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The genome file annotation_chr.genome has no valid entries #2

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Kingatsu opened this issue Oct 28, 2022 · 10 comments
Open

The genome file annotation_chr.genome has no valid entries #2

Kingatsu opened this issue Oct 28, 2022 · 10 comments

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@Kingatsu
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Hello,
The CRAFT software is a power tools for me.
However, I got the following error messages when I want to use fasta file from GENCODE, which is used to find my circRNA.
Error: The genome file annotation_chr.genome has no valid entries. Exiting.
Error: The genome file annotation_chr.genome has no valid entries. Exiting.
mv: cannot stat '/data/input/backsplice_gene_name.txt': No such file or directory
I have changed the list_backsplice.txt and backsplice_gene_name.txt from 1 to chr1, to adapt my fasta file.
But the error still here.

I don't know whether I MUST use the genome file from Ensembl for CRAFT.
Can you give me some helps?

Thanks in advance.

Regards,
Kingatsu
@annadalmolin
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annadalmolin commented Oct 28, 2022 via email

@Kingatsu
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Hello Anna,
Thanks for the prompt reply.

Yes, I used the Ensembl genome file and it seems work!
But it took me more than 12h but just finished the MiRNA binding site prediction analysis for ~20 circRNAs.
I am not sure if it is normal.

Thanks again for the help!

Regards,
Kingatsu

@annadalmolin
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annadalmolin commented Oct 29, 2022 via email

@Kingatsu
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Hi Anna,

Here is my computer data:

cat /proc/cpuinfo| grep "cpu cores"| uniq
cpu cores       : 10
cat /proc/cpuinfo| grep "processor"| wc -l
20

And my param.txt is:

MRO
hsa
80      -15
all     all
hg38
1       1       30      FALSE   both
l=160000
l=160000

I think it doesn't check the overlapping with AGO2 binding sites because I don't put the AGO2_binding_sites.bed into /input.
Also, I tested the data with same parameters except changed "MRO" to "RO" yesterday.
And I got the output this morning

...
Quitting from lines 94-165 (functional_predictions_single_circRNA.Rmd)
Error in read.table(file_beRBP, header = T, sep = "\t") :
  no lines available in input
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> read.table
In addition: Warning messages:
1: In system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1
2: package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'org.Hs.eg.db'

Execution halted
mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory
...
Quitting from lines 90-153 (functional_predictions_all_circRNAs.Rmd)
Error in read.table(file_beRBP, header = T, sep = "\t") :
  no lines available in input
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> read.table
In addition: Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'grid'

Execution halted

It seems the RBP prediction failed, and here is the beRBP.log:

working on M001_0.6 Sat Oct 29 03:43:26 UTC 2022
analysis_RBP featureMat_start=Sat Oct 29 03:43:26 UTC 2022
1 rank...Sat Oct 29 03:43:29 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cp: cannot stat 'siteSegment_1.csrv': No such file or directory
2 rank...Sat Oct 29 03:43:58 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_2.csrv: No such file or directory
paste: csrvI.txt: No such file or directory
3 rank...Sat Oct 29 03:44:19 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_3.csrv: No such file or directory
4 rank...Sat Oct 29 03:44:47 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_4.csrv: No such file or directory
5 rank...Sat Oct 29 03:45:16 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_5.csrv: No such file or directory
6 rank...Sat Oct 29 03:45:44 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_6.csrv: No such file or directory
7 rank...Sat Oct 29 03:46:05 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_7.csrv: No such file or directory
8 rank...Sat Oct 29 03:46:28 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_8.csrv: No such file or directory
9 rank...Sat Oct 29 03:46:54 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_9.csrv: No such file or directory
10 rank...Sat Oct 29 03:47:14 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_10.csrv: No such file or directory
analysis_RBP featureMat_finished=Sat Oct 29 03:47:40 UTC 2022
M001_0.6 all
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Error in file(file, "rt") : cannot open the connection
Calls: generalPred -> read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'analysis_RBP.ftMat.txt': No such file or directory
Execution halted

Is this the circRNA sequence does not predict RBP or sth wrong before RBP prediction?

Thanks in advance.

Regards.
Kingatsu

@annadalmolin
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annadalmolin commented Nov 2, 2022 via email

@Kingatsu
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Kingatsu commented Nov 3, 2022

Hi Anna,

  • did you placed the UCSC genome and indexes in the input/ directory?
    Yes, here is my input files list:
backsplice_gene_name.txt  hg38.02.idx  hg38.nhr  hg38.not  hg38.nto                     Homo_sapiens.GRCh38.dna.primary_assembly.fa
hg38.00.idx               hg38.fa      hg38.nin  hg38.nsq  hg38.shd                     Homo_sapiens.GRCh38.dna.primary_assembly.fa.fai
hg38.01.idx               hg38.ndb     hg38.njs  hg38.ntf  Homo_sapiens.GRCh38.104.gtf

  • And *hg38 *is the corresponding genome version?
    Yes, I used circompara2 to find the circRNAs with GRCh38.p12.genome.fa [from GENCODE]

  • the parameters in the params.txt file are tab-separated?
    Yes, I am sure that.

Now I am re-running CRAFT with "MO" parameter.
I will tell you the error details later if it occurs.

Regards,
Kingatsu

@Kingatsu
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Kingatsu commented Nov 3, 2022 •
edited

Hi Anna,
Here is the error log:

Error (circ1) : No ORFs found for the specified parameters
Error (circ1) : No ORFs found for the specified parameters
Error (circ1) : No ORFs found for the specified parameters
Error (circ1) : No ORFs found for the specified parameters
Error: Invalid record in file result_30.bed. Record is
circ2     101     10
ERROR: Received illegal bin number 262143 from getBin call.
ERROR: Unable to add record to tree.
ORF prediction analysis completed.

The circ1 is a 'chr_start-end' form and circ2 is a 'chr:start-end' form, I am sorry for blurring them off here.
Then it came to the R pipeline, and so many warnings and errors occured.
Such as:

- Maybe a connection error: 
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cloud.r-project.org/src/contrib:
  cannot open URL 'https://cloud.r-project.org/src/contrib/PACKAGES'
PS: but actually I can download the PACKAGES from this URL by 'wget'

- Error in function
Quitting from lines 650-700 (functional_predictions_single_circRNA.Rmd)
Error in function (type, msg, asError = TRUE)  :
  Failed to connect to multimir.org port 80: Connection refused
Calls: <Anonymous> ... submit_request -> <Anonymous> -> .postForm -> <Anonymous> -> fun
In addition: Warning messages:
1: In system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1
2: package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'org.Hs.eg.db'
3: position_stack requires non-overlapping x intervals
4: ggrepel: 287 unlabeled data points (too many overlaps). Consider increasing max.overlaps
5: position_stack requires non-overlapping x intervals
6: ggrepel: 292 unlabeled data points (too many overlaps). Consider increasing max.overlaps
7: ggrepel: 287 unlabeled data points (too many overlaps). Consider increasing max.overlaps

That is the error I have seen. it seems some circ analysis failed before (like can't find the ORF) and started cascade of Error in R later.

Thanks in advance.

Regards,
Kingatsu

@annadalmolin
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annadalmolin commented Nov 10, 2022 via email

@annadalmolin
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annadalmolin commented Nov 18, 2022 via email

@Kingatsu
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Hi Anna,
Sorry for the late reply.

Well, I cann't run the CRAFT with RBP detection yet. So maybe the problems are in the circRNA sequences, I guess.
I am running the circRNA detection tools again and try to find some other circRNAs, then run the CRAFT again.
I will tell you if it works!

Regards,
Kingatsu

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@annadalmolin @Kingatsu