Comments (17)
cc2qe
commented on July 28, 2024
What do the files in ths /mnt/lustre/references/speedseq/annotations/cnvnator_chroms directory look like? Do your chromosomes have "chr" prefixes by any chance? SpeedSeq sv currently doesn't support chromosome prefixes because cnvnator's names are rigid, so I'm not sure how it will behave with them.
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s-boardman
commented on July 28, 2024
Ah that's a good point. We're using hg19 so they are chr1.fa etc.
I've used the standalone version of CNVnator previously with hg19 formatted chromosomes and its worked fine. Perhaps it may be to do with the changes made to the CNVnator-multi program supplied with SpeedSeq?
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cc2qe
commented on July 28, 2024
yeah, quite possibly the case. It comes down to this file mainly. I think Alexej may have modified it for more flexibility since the speedseq implementation was written.
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s-boardman
commented on July 28, 2024
Hi Colby, sorry for the delay.
I've downloaded GRCh37 and set it up as per the user guide. Will be doing some testing over the next few days so shall update this ticket with new information in due course. Hopefully it'll be resolved by the corrected naming as you suspect.
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s-boardman
commented on July 28, 2024
Hi Colby,
I've been able to run this today and no longer have the chromosome naming error.
However, what we now have is what looks like a root error (output below):
/opt/gridware/pkg/apps/speedseq/0.0.3a/gcc-4.4.6+root-5.34.30+samtools-0.1.19+python-2.7.3/bin/cnvnator-multi: error while loading shared libraries: libCore.so.5.34: cannot open shared object file: No such file or directory
Should I open a new ticket or do you think this related?
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cc2qe
commented on July 28, 2024
I think this is a different issue, I've opened a new ticket here #44
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s-boardman
commented on July 28, 2024
As per #44;
Command I used to run speedseq sv:
qsub -V -e e -o o -cwd -b Y -N speedseq_sv_1 speedseq sv -R /mnt/lustre/references/speedseq/GRCh37/grch37.fasta -o ERR194146 -g -k -d -v \
-B /mnt/archive/analysis/projects/HiSeq/CNV_Genome_Project/External_Data/Illumina_Platinum_Genomes/NA12877/bam_fromfastq_dl/ERR194146.bam \
-S /mnt/archive/analysis/projects/HiSeq/CNV_Genome_Project/External_Data/Illumina_Platinum_Genomes/NA12877/bam_fromfastq_dl/ERR194146.splitters.bam \
-D /mnt/archive/analysis/projects/HiSeq/CNV_Genome_Project/External_Data/Illumina_Platinum_Genomes/NA12877/bam_fromfastq_dl/ERR194146.discordants.bam
Error message:
Traceback (most recent call last):
File "/opt/gridware/pkg/apps/speedseq/0.0.3a/gcc-4.4.6+root-5.34.30+samtools-0.1.19+python-2.7.3/bin/cnvnator_wrapper.py", line 350, in <module>
chroms_list = get_chroms_list(args.bam)
File "/opt/gridware/pkg/apps/speedseq/0.0.3a/gcc-4.4.6+root-5.34.30+samtools-0.1.19+python-2.7.3/bin/cnvnator_wrapper.py", line 153, in get_chroms_list
proc = subprocess.Popen(['samtools', 'view', '-H', bam_fn], stdout = subprocess.PIPE)
File "/opt/gridware/pkg/apps/python/2.7.3/gcc-4.4.6/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
File "/opt/gridware/pkg/apps/python/2.7.3/gcc-4.4.6/lib/python2.7/subprocess.py", line 1249, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
The structure of my references directory is as follows:
ls -l /mnt/lustre/references/speedseq/GRCh37/
-rw-rw-r-- 1 sb2 bioinfo 3147288981 Aug 25 14:40 grch37.fasta
-rw-rw-r-- 1 sb2 bioinfo 6563 Aug 26 16:18 grch37.fasta.amb
-rw-rw-r-- 1 sb2 bioinfo 869 Aug 26 16:18 grch37.fasta.ann
-rw-rw-r-- 1 sb2 bioinfo 3095694072 Aug 26 16:17 grch37.fasta.bwt
-rw-rw-r-- 1 sb2 bioinfo 713 Aug 27 13:06 grch37.fasta.fai
-rw-rw-r-- 1 sb2 bioinfo 773923497 Aug 26 16:18 grch37.fasta.pac
-rw-rw-r-- 1 sb2 bioinfo 1547847040 Aug 26 16:30 grch37.fasta.sa
ls -l /mnt/lustre/references/speedseq/annotations/cnvnator_chroms/
-rw-rw-r-- 1 sb2 bioinfo 137793664 Aug 25 13:35 10.fa
-rw-rw-r-- 1 sb2 bioinfo 137256629 Aug 25 13:35 11.fa
-rw-rw-r-- 1 sb2 bioinfo 136082764 Aug 25 13:35 12.fa
-rw-rw-r-- 1 sb2 bioinfo 117089380 Aug 25 13:35 13.fa
-rw-rw-r-- 1 sb2 bioinfo 109138703 Aug 25 13:35 14.fa
-rw-rw-r-- 1 sb2 bioinfo 104240253 Aug 25 13:35 15.fa
-rw-rw-r-- 1 sb2 bioinfo 91860670 Aug 25 13:35 16.fa
-rw-rw-r-- 1 sb2 bioinfo 82548468 Aug 25 13:35 17.fa
-rw-rw-r-- 1 sb2 bioinfo 79378540 Aug 25 13:35 18.fa
-rw-rw-r-- 1 sb2 bioinfo 60114471 Aug 25 13:35 19.fa
-rw-rw-r-- 1 sb2 bioinfo 253404802 Aug 25 13:35 1.fa
-rw-rw-r-- 1 sb2 bioinfo 64075950 Aug 25 13:35 20.fa
-rw-rw-r-- 1 sb2 bioinfo 48932064 Aug 25 13:35 21.fa
-rw-rw-r-- 1 sb2 bioinfo 52159647 Aug 25 13:35 22.fa
-rw-rw-r-- 1 sb2 bioinfo 247252699 Aug 25 13:35 2.fa
-rw-rw-r-- 1 sb2 bioinfo 201322807 Aug 25 13:35 3.fa
-rw-rw-r-- 1 sb2 bioinfo 194340184 Aug 25 13:35 4.fa
-rw-rw-r-- 1 sb2 bioinfo 183930518 Aug 25 13:35 5.fa
-rw-rw-r-- 1 sb2 bioinfo 173966988 Aug 25 13:35 6.fa
-rw-rw-r-- 1 sb2 bioinfo 161790978 Aug 25 13:35 7.fa
-rw-rw-r-- 1 sb2 bioinfo 148803426 Aug 25 13:35 8.fa
-rw-rw-r-- 1 sb2 bioinfo 143566992 Aug 25 13:35 9.fa
-rw-rw---- 1 sb2 bioinfo 16849 Aug 25 14:38 M.fa
-rw-rw---- 1 sb2 bioinfo 157858406 Aug 25 14:36 X.fa
-rw-rw---- 1 sb2 bioinfo 60363129 Aug 25 14:36 Y.fa
Is there a key file that I am missing?
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cc2qe
commented on July 28, 2024
is samtools in your path? also, can you should the header of /mnt/archive/analysis/projects/HiSeq/CNV_Genome_Project/External_Data/Illumina_Platinum_Genomes/NA12877/bam_fromfastq_dl/ERR194146.bam
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s-boardman
commented on July 28, 2024
Ah, samtools wasn't loaded at the time. It looks like it isn't a linked dependency to speedseq qhen I load that on our cluster.
Here's my bam header for you; chromosome numbering looks fine to me?
@HD VN:1.3 SO:coordinate
@SQ SN:1 LN:249250621
@SQ SN:2 LN:243199373
@SQ SN:3 LN:198022430
@SQ SN:4 LN:191154276
@SQ SN:5 LN:180915260
@SQ SN:6 LN:171115067
@SQ SN:7 LN:159138663
@SQ SN:8 LN:146364022
@SQ SN:9 LN:141213431
@SQ SN:10 LN:135534747
@SQ SN:11 LN:135006516
@SQ SN:12 LN:133851895
@SQ SN:13 LN:115169878
@SQ SN:14 LN:107349540
@SQ SN:15 LN:102531392
@SQ SN:16 LN:90354753
@SQ SN:17 LN:81195210
@SQ SN:18 LN:78077248
@SQ SN:19 LN:59128983
@SQ SN:20 LN:63025520
@SQ SN:21 LN:48129895
@SQ SN:22 LN:51304566
@SQ SN:X LN:155270560
@SQ SN:Y LN:59373566
@SQ SN:M LN:16569
@RG ID:ERR194146 SM:ERR194146
@PG ID:bwa PN:bwa CL:/opt/gridware/pkg/apps/bwa/0.7.8/gcc-4.4.6/bin/bwa mem -t 1 -M -R @RG\tID:ERR194146\tSM:ERR194146 /mnt/lustre/references/speedseq/GRCh37/grch37.fasta ../fastq_dl/ERR194146_1.subset.fastq ../fastq_dl/ERR194146_2.subset.fastq VN:0.7.8-r455
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cc2qe
commented on July 28, 2024
yeah, the samtools thing is an oversight, i didn't realize that it was being called.
BAM header looks fine, is the problem solved if you add samtools to your path?
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s-boardman
commented on July 28, 2024
Looks OK so far!
I'll be able to check it all on Tuesday (long weekend here in the UK) and hopefully everything will have run hunky dory and I'll be able to close the task for you.
Thanks (again!) for the troubleshooting help. 😄
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cc2qe
commented on July 28, 2024
sounds good, appreciate the detailed bug report. i'll change speedseq to explicitly use the embedded sambamba rather than the samtools in PATH
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s-boardman
commented on July 28, 2024
OK, cool. I've asked our syadmin to pop samtools into the load path for speedseq for the time being so that should make sure I don't see it again.
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s-boardman
commented on July 28, 2024
Hi Colby, sorry for the late reply.
With samtools in my PATH its worked fine.
I've got an Error (below) which I think is related to me qsubbing the jobs to our cluster via ssh (rather than running speedseq natively). Could you confirm this, and explain what I'm missing out on. This happens with ssh -X (my default) and ssh -Y.
Error in <TGClient::TGClient>: can't open display "localhost:11.0", switchingt to batch mode...
In case you run from a remote ssh session, reconnect with ssh -Y
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cc2qe
commented on July 28, 2024
I also see this error when we submit speedseq jobs through LSF. I'm not sure what CNVnator is attempting to do with X11, but as far as I can tell, you can ignore this message. Does your output complete and look correct?
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s-boardman
commented on July 28, 2024
Yeah that makes sense. Everything else looked fine so I'm definitely at the
point where it's working as intended.
Thanks for the help again!
On Wed, 2 Sep 2015 at 16:40, Colby Chiang [email protected] wrote:
I also see this error when we submit speedseq jobs through LSF. I'm not
sure what CNVnator is attempting to do with X11, but as far as I can tell,
you can ignore this message. Does your output complete and look correct?—
Reply to this email directly or view it on GitHub
#40 (comment).
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s-boardman
commented on July 28, 2024
@cc2qe you can mark this issue closed. Following all the helpful comments has resolved the error.
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