Files were run by submitting pairs of prefix strings to the following script:
to be clear, the values of GENES and BWAINDEX are set in the scriptsettings file and have worked for 2 cuffmerge runs in the same batch as the one that had this error. 4 jobs worked 1 job failed.
here is the console log:
I have no idea why this error should have occurred as all of this seems to be internal cuffmerge behavior, and none of it subject to my alteration via command line input.
Code:
#!/bin/bash source /UCHC/HPC/Everson_HPC/cluster_scripts/shbin/ScriptSettings.lib.sh echo "./$1_CUFFLINKS/transcripts.gtf ./$2_CUFFLINKS/transcripts.gtf" | cuffmerge -g $GENES -s $BWAINDEX -p 8 -o $1_$2_Merge /dev/stdin
here is the console log:
Code:
[Fri Mar 1 16:48:14 2013] Beginning transcriptome assembly merge
-------------------------------------------
[Fri Mar 1 16:48:14 2013] Preparing output location NC_TC_Merge/
[Fri Mar 1 16:48:23 2013] Converting GTF files to SAM
gtf_to_sam: /lib64/libz.so.1: no version information available (required by gtf_to_sam)
[16:48:23] Loading reference annotation.
gtf_to_sam: /lib64/libz.so.1: no version information available (required by gtf_to_sam)
[16:48:29] Loading reference annotation.
[Fri Mar 1 16:48:35 2013] Quantitating transcripts
cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks)
You are using Cufflinks v2.0.2, which is the most recent release.
Command line:
cufflinks -o NC_TC_Merge/ -F 0.05 -g /UCHC/HPC/Everson_HPC/reference_data/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/gen
es.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 NC_TC_Merge
/tmp/mergeSam_filefQU62s
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File NC_TC_Merge/tmp/mergeSam_filefQU62s doesn't appear to be a valid BAM file, trying SAM...
[16:48:35] Loading reference annotation.
[16:48:42] Inspecting reads and determining fragment length distribution.
Processed 83568 loci.
> Map Properties:
> Normalized Map Mass: 196148.00
> Raw Map Mass: 196148.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[16:48:44] Assembling transcripts and estimating abundances.
Processed 83568 loci.
[Fri Mar 1 17:15:20 2013] Comparing against reference file /UCHC/HPC/Everson_HPC/reference_data/igenomes/Homo_sapiens/UCSC/hg
19/Annotation/Genes/genes.gtf
You are using Cufflinks v2.0.2, which is the most recent release.
[Fri Mar 1 17:16:59 2013] Comparing against reference file /UCHC/HPC/Everson_HPC/reference_data/igenomes/Homo_sapiens/UCSC/hg
19/Annotation/Genes/genes.gtf
You are using Cufflinks v2.0.2, which is the most recent release.
Traceback (most recent call last):
File "/UCHC/HPC/Everson_HPC/tuxedo_tools/cufflinks/bin/cuffmerge", line 576, in <module>
sys.exit(main())
File "/UCHC/HPC/Everson_HPC/tuxedo_tools/cufflinks/bin/cuffmerge", line 559, in main
compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
File "/UCHC/HPC/Everson_HPC/tuxedo_tools/cufflinks/bin/cuffmerge", line 437, in compare_meta_asm_against_ref
shutil.move("tmp_meta_asm.combined.gtf", output_dir + "/merged.gtf")
File "/UCHC/HPC/Everson_HPC/python-2.7/lib/python2.7/shutil.py", line 299, in move
copy2(src, real_dst)
File "/UCHC/HPC/Everson_HPC/python-2.7/lib/python2.7/shutil.py", line 128, in copy2
copyfile(src, dst)
File "/UCHC/HPC/Everson_HPC/python-2.7/lib/python2.7/shutil.py", line 82, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: 'tmp_meta_asm.combined.gtf'
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