Is free version of novoalign not adequate to NCLscan ? #9

tyaoi · 2016-11-04T02:47:24Z

Hello,
I just came about a trouble as the follows. Did the use of free version of novoalign cause this ?
My PC environments is Ubuntu 14.04LTS. i7-6700K, 64GB RAM.
All pre-required 5 tools were installed by using Linuxbrew that is equivalent to Homebrew in OSX.
Moreover, NCLscan was run on Python 2.7.12 |Anaconda 4.2.0 (64-bit).

Sincerely,

Yaoi T

License file not found.

Licensed for evaluation, educational, and not-for-profit use only.

novoalign -r A 1 -g 99 -x 99 -d /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.JS.ndx -f /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.main.unmapped_1.fastq -o SAM

Starting at Thu Nov 3 20:17:47 2016

Interpreting input files as Sanger FASTQ.

Error: /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.JS.ndx does not appear to be a valid novoindex. Code 9

novoalign (V3.02.13 - Build Jun 29 2015 @ 12:27:18 - A short read aligner with qualities.

(C) 2008-2015 NovoCraft Technologies Sdn Bhd.

License file not found.

Licensed for evaluation, educational, and not-for-profit use only.

novoalign -r A 1 -g 99 -x 99 -d /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.JS.ndx -f /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.main.unmapped_2.fastq -o SAM

Starting at Thu Nov 3 20:17:47 2016

Interpreting input files as Sanger FASTQ.

Error: /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.JS.ndx does not appear to be a valid novoindex. Code 9
End of file reading 4 bytes
Total time cost = 0.00139594078064 sec
End of file reading 4 bytes
Total time cost = 0.00144004821777 sec

tyaoi · 2016-11-04T03:03:31Z

Hello,
I write another information in the below:
In NCLscan.config, I wrote the PATH to tools
bedtools_bin = /home/tyaoi4/.linuxbrew/bin/bedtools
blat_bin = /home/tyaoi4/.linuxbrew/bin/blat
bwa_bin = /home/tyaoi4/.linuxbrew/bin/bwa
samtools_bin = /home/tyaoi4/.linuxbrew/bin/samtools
novoalign_bin = /home/tyaoi4/.linuxbrew/bin/novoalign
novoindex_bin = /home/tyaoi4/.linuxbrew/bin/novoindex

Sincerely,

Yaoi T

tyaoi · 2016-11-05T13:02:46Z

Hello,

I retried to run after obtaining trial license.
However, the following error message was returned.

Error: /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.JS.ndx does not appear to be a valid novoindex. Code 9

What does " Code 9" mean ?
How can I do to resolve this problem ?

I apprecite any advice.
Thanks,

Yaoi T

chiangtw · 2016-11-05T14:14:42Z

Hi,

You may check the two files first,

"CT11_NCLscan.JS.fa"
"CT11_NCLscan.JS.ndx"

Do these two files have normal file size?

Thanks!

tyaoi · 2016-11-05T14:31:49Z

Hi,
Thanks for your quick response.
Those files have 0 kb and 18.9 kb respectively.
I don't know normal file size of them, but the size of "CT11_NCLscan.JS.fa" is probably not adequate.

Would you tell me the other check list ?

Thanks,

Yaoi T

chiangtw · 2016-11-13T23:07:46Z

Hi,
Please check the file size of the following files,

CT11_NCLscan.sam
CT11_NCLscan.unmapped.sam
CT11_NCLscan.rG.psl
CT11_NCLscan.chi0.bed
CT11_NCLscan.chi.bed
CT11_NCLscan.preJS.bed
CT11_NCLscan.preJS.info2
CT11_NCLscan.JS.info
CT11_NCLscan.JS.cleaned.info
CT11_NCLscan.preJS.seq
CT11_NCLscan.preJS.seq2
CT11_NCLscan.preJS.seq12

Thanks!

tyaoi · 2016-11-14T05:37:57Z

Hi,

Thanks for your reply.

I attach the following files:

" output_name_size_list.txt " is the list of all produced files including
each size.

" NCLscan.config " includes the actually used information. Herein, I
conducted the runs by using mouse genome data files.
Moreover, I tried a run by using the max_fragment_size = 1139 because the
maximum in the fragment size distribution is shown to be from 1125 to
1139 (count
300). The max_read_len value is default because the read length is 90.
However, I got the same results.

" Mus.genome.ref_name_size_list.txt " is the list of mouse reference genome
that includes both the downloaded files and the files produced by the
program.

Thanks,

矢追毅
京都府立医科大学・院・分子病態病理学
助教
京都市上京区河原町通広小路梶井町465
TEL/FAX 075-251-5849

2016-11-14 8:07 GMT+09:00 Tai-Wei Chiang notifications@github.com:

Hi,
Please check the file size of the following files,

CT11_NCLscan.sam

CT11_NCLscan.unmapped.sam

CT11_NCLscan.rG.psl

CT11_NCLscan.chi0.bed

CT11_NCLscan.chi.bed

CT11_NCLscan.preJS.bed

CT11_NCLscan.preJS.info2

CT11_NCLscan.JS.info

CT11_NCLscan.JS.cleaned.info

CT11_NCLscan.preJS.seq

CT11_NCLscan.preJS.seq2

CT11_NCLscan.preJS.seq12

Thanks!

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
#9 (comment), or mute
the thread
https://github.com/notifications/unsubscribe-auth/AQMHiaUGlMEZZfMTw40VahdO7e1KeTXaks5q95hCgaJpZM4KpI9H
.

AllRef.fa 2950187399
AllRef.fa.amb 11343
AllRef.fa.ann 11449641
AllRef.fa.bwt 2894859392
AllRef.fa.pac 723714829
AllRef.fa.sa 1447429704
AllRef.ndx 8163709198
GRCm38.p4.genome.fa 2785778639
GRCm38.p4.genome.fa.fai 3255
RepChrM.fa 33151
gencode.vM11.annotation.gtf 810222289
gencode.vM11.lncRNA_transcripts.fa 20821697
gencode.vM11.pc_transcripts.fa 143553912

CT11_NCLscan.2.chi.bed 0
CT11_NCLscan.2.info 0
CT11_NCLscan.2.info.fa 0
CT11_NCLscan.2b.info 0
CT11_NCLscan.3.info 0
CT11_NCLscan.3b.info 0
CT11_NCLscan.4.info 0
CT11_NCLscan.4b.info 0
CT11_NCLscan.JS.GRCh37.2.psl 0
CT11_NCLscan.JS.cleaned.info 0
CT11_NCLscan.JS.clear.fa 0
CT11_NCLscan.JS.fa 0
CT11_NCLscan.JS.info 0
CT11_NCLscan.JS.info_1 0
CT11_NCLscan.JS.info_2 0
CT11_NCLscan.JS.ndx 16877
CT11_NCLscan.JS.seq 0
CT11_NCLscan.JS.seq12 0
CT11_NCLscan.JS.seq_1 0
CT11_NCLscan.JS.seq_2 0
CT11_NCLscan.JS1.Idx 0
CT11_NCLscan.JS1.preIdx 0
CT11_NCLscan.JS2.Idx 0
CT11_NCLscan.JS2.cleaned.info 0
CT11_NCLscan.JS2.fa 0
CT11_NCLscan.JS2.info 0
CT11_NCLscan.JS2.info_1 0
CT11_NCLscan.JS2.info_2 0
CT11_NCLscan.JS2.ndx 16877
CT11_NCLscan.JS2.preIdx 0
CT11_NCLscan.JS2.prefa 0
CT11_NCLscan.JS2.result.info 0
CT11_NCLscan.JS2.seq 0
CT11_NCLscan.JS2.seq_1 0
CT11_NCLscan.JS2.seq_2 0
CT11_NCLscan.PreJS2.bed 0
CT11_NCLscan.PreJS2.info 0
CT11_NCLscan.PreJS2.info2 2
CT11_NCLscan.PreJS2.seq 0
CT11_NCLscan.PreJS2.seq2 2
CT11_NCLscan.chi.bed 0
CT11_NCLscan.chi0.bed 0
CT11_NCLscan.chi2.bed 0
CT11_NCLscan.chi3.bed 0
CT11_NCLscan.colinear.psl 0
CT11_NCLscan.info 0
CT11_NCLscan.linearJS 0
CT11_NCLscan.main.JS2.sam 0
CT11_NCLscan.main.JS2b.sam 0
CT11_NCLscan.main.bwa.bam 106688204
CT11_NCLscan.main.bwa.unmapped.sam 12378112
CT11_NCLscan.main.bwa.unmapped.sam.id 0
CT11_NCLscan.main.bwa.unmapped_1.fastq 0
CT11_NCLscan.main.bwa.unmapped_2.fastq 0
CT11_NCLscan.main.sam 0
CT11_NCLscan.main.um3.fa 0
CT11_NCLscan.main.unmapped.fa 0
CT11_NCLscan.main.unmapped.sam 0
CT11_NCLscan.main.unmapped.sam.id 0
CT11_NCLscan.main.unmapped_1.fastq 0
CT11_NCLscan.main.unmapped_2.fastq 0
CT11_NCLscan.main_1.JS.sam 0
CT11_NCLscan.main_1.um3.fastq 0
CT11_NCLscan.main_2.JS.sam 0
CT11_NCLscan.main_2.um3.fastq 0
CT11_NCLscan.ncl.sam 0
CT11_NCLscan.preJS.bed 0
CT11_NCLscan.preJS.info 0
CT11_NCLscan.preJS.info2 2
CT11_NCLscan.preJS.seq 0
CT11_NCLscan.preJS.seq2 2
CT11_NCLscan.preResult 0
CT11_NCLscan.rG.non_un.psl 0
CT11_NCLscan.result.info 0
CT11_NCLscan.result.sam 0
CT11_NCLscan.result.tmp 0
CT11_NCLscan.tmp.info 0
CT11_NCLscan.tmp2.info 0
CT11_NCLscan.un.psl 0
CT11_NCLscan.unmapped.2.fa 0
CT11_NCLscan.unmapped.fa 0
all.CT11_NCLscan.1.result 0
all.CT11_NCLscan.1.sam 0
all.CT11_NCLscan.1b.result 0
all.CT11_NCLscan.1b.sam 0
all.CT11_NCLscan.JS.Parsered.sam 0
all.CT11_NCLscan.JS.sam 0
all.CT11_NCLscan.JS2.sam 0
all.CT11_NCLscan.JS2b.sam 0
all.CT11_NCLscan.b.result 0
all.CT11_NCLscan.result 0
all.CT11_NCLscan.um3.colinear.psl 0
all.CT11_NCLscan.um3.fa 0
temp.list 0
tmp.info 0

chiangtw · 2016-11-18T07:20:31Z

Hi,

It seems that there are no "unmapped reads" in the your input dataset.
You may check these two files first:

"CT11_NCLscan.main.bwa.bam"
"CT11_NCLscan.main.bwa.unmapped.sam"

"CT11_NCLscan.main.bwa.bam" was the alignment result mapped by bwa, and "CT11_NCLscan.main.bwa.unmapped.sam" was the unmapped part filtered by samtools.

tyaoi · 2016-11-18T08:36:28Z

Hi, Tai-Wei

Thank you for reply.

CT11_NCLscan.main.bwa.bam 106688204
CT11_NCLscan.main.bwa.unmapped.sam 12378112

I am sorry to trouble you, but thank you for your continuous support.

Yaoi T

chiangtw · 2016-11-19T09:20:54Z

I'm mean ...
Are there some "unmapped-reads-removing" pre-processes on your input dataset?
because it looks like that there are no unmapped reads in the dataset.
NCLscan needs the unmapped reads to find the NCL candidates.

Thanks!

chiangtw closed this as completed Feb 20, 2019

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Is free version of novoalign not adequate to NCLscan ? #9

Is free version of novoalign not adequate to NCLscan ? #9

tyaoi commented Nov 4, 2016

tyaoi commented Nov 4, 2016

tyaoi commented Nov 5, 2016

chiangtw commented Nov 5, 2016

tyaoi commented Nov 5, 2016

chiangtw commented Nov 13, 2016

tyaoi commented Nov 14, 2016

chiangtw commented Nov 18, 2016

tyaoi commented Nov 18, 2016

chiangtw commented Nov 19, 2016

Is free version of novoalign not adequate to NCLscan ? #9

Is free version of novoalign not adequate to NCLscan ? #9

Comments

tyaoi commented Nov 4, 2016

License file not found.

Licensed for evaluation, educational, and not-for-profit use only.

novoalign -r A 1 -g 99 -x 99 -d /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.JS.ndx -f /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.main.unmapped_1.fastq -o SAM

Starting at Thu Nov 3 20:17:47 2016

Interpreting input files as Sanger FASTQ.

novoalign (V3.02.13 - Build Jun 29 2015 @ 12:27:18 - A short read aligner with qualities.

(C) 2008-2015 NovoCraft Technologies Sdn Bhd.

License file not found.

Licensed for evaluation, educational, and not-for-profit use only.

novoalign -r A 1 -g 99 -x 99 -d /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.JS.ndx -f /media/tyaoi4/SeaGate3TB/NCLscan_Results/CT11_NCLscan_Result/CT11_NCLscan.main.unmapped_2.fastq -o SAM

Starting at Thu Nov 3 20:17:47 2016

Interpreting input files as Sanger FASTQ.

tyaoi commented Nov 4, 2016

tyaoi commented Nov 5, 2016

chiangtw commented Nov 5, 2016

tyaoi commented Nov 5, 2016

chiangtw commented Nov 13, 2016

tyaoi commented Nov 14, 2016

chiangtw commented Nov 18, 2016

tyaoi commented Nov 18, 2016

chiangtw commented Nov 19, 2016