Unable to download GRCh38.mane.1.2.refseq: "The specified blob does not exist" #501

jamigo · 2023-10-16T15:53:49Z

Describe the bug
Unable to download GRCh38.mane.1.2.refseq annotations

To Reproduce

SnpEff version: 5.2
Genome version: GRCh38
SnpEff full command line:
java -Xmx4g -jar snpEff.jar GRCh38.mane.1.2.refseq examples/test.vcf
Output / Error message: Please include a full VCF line output

FATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.mane.1.2.refseq.zip, https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.mane.1.2.refseq.zip]

Expected behavior
GRCh38.mane.1.2.refseq dataset should be downloaded into "data" folder and example test.vcf file should be annotated.

Data
Distribution's examples/test.vcf

Additional
wgetting the file directly provides the "specified blob does not exist" message:

$ wget https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip
--2023-10-16 17:51:40--  https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip
Resolving snpeff.blob.core.windows.net... 52.239.234.228
Connecting to snpeff.blob.core.windows.net|52.239.234.228|:443... connected.
HTTP request sent, awaiting response... 404 The specified blob does not exist.
2023-10-16 17:51:40 ERROR 404: The specified blob does not exist..

The text was updated successfully, but these errors were encountered:

etrh · 2023-10-27T10:29:23Z

#503

pcingola · 2023-12-04T23:18:07Z

Fixed.

$ snpeff download -v GRCh38.mane.1.2.refseq
00:00:00 SnpEff version SnpEff 5.2b (build 2023-11-21 11:36), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.mane.1.2.refseq'
...
00:00:00 Downloading database for 'GRCh38.mane.1.2.refseq'
00:00:00 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip' to local file ...
00:00:00 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip
00:00:00 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip, using proxy: false
00:00:01 Local file name: '/tmp/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip'
...
00:01:52 Unzip: OK
00:01:52 Deleted local file '/tmp/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip'
00:01:52 Done
00:01:52 Logging
00:01:53 Done.

singha30 · 2024-01-09T06:22:06Z

not working

pcingola · 2024-01-09T09:37:43Z

@singha30 : I've just tested and it works OK for me. Please provide more details about what error conditions you have.

singha30 · 2024-01-09T09:48:05Z

$ snpeff download -v GRCh38.mane.1.2.refseq
this is the code i have to run in the snpEff folder right?
root@9d196134ef1b:/Data/data/raja/cfdna/nextflow1/bin/snpEff# snpeff download -v GRCh38.mane.1.2.refseq
bash: snpeff: command not found

pcingola · 2024-01-09T09:57:45Z

Here the console is telling you the problem:

bash: snpeff: command not found

You need to write the full command, which is something like: java -jar snpEff.jar ...
Please read the documentation for more details.

In my setup I have the following alias (obviously you need to use your own home dir in your case):

alias snpeff='java -Xmx8g -jar /home/pcingola/snpEff/snpEff.jar '

singha30 · 2024-01-09T10:15:25Z

(base) root@9d196134ef1b:/Data/data/raja/cfdna/nextflow1/bin/snpEff# java -jar snpEff.jar download -v GRCh38.mane.1.2.refseq
00:00:00 SnpEff version SnpEff 5.1f (build 2023-07-21 13:58), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.mane.1.2.refseq'
00:00:00 Reading config file: /Data/data/raja/cfdna/nextflow1/bin/snpEff/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.mane.1.2.refseq.genome' not found
at org.snpeff.interval.Genome.(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:754)
at org.snpeff.snpEffect.Config.init(Config.java:529)
at org.snpeff.snpEffect.Config.(Config.java:116)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Logging
00:00:02 Done.

error is coming'GRCh38.mane.1.2.refseq.genome' not found

pcingola · 2024-01-09T10:18:53Z

It sounds like the entry is not in your config file because you did not install the latest version.
I strongly suggest that you read the documentation, since many of your problems are addressed there.
All the best.

singha30 · 2024-01-09T10:26:37Z

(base) root@9d196134ef1b:/Data/data/raja/cfdna/nextflow1/bin/snpEff# java -jar snpEff.jar download -v GRCh38.mane.1.[84/3260]
00:00:00 SnpEff version SnpEff 5.2a (build 2023-10-24 14:24), by Pablo Cingolani [83/3260]
00:00:00 Command: 'download' [82/3260]
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.mane.1.2.refseq' [81/3260]
00:00:00 Reading config file: /Data/data/raja/cfdna/nextflow1/bin/snpEff/snpEff.config [80/3260]
00:00:01 done [79/3260]
00:00:01 Downloading database for 'GRCh38.mane.1.2.refseq' [78/3260]
00:00:01 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.mane.1.2.refseq.zi[77/3260]
al file '/tmp/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip' [76/3260]
00:00:01 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip [75/3260]
00:00:01 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip, u[74/3260]
y: false [73/3260]
00:00:01 Local file name: '/tmp/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip' [72/3260]
....................................................................................................................[71/3260]
....................................................................................................................[70/3260]
................................................................................................................00:0[69/3260]
00:01:23 Download finished. Total 385740620 bytes. [68/3260]
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.1.bin' [67/3260]
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.10.bin' [66/3260]
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.11.bin' [65/3260]
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.12.bin'
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.13.bin'
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.14.bin'
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.15.bin'
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.16.bin'
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.17.bin'
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.18.bin'
00:01:23 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.19.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.2.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.20.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.21.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.22.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.3.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.4.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.5.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.6.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.7.bin'
00:01:24 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.8.bin'
00:01:25 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.9.bin'
00:01:25 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.X.bin'
00:01:25 Extracting file 'data/GRCh38.mane.1.2.refseq/sequence.Y.bin'
00:01:25 Extracting file 'data/GRCh38.mane.1.2.refseq/snpEffectPredictor.bin'
00:01:25 Unzip: OK
00:01:25 Deleted local file '/tmp/snpEff_v5_2_GRCh38.mane.1.2.refseq.zip'
00:01:25 Done
00:01:25 Logging
00:01:26 Done.
thanx issue has been resolved

singha30 · 2024-01-17T09:52:32Z

@pcingola while running this code :- java -jar snpEff.jar build -gff3 -v GRCh38.p14
this error is showing up:- (base) root@9d196134ef1b:/Data/data/raja/cfdna/nextflow1/bin/snpEff# java -jar snpEff.jar download -v GRCh38.p14
00:00:00 SnpEff version SnpEff 5.2a (build 2023-10-24 14:24), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.p14'
00:00:00 Reading config file: /Data/data/raja/cfdna/nextflow1/bin/snpEff/snpEff.config
00:00:01 Codon table 'Vertebrate_Mitochondrial' assigned to chromosome 'MT'
00:00:01 Codon table 'Vertebrate_Mitochondrial' assigned to chromosome 'M'
00:00:01 done
00:00:01 Downloading database for 'GRCh38.p14'
00:00:01 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip' to local file '/tmp/snpEff_v5_2_GRCh38.p14.zip'
00:00:01 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip
00:00:01 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip, using proxy: false
00:00:02 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip
00:00:02 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip' to local file '/tmp/snpEff_v5_0_GRCh38.p14.zip'
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip, using proxy: false
00:00:02 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip
00:00:02 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.p14.zip' to local file '/tmp/snpEff_v5_1_GRCh38.p14.zip'
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.p14.zip
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.p14.zip, using proxy: false
00:00:02 Local file name: '/tmp/snpEff_v5_1_GRCh38.p14.zip'
..........................................................................................................................
..........................................................................................................................
..........................................................................................................................
..........................................................................................................................
..........................................................................................................................
.........00:02:25
00:02:25 Download finished. Total 660161720 bytes.
00:02:25 Extracting file 'data/GRCh38.p14/sequence.1.bin'
00:02:25 Extracting file 'data/GRCh38.p14/sequence.10.bin'
00:02:25 Extracting file 'data/GRCh38.p14/sequence.11.bin'
00:02:25 Extracting file 'data/GRCh38.p14/sequence.12.bin'
00:02:25 Extracting file 'data/GRCh38.p14/sequence.13.bin'
00:02:25 Extracting file 'data/GRCh38.p14/sequence.14.bin'
00:02:25 Extracting file 'data/GRCh38.p14/sequence.15.bin'
00:02:26 Extracting file 'data/GRCh38.p14/sequence.16.bin'
00:02:26 Extracting file 'data/GRCh38.p14/sequence.17.bin'
00:02:26 Extracting file 'data/GRCh38.p14/sequence.18.bin'
00:02:26 Extracting file 'data/GRCh38.p14/sequence.19.bin'
00:02:26 Extracting file 'data/GRCh38.p14/sequence.2.bin'
00:02:26 Extracting file 'data/GRCh38.p14/sequence.20.bin'
00:02:26 Extracting file 'data/GRCh38.p14/sequence.21.bin'
00:02:26 Extracting file 'data/GRCh38.p14/sequence.22.bin'
[https://snpeff.blob.core.windows.net/databases/v5_2/snp[55/96968]
est_GRCh38.mane.1.0.ensembl.chr19.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_test_GRCh[54/96968]
0.ensembl.chr19.zip, https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_test_GRCh38.mane.1.0.ensemb[53/96968]
p] [52/96968]
test_GRCh38.mane.1.0.ensembl.chr21 GRCh38 MANE 1.0 chr21 [51/96968]
[https://snpeff.blob.core.windows.net/databases/v5_2/snp[50/96968]
est_GRCh38.mane.1.0.ensembl.chr21.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_test_GRCh[49/96968]
0.ensembl.chr21.zip, https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_test_GRCh38.mane.1.0.ensemb[48/96968]
p] [47/96968]
(base) root@9d196134ef1b:/Data/data/raja/cfdna/nextflow1/bin/snpEff# java -jar snpEff.jar download -v GRCh38.p14[46/96968]
00:00:00 SnpEff version SnpEff 5.2a (build 2023-10-24 14:24), by Pablo Cingolani [45/96968]
00:00:00 Command: 'download' [44/96968]
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.p14' [43/96968]
00:00:00 Reading config file: /Data/data/raja/cfdna/nextflow1/bin/snpEff/snpEff.config [42/96968]
00:00:01 Codon table 'Vertebrate_Mitochondrial' assigned to chromosome 'MT' [41/96968]
00:00:01 Codon table 'Vertebrate_Mitochondrial' assigned to chromosome 'M' [40/96968]
00:00:01 done [39/96968]
00:00:01 Downloading database for 'GRCh38.p14' [38/96968]
00:00:01 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip' to lo[37/96968]
/tmp/snpEff_v5_2_GRCh38.p14.zip' [36/96968]
00:00:01 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip [35/96968]
00:00:01 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip, using pro[34/96968]
00:00:02 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zi[33/96968]
00:00:02 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip' to lo[32/96968]
/tmp/snpEff_v5_0_GRCh38.p14.zip' [31/96968]
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip [30/96968]
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip, using pro[29/96968]
00:00:02 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zi[28/96968]
00:00:02 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.p14.zip' to lo[27/96968]
/tmp/snpEff_v5_1_GRCh38.p14.zip' [26/96968]
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.p14.zip [25/96968]
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.p14.zip, using pro[24/96968]
00:00:02 Local file name: '/tmp/snpEff_v5_1_GRCh38.p14.zip' [23/96968]
................................................................................................................[22/96968]
................................................................................................................[21/96968]
................................................................................................................[20/96968]
................................................................................................................[19/96968]
................................................................................................................[18/96968]
.........00:02:25 [17/96968]
00:02:25 Download finished. Total 660161720 bytes. [16/96968]
00:02:25 Extracting file 'data/GRCh38.p14/sequence.1.bin' [15/96968]
00:02:25 Extracting file 'data/GRCh38.p14/sequence.10.bin' [14/96968]
00:02:25 Extracting file 'data/GRCh38.p14/sequence.11.bin' [13/96968]
00:02:25 Extracting file 'data/GRCh38.p14/sequence.12.bin' [12/96968]
00:02:25 Extracting file 'data/GRCh38.p14/sequence.13.bin' [11/96968]
00:02:25 Extracting file 'data/GRCh38.p14/sequence.14.bin' [10/96968]
00:02:25 Extracting file 'data/GRCh38.p14/sequence.15.bin' [9/96968]
00:02:26 Extracting file 'data/GRCh38.p14/sequence.16.bin' [8/96968]
00:02:26 Extracting file 'data/GRCh38.p14/sequence.17.bin' [7/96968]
00:02:26 Extracting file 'data/GRCh38.p14/sequence.18.bin' [6/96968]
00:02:26 Extracting file 'data/GRCh38.p14/sequence.19.bin' [5/96968]
00:02:26 Extracting file 'data/GRCh38.p14/sequence.2.bin' [4/96968]
00:02:26 Extracting file 'data/GRCh38.p14/sequence.20.bin' [3/96968]
00:02:26 Extracting file 'data/GRCh38.p14/sequence.21.bin' [2/96968]
00:02:26 Extracting file 'data/GRCh38.p14/sequence.22.bin' [1/96968]
00:00:00 SnpEff version SnpEff 5.2a (build 2023-10-24 14:24), by Pablo Cingolani [45/96968]
00:00:00 Command: 'download' [44/96968]
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.p14' [43/96968]
00:00:00 Reading config file: /Data/data/raja/cfdna/nextflow1/bin/snpEff/snpEff.config [42/96968]
00:00:01 Codon table 'Vertebrate_Mitochondrial' assigned to chromosome 'MT' [41/96968]
00:00:01 Codon table 'Vertebrate_Mitochondrial' assigned to chromosome 'M' [40/96968]
00:00:01 done [39/96968]
00:00:01 Downloading database for 'GRCh38.p14' [38/96968]
00:00:01 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip' to lo[37/96968]
/tmp/snpEff_v5_2_GRCh38.p14.zip' [36/96968]
00:00:01 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip [35/96968]
00:00:01 Connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zip, using pro[34/96968]
00:00:02 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_GRCh38.p14.zi[33/96968]
00:00:02 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip' to lo[32/96968]
/tmp/snpEff_v5_0_GRCh38.p14.zip' [31/96968]
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip [30/96968]
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zip, using pro[29/96968]
00:00:02 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p14.zi[28/96968]
00:00:02 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.p14.zip' to lo[27/96968]
/tmp/snpEff_v5_1_GRCh38.p14.zip' [26/96968]
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.p14.zip [25/96968]
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh38.p14.zip, using pro[24/96968]
00:00:02 Local file name: '/tmp/snpEff_v5_1_GRCh38.p14.zip' [23/96968]
................................................................................................................[22/96968]
................................................................................................................[21/96968]
................................................................................................................[20/96968]
................................................................................................................[19/96968]
................................................................................................................[18/96968]
.........00:02:25 [17/96968]
00:02:25 Download finished. Total 660161720 bytes. [16/96968]
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00:02:29 Unzip: OK
00:02:29 Deleted local file '/tmp/snpEff_v5_1_GRCh38.p14.zip'
00:02:29 Done
00:02:29 Logging
00:02:30 Done.
(base) root@9d196134ef1b:/Data/data/raja/cfdna/nextflow1/bin/snpEff# java -jar snpEff.jar build -gff3 -v GRCh38.p14
00:00:00 SnpEff version SnpEff 5.2a (build 2023-10-24 14:24), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'GRCh38.p14'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.p14'
00:00:00 Reading config file: /Data/data/raja/cfdna/nextflow1/bin/snpEff/snpEff.config
00:00:01 Codon table 'Vertebrate_Mitochondrial' assigned to chromosome 'MT'
00:00:01 Codon table 'Vertebrate_Mitochondrial' assigned to chromosome 'M'
00:00:01 done
00:00:01 Reading GFF3 data file : '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff'
00:00:01 Reading file '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_046018.2'. Created transcript 'rna-NR_046018.2' and gene 'GENE_exon-NR_046018.2-1' for NC_000001.11 BestRefSeq EXON 11873 12226 +
dbxref : GeneID:100287102,GenBank:NR_046018.2,HGNC:HGNC:37102
gbkey : misc_RNA
gene : DDX11L1
id : exon-NR_046018.2-1
parent : rna-NR_046018.2
product : DEAD/H-box helicase 11 like 1 (pseudogene)
pseudo : true
source : BestRefSeq
transcript_id : NR_046018.2
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 13 'NC_000001.11 BestRefSeqexon 11874 12227 . + . ID=exon-NR_046018.2-1;Parent=rna-NR_046018.2;Dbxref=GeneID:100287102,GenBank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1 (pseudogene);pseudo=true;transcript_id=NR_046018.2'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_024540.1'. Created transcript 'rna-NR_024540.1' and gene 'GENE_exon-NR_024540.1-1' for NC_000001.11 BestRefSeq EXON 29320 29369 -
dbxref : GeneID:653635,GenBank:NR_024540.1,HGNC:HGNC:38034
gbkey : misc_RNA
gene : WASH7P
id : exon-NR_024540.1-1
parent : rna-NR_024540.1
product : WASP family homolog 7%2C pseudogene
pseudo : true
source : BestRefSeq
transcript_id : NR_024540.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 18 'NC_000001.11 BestRefSeqexon 29321 29370 . - . ID=exon-NR_024540.1-1;Parent=rna-NR_024540.1;Dbxref=GeneID:653635,GenBank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WASP family homolog 7%2C pseudogene;pseudo=true;transcript_id=NR_024540.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_106918.1'. Created transcript 'rna-NR_106918.1' and gene 'GENE_exon-NR_106918.1-1' for NC_000001.11 BestRefSeq EXON 17368 17435 -
dbxref : GeneID:102466751,GenBank:NR_106918.1,HGNC:HGNC:50039,miRBase:MI0022705
gbkey : precursor_RNA
gene : MIR6859-1
id : exon-NR_106918.1-1
parent : rna-NR_106918.1
product : microRNA 6859-1
source : BestRefSeq
transcript_id : NR_106918.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 31 'NC_000001.11 BestRefSeqexon 17369 17436 . - . ID=exon-NR_106918.1-1;Parent=rna-NR_106918.1;Dbxref=GeneID:102466751,GenBank:NR_106918.1,HGNC:HGNC:50039,miRBase:MI0022705;gbkey=precursor_RNA;gene=MIR6859-1;product=microRNA 6859-1;transcript_id=NR_106918.1'
WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106918.1' (NC_000001.11:17369-17391) does not include 'rna-MIR6859-1-2' (NC_000001.11:17409-17431). Created new gene 'rna-NR_106918.1.2' (NC_000001.11:17409-17431). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 34 'NC_000001.11 BestRefSeq miRNA 17409 17431 . - .ID=rna-MIR6859-1-2;Parent=rna-NR_106918.1;Dbxref=GeneID:102466751,miRBase:MIMAT0027618,HGNC:HGNC:50039,miRBase:MI0022705;gbkey=ncRNA;gene=MIR6859-1;product=hsa-miR-6859-5p'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065314.1'. Created transcript 'rna-XR_007065314.1' and gene 'GENE_exon-XR_007065314.1-1' for NC_000001.11 Gnomon EXON 29773 30666 +
dbxref : GeneID:107985730,GenBank:XR_007065314.1,HGNC:HGNC:52482
gbkey : ncRNA
gene : MIR1302-2HG
id : exon-XR_007065314.1-1
parent : rna-XR_007065314.1
product : MIR1302-2 host gene
source : Gnomon
transcript_id : XR_007065314.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 40 'NC_000001.11 Gnomon exon 29774 30667 . + . ID=exon-XR_007065314.1-1;Parent=rna-XR_007065314.1;Dbxref=GeneID:107985730,GenBank:XR_007065314.1,HGNC:HGNC:52482;gbkey=ncRNA;gene=MIR1302-2HG;product=MIR1302-2 host gene;transcript_id=XR_007065314.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_036051.1'. Created transcript 'rna-NR_036051.1' and gene 'GENE_exon-NR_036051.1-1' for NC_000001.11 BestRefSeq EXON 30365 30502 +
dbxref : GeneID:100302278,GenBank:NR_036051.1,HGNC:HGNC:35294,miRBase:MI0006363
gbkey : precursor_RNA
gene : MIR1302-2
id : exon-NR_036051.1-1
parent : rna-NR_036051.1
product : microRNA 1302-2
source : BestRefSeq
transcript_id : NR_036051.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 45 'NC_000001.11 BestRefSeqexon 30366 30503 . + . ID=exon-NR_036051.1-1;Parent=rna-NR_036051.1;Dbxref=GeneID:100302278,GenBank:NR_036051.1,HGNC:HGNC:35294,miRBase:MI0006363;gbkey=precursor_RNA;gene=MIR1302-2;product=microRNA 1302-2;transcript_id=NR_036051.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_026818.1'. Created transcript 'rna-NR_026818.1' and gene 'GENE_exon-NR_026818.1-1' for NC_000001.11 BestRefSeq EXON 35720 36080 -
dbxref : GeneID:645520,GenBank:NR_026818.1,HGNC:HGNC:32334
gbkey : ncRNA
gene : FAM138A
id : exon-NR_026818.1-1
parent : rna-NR_026818.1
product : family with sequence similarity 138 member A
source : BestRefSeq
transcript_id : NR_026818.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 50 'NC_000001.11 BestRefSeqexon 35721 36081 . - . ID=exon-NR_026818.1-1;Parent=rna-NR_026818.1;Dbxref=GeneID:645520,GenBank:NR_026818.1,HGNC:HGNC:32334;gbkey=ncRNA;gene=FAM138A;product=family with sequence similarity 138 member A;transcript_id=NR_026818.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NM_001005484.2'. Created transcript 'rna-NM_001005484.2' and gene 'GENE_exon-NM_001005484.2-1' for NC_000001.11 BestRefSeq EXON 65418 65432 +
dbxref : Ensembl:ENST00000641515.2,GeneID:79501,GenBank:NM_001005484.2,HGNC:HGNC:14825
gbkey : mRNA
gene : OR4F5
id : exon-NM_001005484.2-1
parent : rna-NM_001005484.2
product : olfactory receptor family 4 subfamily F member 5
source : BestRefSeq
tag : MANE Select
transcript_id : NM_001005484.2
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 57 'NC_000001.11 BestRefSeqexon 65419 65433 . + . ID=exon-NM_001005484.2-1;Parent=rna-NM_001005484.2;Dbxref=Ensembl:ENST00000641515.2,GeneID:79501,GenBank:NM_001005484.2,HGNC:HGNC:14825;gbkey=mRNA;gene=OR4F5;product=olfactory receptor family 4 subfamily F member 5;tag=MANE Select;transcript_id=NM_001005484.2'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065337.1'. Created transcript 'rna-XR_007065337.1' and gene 'GENE_exon-XR_007065337.1-1' for NC_000001.11 Gnomon EXON 95221 99718 +
dbxref : GeneID:124903816,GenBank:XR_007065337.1
experiment : COORDINATES: polyA evidence [ECO:0006239]
gbkey : ncRNA
gene : LOC124903816
id : exon-XR_007065337.1-1
parent : rna-XR_007065337.1
product : uncharacterized LOC124903816%2C transcript variant X1
source : Gnomon
transcript_id : XR_007065337.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 64 'NC_000001.11 Gnomon exon 95222 99719 . + . ID=exon-XR_007065337.1-1;Parent=rna-XR_007065337.1;Dbxref=GeneID:124903816,GenBank:XR_007065337.1;experiment=COORDINATES: polyA evidence [ECO:0006239];gbkey=ncRNA;gene=LOC124903816;product=uncharacterized LOC124903816%2C transcript variant X1;transcript_id=XR_007065337.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065338.1'. Created transcript 'rna-XR_007065338.1' and gene 'GENE_exon-XR_007065338.1-1' for NC_000001.11 Gnomon EXON 95221 99718 +
dbxref : GeneID:124903816,GenBank:XR_007065338.1
experiment : COORDINATES: polyA evidence [ECO:0006239]
gbkey : ncRNA
gene : LOC124903816
id : exon-XR_007065338.1-1
parent : rna-XR_007065338.1
product : uncharacterized LOC124903816%2C transcript variant X2
source : Gnomon
transcript_id : XR_007065338.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 67 'NC_000001.11 Gnomon exon 95222 99719 . + . ID=exon-XR_007065338.1-1;Parent=rna-XR_007065338.1;Dbxref=GeneID:124903816,GenBank:XR_007065338.1;experiment=COORDINATES: polyA evidence [ECO:0006239];gbkey=ncRNA;gene=LOC124903816;product=uncharacterized LOC124903816%2C transcript variant X2;transcript_id=XR_007065338.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_001737579.3'. Created transcript 'rna-XR_001737579.3' and gene 'GENE_exon-XR_001737579.3-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_001737579.3
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_001737579.3-1
parent : rna-XR_001737579.3
product : uncharacterized LOC124900384%2C transcript variant X13
source : Gnomon
transcript_id : XR_001737579.3
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 72 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_001737579.3-1;Parent=rna-XR_001737579.3;Dbxref=GeneID:124900384,GenBank:XR_001737579.3;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X13;transcript_id=XR_001737579.3'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065328.1'. Created transcript 'rna-XR_007065328.1' and gene 'GENE_exon-XR_007065328.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065328.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065328.1-1
parent : rna-XR_007065328.1
product : uncharacterized LOC124900384%2C transcript variant X9
source : Gnomon
transcript_id : XR_007065328.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 79 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065328.1-1;Parent=rna-XR_007065328.1;Dbxref=GeneID:124900384,GenBank:XR_007065328.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X9;transcript_id=XR_007065328.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065325.1'. Created transcript 'rna-XR_007065325.1' and gene 'GENE_exon-XR_007065325.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065325.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065325.1-1
parent : rna-XR_007065325.1
product : uncharacterized LOC124900384%2C transcript variant X6
source : Gnomon
transcript_id : XR_007065325.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 89 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065325.1-1;Parent=rna-XR_007065325.1;Dbxref=GeneID:124900384,GenBank:XR_007065325.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X6;transcript_id=XR_007065325.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065330.1'. Created transcript 'rna-XR_007065330.1' and gene 'GENE_exon-XR_007065330.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065330.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065330.1-1
parent : rna-XR_007065330.1
product : uncharacterized LOC124900384%2C transcript variant X11
source : Gnomon
transcript_id : XR_007065330.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 100 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065330.1-1;Parent=rna-XR_007065330.1;Dbxref=GeneID:124900384,GenBank:XR_007065330.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X11;transcript_id=XR_007065330.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065322.1'. Created transcript 'rna-XR_007065322.1' and gene 'GENE_exon-XR_007065322.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065322.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065322.1-1
parent : rna-XR_007065322.1
product : uncharacterized LOC124900384%2C transcript variant X3
source : Gnomon
transcript_id : XR_007065322.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 109 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065322.1-1;Parent=rna-XR_007065322.1;Dbxref=GeneID:124900384,GenBank:XR_007065322.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X3;transcript_id=XR_007065322.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065324.1'. Created transcript 'rna-XR_007065324.1' and gene 'GENE_exon-XR_007065324.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065324.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065324.1-1
parent : rna-XR_007065324.1
product : uncharacterized LOC124900384%2C transcript variant X5
source : Gnomon
transcript_id : XR_007065324.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 119 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065324.1-1;Parent=rna-XR_007065324.1;Dbxref=GeneID:124900384,GenBank:XR_007065324.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X5;transcript_id=XR_007065324.1'
.WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065331.1'. Created transcript 'rna-XR_007065331.1' and gene 'GENE_exon-XR_007065331.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065331.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065331.1-1
parent : rna-XR_007065331.1
product : uncharacterized LOC124900384%2C transcript variant X12
source : Gnomon
transcript_id : XR_007065331.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 130 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065331.1-1;Parent=rna-XR_007065331.1;Dbxref=GeneID:124900384,GenBank:XR_007065331.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X12;transcript_id=XR_007065331.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065327.1'. Created transcript 'rna-XR_007065327.1' and gene 'GENE_exon-XR_007065327.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065327.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065327.1-1
parent : rna-XR_007065327.1
product : uncharacterized LOC124900384%2C transcript variant X8
source : Gnomon
transcript_id : XR_007065327.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 139 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065327.1-1;Parent=rna-XR_007065327.1;Dbxref=GeneID:124900384,GenBank:XR_007065327.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X8;transcript_id=XR_007065327.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065323.1'. Created transcript 'rna-XR_007065323.1' and gene 'GENE_exon-XR_007065323.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065323.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065323.1-1
parent : rna-XR_007065323.1
product : uncharacterized LOC124900384%2C transcript variant X4
source : Gnomon
transcript_id : XR_007065323.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 149 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065323.1-1;Parent=rna-XR_007065323.1;Dbxref=GeneID:124900384,GenBank:XR_007065323.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X4;transcript_id=XR_007065323.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065321.1'. Created transcript 'rna-XR_007065321.1' and gene 'GENE_exon-XR_007065321.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065321.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065321.1-1
parent : rna-XR_007065321.1
product : uncharacterized LOC124900384%2C transcript variant X2
source : Gnomon
transcript_id : XR_007065321.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 160 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065321.1-1;Parent=rna-XR_007065321.1;Dbxref=GeneID:124900384,GenBank:XR_007065321.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X2;transcript_id=XR_007065321.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065329.1'. Created transcript 'rna-XR_007065329.1' and gene 'GENE_exon-XR_007065329.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065329.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065329.1-1
parent : rna-XR_007065329.1
product : uncharacterized LOC124900384%2C transcript variant X10
source : Gnomon
transcript_id : XR_007065329.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 170 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065329.1-1;Parent=rna-XR_007065329.1;Dbxref=GeneID:124900384,GenBank:XR_007065329.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X10;transcript_id=XR_007065329.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065326.1'. Created transcript 'rna-XR_007065326.1' and gene 'GENE_exon-XR_007065326.1-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_007065326.1
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_007065326.1-1
parent : rna-XR_007065326.1
product : uncharacterized LOC124900384%2C transcript variant X7
source : Gnomon
transcript_id : XR_007065326.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 180 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_007065326.1-1;Parent=rna-XR_007065326.1;Dbxref=GeneID:124900384,GenBank:XR_007065326.1;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X7;transcript_id=XR_007065326.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_002958514.2'. Created transcript 'rna-XR_002958514.2' and gene 'GENE_exon-XR_002958514.2-1' for NC_000001.11 Gnomon EXON 173752 175245 -
dbxref : GeneID:124900384,GenBank:XR_002958514.2
gbkey : ncRNA
gene : LOC124900384
id : exon-XR_002958514.2-1
parent : rna-XR_002958514.2
product : uncharacterized LOC124900384%2C transcript variant X1
source : Gnomon
transcript_id : XR_002958514.2
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 190 'NC_000001.11 Gnomon exon 173753 175246 . - . ID=exon-XR_002958514.2-1;Parent=rna-XR_002958514.2;Dbxref=GeneID:124900384,GenBank:XR_002958514.2;gbkey=ncRNA;gene=LOC124900384;product=uncharacterized LOC124900384%2C transcript variant X1;transcript_id=XR_002958514.2'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_039983.2'. Created transcript 'rna-NR_039983.2' and gene 'GENE_exon-NR_039983.2-1' for NC_000001.11 BestRefSeq EXON 140074 140565 -
dbxref : GeneID:729737,GenBank:NR_039983.2
gbkey : ncRNA
gene : LOC729737
id : exon-NR_039983.2-1
parent : rna-NR_039983.2
product : uncharacterized LOC729737
source : BestRefSeq
transcript_id : NR_039983.2
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 202 'NC_000001.11 BestRefSeqexon 140075 140566 . - . ID=exon-NR_039983.2-1;Parent=rna-NR_039983.2;Dbxref=GeneID:729737,GenBank:NR_039983.2;gbkey=ncRNA;gene=LOC729737;product=uncharacterized LOC729737;transcript_id=NR_039983.2'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065332.1'. Created transcript 'rna-XR_007065332.1' and gene 'GENE_exon-XR_007065332.1-1' for NC_000001.11 Gnomon EXON 177681 180104 -
dbxref : GeneID:124903814,GenBank:XR_007065332.1
experiment : COORDINATES: polyA evidence [ECO:0006239]
gbkey : ncRNA
gene : LOC124903814
id : exon-XR_007065332.1-1
parent : rna-XR_007065332.1
product : uncharacterized LOC124903814%2C transcript variant X1
source : Gnomon
transcript_id : XR_007065332.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 213 'NC_000001.11 Gnomon exon 177682 180105 . - . ID=exon-XR_007065332.1-1;Parent=rna-XR_007065332.1;Dbxref=GeneID:124903814,GenBank:XR_007065332.1;experiment=COORDINATES: polyA evidence [ECO:0006239];gbkey=ncRNA;gene=LOC124903814;product=uncharacterized LOC124903814%2C transcript variant X1;transcript_id=XR_007065332.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065333.1'. Created transcript 'rna-XR_007065333.1' and gene 'GENE_exon-XR_007065333.1-1' for NC_000001.11 Gnomon EXON 177681 180104 -
dbxref : GeneID:124903814,GenBank:XR_007065333.1
experiment : COORDINATES: polyA evidence [ECO:0006239]
gbkey : ncRNA
gene : LOC124903814
id : exon-XR_007065333.1-1
parent : rna-XR_007065333.1
product : uncharacterized LOC124903814%2C transcript variant X2
source : Gnomon
transcript_id : XR_007065333.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 216 'NC_000001.11 Gnomon exon 177682 180105 . - . ID=exon-XR_007065333.1-1;Parent=rna-XR_007065333.1;Dbxref=GeneID:124903814,GenBank:XR_007065333.1;experiment=COORDINATES: polyA evidence [ECO:0006239];gbkey=ncRNA;gene=LOC124903814;product=uncharacterized LOC124903814%2C transcript variant X2;transcript_id=XR_007065333.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007065334.1'. Created transcript 'rna-XR_007065334.1' and gene 'GENE_exon-XR_007065334.1-1' for NC_000001.11 Gnomon EXON 177677 180104 -
dbxref : GeneID:124903814,GenBank:XR_007065334.1
experiment : COORDINATES: polyA evidence [ECO:0006239]
gbkey : ncRNA
gene : LOC124903814
id : exon-XR_007065334.1-1
parent : rna-XR_007065334.1
product : uncharacterized LOC124903814%2C transcript variant X3
source : Gnomon
transcript_id : XR_007065334.1
type : exon
. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 219 'NC_000001.11 Gnomon exon 177678 180105 . - . ID=exon-XR_007065334.1-1;Parent=rna-XR_007065334.1;Dbxref=GeneID:124903814,GenBank:XR_007065334.1;experiment=COORDINATES: polyA evidence [ECO:0006239];gbkey=ncRNA;gene=LOC124903814;product=uncharacterized LOC124903814%2C transcript variant X3;transcript_id=XR_007065334.1'
WARNING_TRANSCRIPT_NOT_FOUND: Too many 'WARNING_TRANSCRIPT_NOT_FOUND' warnings, no further warnings will be shown.
.WARNING_GENE_NOT_FOUND: Gene 'rna-NR_107062.1' (NC_000001.11:187891-187913) does not include 'rna-MIR6859-2-2' (NC_000001.11:187931-187953). Created new gene 'rna-NR_107062.1.2' (NC_000001.11:187931-187953). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 244 'NC_000001.11 BestRefSeq miRNA 187931 187953 . -.ID=rna-MIR6859-2-2;Parent=rna-NR_107062.1;Dbxref=GeneID:102465909,miRBase:MIMAT0027618,HGNC:HGNC:49954,miRBase:MI0026420;gbkey=ncRNA;gene=MIR6859-2;product=hsa-miR-6859-5p'
.........WARNING_GENE_NOT_FOUND: Gene 'rna-NR_029639.1' (NC_000001.11:1167124-1167145) does not include 'rna-MIR200B-2' (NC_000001.11:1167160-1167181). Created new gene 'rna-NR_029639.1.2' (NC_000001.11:1167160-1167181). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 2035 'NC_000001.11 BestRefSeq miRNA 1167160 1167181 . + . ID=rna-MIR200B-2;Parent=rna-NR_029639.1;Dbxref=GeneID:406984,miRBase:MIMAT0000318,HGNC:HGNC:31579,MIM:612091,miRBase:MI0000342;gbkey=ncRNA;gene=MIR200B;product=hsa-miR-200b-3p'
WARNING_GENE_NOT_FOUND: Gene 'rna-NR_029834.1' (NC_000001.11:1167878-1167899) does not include 'rna-MIR200A-2' (NC_000001.11:1167916-1167937). Created new gene 'rna-NR_029834.1.2' (NC_000001.11:1167916-1167937). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 2042 'NC_000001.11 BestRefSeq miRNA 1167916 1167937 .+. ID=rna-MIR200A-2;Parent=rna-NR_029834.1;Dbxref=GeneID:406983,miRBase:MIMAT0000682,HGNC:HGNC:31578,MIM:612090,miRBase:MI0000737;gbkey=ncRNA;gene=MIR200A;product=hsa-miR-200a-3p'
.......WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106784.1' (NC_000001.11:1296110-1296129) does not include 'rna-MIR6726-2' (NC_000001.11:1296145-1296165). Created new gene 'rna-NR_106784.1.2' (NC_000001.11:1296145-1296165). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 3440 'NC_000001.11 BestRefSeq miRNA 1296145 1296165 . - . ID=rna-MIR6726-2;Parent=rna-NR_106784.1;Dbxref=GeneID:102465434,miRBase:MIMAT0027353,HGNC:HGNC:50009,miRBase:MI0022571;gbkey=ncRNA;gene=MIR6726;product=hsa-miR-6726-5p'
..WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106785.1' (NC_000001.11:1312502-1312521) does not include 'rna-MIR6727-2' (NC_000001.11:1312539-1312561). Created new gene 'rna-NR_106785.1.2' (NC_000001.11:1312539-1312561). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 3859 'NC_000001.11 BestRefSeq miRNA 1312539 1312561 .-. ID=rna-MIR6727-2;Parent=rna-NR_106785.1;Dbxref=GeneID:102465435,miRBase:MIMAT0027355,HGNC:HGNC:50171,miRBase:MI0022572;gbkey=ncRNA;gene=MIR6727;product=hsa-miR-6727-5p'
..WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106866.1' (NC_000001.11:1339650-1339670) does not include 'rna-MIR6808-2' (NC_000001.11:1339682-1339703). Created new gene 'rna-NR_106866.1.2' (NC_000001.11:1339682-1339703). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4092 'NC_000001.11 BestRefSeq miRNA 1339682 1339703 .-. ID=rna-MIR6808-2;Parent=rna-NR_106866.1;Dbxref=GeneID:102466740,miRBase:MIMAT0027516,HGNC:HGNC:50046,miRBase:MI0022653;gbkey=ncRNA;gene=MIR6808;product=hsa-miR-6808-5p'
..............................................................................
10000 ..................................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106786.1' (NC_000001.11:8866502-8866522) does not include 'rna-MIR6728-2' (NC_000001.11:8866563-8866585). Created new gene 'rna-NR_106786.1.2' (NC_000001.11:8866563-8866585). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 25692 'NC_000001.11 BestRefSeq miRNA 8866563 8866585 . - . ID=rna-MIR6728-2;Parent=rna-NR_106786.1;Dbxref=GeneID:102465436,miRBase:MIMAT0027357,HGNC:HGNC:49961,miRBase:MI0022573;gbkey=ncRNA;gene=MIR6728;product=hsa-miR-6728-5p'
...WARNING_GENE_NOT_FOUND: Gene 'rna-NR_029610.1' (NC_000001.11:9151693-9151714) does not include 'rna-MIR34A-2' (NC_000001.11:9151735-9151756). Created new gene 'rna-NR_029610.1.2' (NC_000001.11:9151735-9151756). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 26393 'NC_000001.11 BestRefSeq miRNA 9151735 9151756 .-. ID=rna-MIR34A-2;Parent=rna-NR_029610.1;Dbxref=GeneID:407040,miRBase:MIMAT0000255,HGNC:HGNC:31635,MIM:611172,miRBase:MI0000268;gbkey=ncRNA;gene=MIR34A;product=hsa-miR-34a-5p'
............................................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106787.1' (NC_000001.11:12029163-12029184) does not include 'rna-MIR6729-2' (NC_000001.11:12029202-12029222). Created new gene 'rna-NR_106787.1.2' (NC_000001.11:12029202-12029222). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 35031 'NC_000001.11 BestRefSeq miRNA 12029202 12029222 . + . ID=rna-MIR6729-2;Parent=rna-NR_106787.1;Dbxref=GeneID:102466982,miRBase:MIMAT0027360,HGNC:HGNC:50103,miRBase:MI0022574;gbkey=ncRNA;gene=MIR6729;product=hsa-miR-6729-3p'
..WARNING_GENE_NOT_FOUND: Gene 'rna-NR_039775.2' (NC_000001.11:12191713-12191735) does not include 'rna-MIR4632-2' (NC_000001.11:12191752-12191773). Created new gene 'rna-NR_039775.2.2' (NC_000001.11:12191752-12191773). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 35437 'NC_000001.11 BestRefSeq miRNA 12191752 12191773 . + . ID=rna-MIR4632-2;Parent=rna-NR_039775.2;Dbxref=GeneID:100616438,miRBase:MIMAT0019688,HGNC:HGNC:41593,miRBase:MI0017259;gbkey=ncRNA;gene=MIR4632;product=hsa-miR-4632-3p'
..WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106788.2' (NC_000001.11:12578958-12578979) does not include 'rna-MIR6730-2' (NC_000001.11:12578996-12579018). Created new gene 'rna-NR_106788.2.2' (NC_000001.11:12578996-12579018). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 35872 'NC_000001.11 BestRefSeq miRNA 12578996 12579018 . - . ID=rna-MIR6730-2;Parent=rna-NR_106788.2;Dbxref=GeneID:102466722,miRBase:MIMAT0027361,HGNC:HGNC:50222,miRBase:MI0022575;gbkey=ncRNA;gene=MIR6730;product=hsa-miR-6730-5p'
...............
20000 ...................................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_037446.1' (NC_000001.11:16858958-16858979) does not include 'rna-MIR3675-2' (NC_000001.11:16858988-16859010). Created new gene 'rna-NR_037446.1.2' (NC_000001.11:16858988-16859010). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 45178 'NC_000001.11 BestRefSeq miRNA 16858988 16859010 . - . ID=rna-MIR3675-2;Parent=rna-NR_037446.1;Dbxref=GeneID:100500876,miRBase:MIMAT0018098,HGNC:HGNC:38973,miRBase:MI0016076;gbkey=ncRNA;gene=MIR3675;product=hsa-miR-3675-5p'
...................................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_039844.2' (NC_000001.11:18883204-18883225) does not include 'rna-MIR4695-2' (NC_000001.11:18883250-18883271). Created new gene 'rna-NR_039844.2.2' (NC_000001.11:18883250-18883271). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 52084 'NC_000001.11 BestRefSeq miRNA 18883250 18883271 . - . ID=rna-MIR4695-2;Parent=rna-NR_039844.2;Dbxref=GeneID:100616120,miRBase:MIMAT0019788,HGNC:HGNC:41573,miRBase:MI0017328;gbkey=ncRNA;gene=MIR4695;product=hsa-miR-4695-5p'
..............................
30000 ..................................................................................................
..
40000 ...........................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_039832.1' (NC_000001.11:22719530-22719551) does not include 'rna-MIR4684-2' (NC_000001.11:22719566-22719587). Created new gene 'rna-NR_039832.1.2' (NC_000001.11:22719566-22719587). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 81616 'NC_000001.11 BestRefSeq miRNA 22719566 22719587 . + . ID=rna-MIR4684-2;Parent=rna-NR_039832.1;Dbxref=GeneID:100616391,miRBase:MIMAT0019770,HGNC:HGNC:41695,miRBase:MI0017316;gbkey=ncRNA;gene=MIR4684;product=hsa-miR-4684-3p'
..................................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106789.1' (NC_000001.11:24919345-24919365) does not include 'rna-MIR6731-2' (NC_000001.11:24919390-24919411). Created new gene 'rna-NR_106789.1.2' (NC_000001.11:24919390-24919411). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 87837 'NC_000001.11 BestRefSeq miRNA 24919390 24919411 . - . ID=rna-MIR6731-2;Parent=rna-NR_106789.1;Dbxref=GeneID:102465437,miRBase:MIMAT0027363,HGNC:HGNC:50036,miRBase:MI0022576;gbkey=ncRNA;gene=MIR6731;product=hsa-miR-6731-5p'
.......................................
50000 ......................................................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_049850.1' (NC_000001.11:32086949-32086970) does not include 'rna-MIR5585-2' (NC_000001.11:32086986-32087007). Created new gene 'rna-NR_049850.1.2' (NC_000001.11:32086986-32087007). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 106076 'NC_000001.11 BestRefSeq miRNA 32086986 32087007 . + . ID=rna-MIR5585-2;Parent=rna-NR_049850.1;Dbxref=GeneID:100847018,miRBase:MIMAT0022286,HGNC:HGNC:43452,miRBase:MI0019142;gbkey=ncRNA;gene=MIR5585;product=hsa-miR-5585-3p'
.....................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_037400.1' (NC_000001.11:33332405-33332427) does not include 'rna-MIR3605-2' (NC_000001.11:33332449-33332471). Created new gene 'rna-NR_037400.1.2' (NC_000001.11:33332449-33332471). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 109915 'NC_000001.11 BestRefSeq miRNA 33332449 33332471 . - . ID=rna-MIR3605-2;Parent=rna-NR_037400.1;Dbxref=GeneID:100500853,miRBase:MIMAT0017981,HGNC:HGNC:38922,miRBase:MI0015995;gbkey=ncRNA;gene=MIR3605;product=hsa-miR-3605-5p'
..........WARNING_GENE_NOT_FOUND: Gene 'rna-NR_030278.1' (NC_000001.11:34669614-34669634) does not include 'rna-MIR552-2' (NC_000001.11:34669650-34669670). Created new gene 'rna-NR_030278.1.2' (NC_000001.11:34669650-34669670). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 111847 'NC_000001.11 BestRefSeq miRNA 34669650 34669670 . - . ID=rna-MIR552-2;Parent=rna-NR_030278.1;Dbxref=GeneID:693137,miRBase:MIMAT0026615,HGNC:HGNC:32808,miRBase:MI0003557;gbkey=ncRNA;gene=MIR552;product=hsa-miR-552-5p'
...............
60000 ................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106790.1' (NC_000001.11:37480235-37480254) does not include 'rna-MIR6732-2' (NC_000001.11:37480267-37480289). Created new gene 'rna-NR_106790.1.2' (NC_000001.11:37480267-37480289). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 117719 'NC_000001.11 BestRefSeq miRNA 37480267 37480289 . + . ID=rna-MIR6732-2;Parent=rna-NR_106790.1;Dbxref=GeneID:102465438,miRBase:MIMAT0027366,HGNC:HGNC:50066,miRBase:MI0022577;gbkey=ncRNA;gene=MIR6732;product=hsa-miR-6732-3p'
.WARNING_GENE_NOT_FOUND: Gene 'rna-NR_049844.1' (NC_000001.11:37500935-37500956) does not include 'rna-MIR5581-2' (NC_000001.11:37500973-37500994). Created new gene 'rna-NR_049844.1.2' (NC_000001.11:37500973-37500994). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 117833 'NC_000001.11 BestRefSeq miRNA 37500973 37500994 . - . ID=rna-MIR5581-2;Parent=rna-NR_049844.1;Dbxref=GeneID:100847010,miRBase:MIMAT0022275,HGNC:HGNC:43527,miRBase:MI0019136;gbkey=ncRNA;gene=MIR5581;product=hsa-miR-5581-5p'
.......................................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_029846.1' (NC_000001.11:40754371-40754392) does not include 'rna-MIR30E-2' (NC_000001.11:40754413-40754434). Created new gene 'rna-NR_029846.1.2' (NC_000001.11:40754413-40754434). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 124915 'NC_000001.11 BestRefSeq miRNA 40754413 40754434 . + . ID=rna-MIR30E-2;Parent=rna-NR_029846.1;Dbxref=GeneID:407034,miRBase:MIMAT0000693,HGNC:HGNC:31629,MIM:619105,miRBase:MI0000749;gbkey=ncRNA;gene=MIR30E;product=hsa-miR-30e-3p'
WARNING_GENE_NOT_FOUND: Gene 'rna-NR_029833.1' (NC_000001.11:40757300-40757322) does not include 'rna-MIR30C1-2' (NC_000001.11:40757339-40757360). Created new gene 'rna-NR_029833.1.2' (NC_000001.11:40757339-40757360). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 124922 'NC_000001.11 BestRefSeq miRNA 40757339 40757360 . + . ID=rna-MIR30C1-2;Parent=rna-NR_029833.1;Dbxref=GeneID:407031,miRBase:MIMAT0004674,HGNC:HGNC:31626,MIM:615151,miRBase:MI0000736;gbkey=ncRNA;gene=MIR30C1;product=hsa-miR-30c-1-3p'
.......................WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106791.1' (NC_000001.11:43171652-43171671) does not include 'rna-MIR6733-2' (NC_000001.11:43171686-43171707). Created new gene 'rna-NR_106791.1.2' (NC_000001.11:43171686-43171707). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 129116 'NC_000001.11 BestRefSeqmiRNA 43171686 43171707 . - . ID=rna-MIR6733-2;Parent=rna-NR_106791.1;Dbxref=GeneID:102465439,miRBase:MIMAT0027367,HGNC:HGNC:50239,miRBase:MI0022578;gbkey=ncRNA;gene=MIR6733;product=hsa-miR-6733-5p'
.......WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106792.1' (NC_000001.11:43364648-43364670) does not include 'rna-MIR6734-2' (NC_000001.11:43364688-43364710). Created new gene 'rna-NR_106792.1.2' (NC_000001.11:43364688-43364710). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 130353 'NC_000001.11 BestRefSeq miRNA 43364688 43364710 . - . ID=rna-MIR6734-2;Parent=rna-NR_106792.1;Dbxref=GeneID:102466723,miRBase:MIMAT0027369,HGNC:HGNC:50219,miRBase:MI0022579;gbkey=ncRNA;gene=MIR6734;product=hsa-miR-6734-5p'
..WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106793.1' (NC_000001.11:43448544-43448568) does not include 'rna-MIR6735-2' (NC_000001.11:43448590-43448611). Created new gene 'rna-NR_106793.1.2' (NC_000001.11:43448590-43448611). File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 130729 'NC_000001.11 BestRefSeq miRNA 43448590 43448611 . + . ID=rna-MIR6735-2;Parent=rna-NR_106793.1;Dbxref=GeneID:102465440,miRBase:MIMAT0027372,HGNC:HGNC:50126,miRBase:MI0022580;gbkey=ncRNA;gene=MIR6735;product=hsa-miR-6735-3p'
WARNING_GENE_NOT_FOUND: Too many 'WARNING_GENE_NOT_FOUND' warnings, no further warnings will be shown.
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2310000 ...............WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NR_028057.2' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4449901 'NC_000024.10 BestRefSeq transcript 276356 303356 . + . ID=rna-NR_028057.2-2;Parent=gene-PLCXD1-2;Dbxref=GeneID:55344,GenBank:NR_028057.2,HGNC:HGNC:23148,MIM:300974;Name=NR_028057.2;gbkey=misc_RNA;gene=PLCXD1;product=phosphatidylinositol specific phospholipase C X domain containing 1%2C transcript variant 2;transcript_id=NR_028057.2'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NR_163416.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4449911 'NC_000024.10 BestRefSeq transcript 281381 303356 . +.ID=rna-NR_163416.1-2;Parent=gene-PLCXD1-2;Dbxref=GeneID:55344,GenBank:NR_163416.1,HGNC:HGNC:23148,MIM:300974;Name=NR_163416.1;gbkey=misc_RNA;gene=PLCXD1;product=phosphatidylinositol specific phospholipase C X domain containing 1%2C transcript variant 7;transcript_id=NR_163416.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001370370.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4449920 'NC_000024.10 BestRefSeq mRNA 276356 303356 . + .ID=rna-NM_001370370.1-2;Parent=gene-PLCXD1-2;Dbxref=GeneID:55344,GenBank:NM_001370370.1,HGNC:HGNC:23148,MIM:300974;Name=NM_001370370.1;gbkey=mRNA;gene=PLCXD1;product=phosphatidylinositol specific phospholipase C X domain containing 1%2C transcript variant 3;transcript_id=NM_001370370.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001370372.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4449935 'NC_000024.10 BestRefSeq mRNA 276356 303356 . + .ID=rna-NM_001370372.1-2;Parent=gene-PLCXD1-2;Dbxref=GeneID:55344,GenBank:NM_001370372.1,HGNC:HGNC:23148,MIM:300974;Name=NM_001370372.1;gbkey=mRNA;gene=PLCXD1;product=phosphatidylinositol specific phospholipase C X domain containing 1%2C transcript variant 6;transcript_id=NM_001370372.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001370371.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4449948 'NC_000024.10 BestRefSeq mRNA 276356 303356 . + .ID=rna-NM_001370371.1-2;Parent=gene-PLCXD1-2;Dbxref=GeneID:55344,GenBank:NM_001370371.1,HGNC:HGNC:23148,MIM:300974;Name=NM_001370371.1;gbkey=mRNA;gene=PLCXD1;product=phosphatidylinositol specific phospholipase C X domain containing 1%2C transcript variant 4;transcript_id=NM_001370371.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_018390.4' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4449992 'NC_000024.10 BestRefSeq mRNA 281381 303356 . + .ID=rna-NM_018390.4-2;Parent=gene-PLCXD1-2;Dbxref=GeneID:55344,GenBank:NM_018390.4,HGNC:HGNC:23148,MIM:300974;Name=NM_018390.4;gbkey=mRNA;gene=PLCXD1;product=phosphatidylinositol specific phospholipase C X domain containing 1%2C transcript variant 1;transcript_id=NM_018390.4'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001370373.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450006 'NC_000024.10 BestRefSeq mRNA 283478 303356 . + .ID=rna-NM_001370373.1-2;Parent=gene-PLCXD1-2;Dbxref=GeneID:55344,GenBank:NM_001370373.1,HGNC:HGNC:23148,MIM:300974;Name=NM_001370373.1;gbkey=mRNA;gene=PLCXD1;product=phosphatidylinositol specific phospholipase C X domain containing 1%2C transcript variant 5;transcript_id=NM_001370373.1'
.WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_012227.4' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450049 'NC_000024.10 BestRefSeq mRNA 304759 318796 . - .ID=rna-NM_012227.4-2;Parent=gene-GTPBP6-2;Dbxref=GeneID:8225,GenBank:NM_012227.4,HGNC:HGNC:30189,MIM:300124;Name=NM_012227.4;gbkey=mRNA;gene=GTPBP6;product=GTP binding protein 6 (putative);transcript_id=NM_012227.4'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_013239.5' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450158 'NC_000024.10 BestRefSeq mRNA 333933 386907 . - .ID=rna-NM_013239.5-2;Parent=gene-PPP2R3B-2;Dbxref=GeneID:28227,GenBank:NM_013239.5,HGNC:HGNC:13417,MIM:300339;Name=NM_013239.5;gbkey=mRNA;gene=PPP2R3B;product=protein phosphatase 2 regulatory subunit B''beta;transcript_id=NM_013239.5'
.WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_006883.2' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450431 'NC_000024.10 BestRefSeq mRNA 624344 659411 . + .ID=rna-NM_006883.2-2;Parent=gene-SHOX-2;Dbxref=GeneID:6473,GenBank:NM_006883.2,HGNC:HGNC:10853,MIM:400020;Name=NM_006883.2;gbkey=mRNA;gene=SHOX;product=SHOX homeobox%2C transcript variant 2;transcript_id=NM_006883.2'
.WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_000451.4' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450443 'NC_000024.10 BestRefSeq mRNA 630791 651584 . + .ID=rna-NM_000451.4-2;Parent=gene-SHOX-2;Dbxref=GeneID:6473,GenBank:NM_000451.4,HGNC:HGNC:10853,MIM:400020;Name=NM_000451.4;gbkey=mRNA;gene=SHOX;product=SHOX homeobox%2C transcript variant 1;transcript_id=NM_000451.4'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NR_110830.2' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450527 'NC_000024.10 BestRefSeq transcript 1190490 1212649 . -.ID=rna-NR_110830.2-2;Parent=gene-CRLF2-2;Dbxref=GeneID:64109,GenBank:NR_110830.2,HGNC:HGNC:14281,MIM:400023;Name=NR_110830.2;gbkey=misc_RNA;gene=CRLF2;product=cytokine receptor like factor 2%2C transcript variant 3;transcript_id=NR_110830.2'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001012288.3' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450536 'NC_000024.10 BestRefSeq mRNA 1190490 1212649 . - .ID=rna-NM_001012288.3-2;Parent=gene-CRLF2-2;Dbxref=GeneID:64109,GenBank:NM_001012288.3,HGNC:HGNC:14281,MIM:400023;Name=NM_001012288.3;gbkey=mRNA;gene=CRLF2;product=cytokine receptor like factor 2%2C transcript variant 2;transcript_id=NM_001012288.3'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_022148.4' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450567 'NC_000024.10 BestRefSeq mRNA 1190490 1212649 . - .ID=rna-NM_022148.4-2;Parent=gene-CRLF2-2;Dbxref=GeneID:64109,GenBank:NM_022148.4,HGNC:HGNC:14281,MIM:400023;Name=NM_022148.4;gbkey=mRNA;gene=CRLF2;product=cytokine receptor like factor 2%2C transcript variant 1;transcript_id=NM_022148.4'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NR_027760.3' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450594 'NC_000024.10 BestRefSeq transcript 1268814 1309935 . +.ID=rna-NR_027760.3-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NR_027760.3,HGNC:HGNC:2435,MIM:425000;Name=NR_027760.3;gbkey=misc_RNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 11;transcript_id=NR_027760.3'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001379163.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450607 'NC_000024.10 BestRefSeq mRNA 1268814 1325218 . + .ID=rna-NM_001379163.1-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_001379163.1,HGNC:HGNC:2435,MIM:425000;Name=NM_001379163.1;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 21;transcript_id=NM_001379163.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001379159.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450632 'NC_000024.10 BestRefSeq mRNA 1268814 1325218 . + .ID=rna-NM_001379159.1-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_001379159.1,HGNC:HGNC:2435,MIM:425000;Name=NM_001379159.1;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 17;transcript_id=NM_001379159.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001379162.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450683 'NC_000024.10 BestRefSeq mRNA 1268814 1325218 . + .ID=rna-NM_001379162.1-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_001379162.1,HGNC:HGNC:2435,MIM:425000;Name=NM_001379162.1;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 20;transcript_id=NM_001379162.1'
.WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001379164.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450728 'NC_000024.10 BestRefSeq mRNA 1268814 1323128 . +.ID=rna-NM_001379164.1-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_001379164.1,HGNC:HGNC:2435,MIM:425000;Name=NM_001379164.1;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 22;transcript_id=NM_001379164.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001379165.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450778 'NC_000024.10 BestRefSeq mRNA 1268814 1323128 . + .ID=rna-NM_001379165.1-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_001379165.1,HGNC:HGNC:2435,MIM:425000;Name=NM_001379165.1;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 23;transcript_id=NM_001379165.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001379161.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4450803 'NC_000024.10 BestRefSeq mRNA 1268814 1323128 . + .ID=rna-NM_001379161.1-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_001379161.1,HGNC:HGNC:2435,MIM:425000;Name=NM_001379161.1;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 19;transcript_id=NM_001379161.1'
.WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001379167.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4451000 'NC_000024.10 BestRefSeq mRNA 1268814 1309935 . +.ID=rna-NM_001379167.1-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_001379167.1,HGNC:HGNC:2435,MIM:425000;Name=NM_001379167.1;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 25;transcript_id=NM_001379167.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001379154.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4451023 'NC_000024.10 BestRefSeq mRNA 1268814 1309935 . + .ID=rna-NM_001379154.1-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_001379154.1,HGNC:HGNC:2435,MIM:425000;Name=NM_001379154.1;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 13;transcript_id=NM_001379154.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_006140.6' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4451050 'NC_000024.10 BestRefSeq mRNA 1268814 1309935 . + .ID=rna-NM_006140.6-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_006140.6,HGNC:HGNC:2435,MIM:425000;Name=NM_006140.6;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 1;transcript_id=NM_006140.6'
.WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_001379169.1' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4451075 'NC_000024.10 BestRefSeq mRNA 1268814 1309935 . +.ID=rna-NM_001379169.1-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_001379169.1,HGNC:HGNC:2435,MIM:425000;Name=NM_001379169.1;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 27;transcript_id=NM_001379169.1'
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'NM_172246.4' already added. File '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff' line 4451097 'NC_000024.10 BestRefSeq mRNA 1268814 1309935 . + .ID=rna-NM_172246.4-2;Parent=gene-CSF2RA-2;Dbxref=GeneID:1438,GenBank:NM_172246.4,HGNC:HGNC:2435,MIM:425000;Name=NM_172246.4;gbkey=mRNA;gene=CSF2RA;product=colony stimulating factor 2 receptor subunit alpha%2C transcript variant 3;transcript_id=NM_172246.4'
WARNING_TRANSCRIPT_ID_DUPLICATE: Too many 'WARNING_TRANSCRIPT_ID_DUPLICATE' warnings, no further warnings will be shown.
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..
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2530000 ......00:00:55
Total: 2530653 markers added.
00:00:55 Create exons from CDS (if needed):
00:00:56 Exons created for 0 transcripts.
00:00:56 Deleting redundant exons (if needed):
00:00:59 Total transcripts with deleted exons: 0
00:00:59 Collapsing zero length introns (if needed):
00:01:02 Total collapsed transcripts: 0
00:01:02 Reading sequences :
00:01:02 FASTA file: '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/genomes/GRCh38.p14.fa' not found.
00:01:02 FASTA file: '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/sequences.fa' not found.
java.lang.RuntimeException: Cannot find reference sequence.
at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.readExonSequences(SnpEffPredictorFactory.java:702)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.readExonSequences(SnpEffPredictorFactoryGff.java:453)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:350)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
java.lang.RuntimeException: Error reading file '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14/genes.gff'
java.lang.RuntimeException: Cannot find reference sequence.
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:362)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:01:02 Logging
00:01:03 Checking for updates...
00:01:04 Done.
#like there are some file which is showing missing like .gff file and some .fasta files

btw manually i have downloaded that files then also same issue is showing up

pcingola · 2024-01-17T17:13:24Z

@singha30:
I don't understand what you are trying to do, or what the problem is, could you clarify?

You've shown three separate commands: downloading GRCh38.p14 and building it (twice). IMO if the database is available for download, there is no point on building it yourself, so I'm not sure what you are trying to accomplish.

All commands succeeded, so I don't see what your problem is.

Tip: Next time maybe you can attach log files instead of copy pasting the content.

pcingola closed this as completed Dec 4, 2023

pcingola reopened this Jan 9, 2024

pcingola closed this as completed Jan 17, 2024

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Unable to download GRCh38.mane.1.2.refseq: "The specified blob does not exist" #501

Unable to download GRCh38.mane.1.2.refseq: "The specified blob does not exist" #501

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pcingola commented Jan 17, 2024

Unable to download GRCh38.mane.1.2.refseq: "The specified blob does not exist" #501

Unable to download GRCh38.mane.1.2.refseq: "The specified blob does not exist" #501

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