Closed mmelendrez closed 9 years ago
I'm not really 100% sure what this error means, but graphsample.py is failing because when it tries to run the montage command in the shell it is getting an error
Can you look to see if any .png files are anywhere in your project in /tmp/FVM00003_*
montage: missing an image filename `/tmp/FVM00003_AndesZYDTDDrunsample/FVM00003_Andes.bam.qualdepth.png' @ montage.c/MontageImageCommand/1649.
Traceback (most recent call last):
File "/media/VD_Research/People/Melanie.Melendrez/.ngs_mapper/bin/graphsample.py", line 4, in <module>
__import__('pkg_resources').run_script('ngs-mapper==1.1.0', 'graphsample.py')
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 517, in run_script
distributions in the working set, otherwise only ones matching
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1423, in run_script
return []
File "/media/VD_Research/People/Melanie.Melendrez/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.1.0-py2.7.egg/EGG-INFO/scripts/graphsample.py", line 6, in <module>
main(parse_args())
File "/media/VD_Research/People/Melanie.Melendrez/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.1.0-py2.7.egg/ngs_mapper/graphsample.py", line 21, in main
pngfile = make_image( jfile, args.outpath )
File "/media/VD_Research/People/Melanie.Melendrez/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.1.0-py2.7.egg/ngs_mapper/graphsample.py", line 48, in make_image
run_montage( *imagelist, compress='JPEG', quality=25, geometry='+1+1' )
File "/media/VD_Research/People/Melanie.Melendrez/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.1.0-py2.7.egg/ngs_mapper/graphsample.py", line 81, in run_montage
subprocess.check_call( cmd )
File "/home/AMED/melanie.melendrez/lib/python2.7/subprocess.py", line 540, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['montage', '-geometry', '+1+1', '-quality', '25', '-compress', 'JPEG', '/tmp/FVM00003_AndesZYDTDDrunsample/FVM00003_Andes.bam.qualdepth.png']' returned non-zero exit status 1
no pngs anywhere all that outputted was graphsample.log and pipeline.log.
There is one functioning png in the /tmp directory - the *.reads.png. I couldn't find any other pngs
(ngs_mapper) [melanie.melendrez@amedwrair15380 FVM00003]$ ls /tmp/FVM00003_AndesZYDTDDrunsample/
Andes__Chile__2002.fasta Andes__Chile__2002.fasta.pac FVM00003_Andes.bam FVM00003_Andes.bam.vcf qualdepth
Andes__Chile__2002.fasta.amb Andes__Chile__2002.fasta.sa FVM00003_Andes.bam.bai FVM00003_Andes.log trimmed_reads
Andes__Chile__2002.fasta.ann bwa.log FVM00003_Andes.bam.consensus.fasta FVM00003_Andes.reads.png trim_stats
Andes__Chile__2002.fasta.bwt flagstats.txt FVM00003_Andes.bam.qualdepth.json FVM00003_Andes.std.log
Can you check in that qualdepth directory as well
I did, no pngs - the directory is empty
(ngs_mapper) [melanie.melendrez@amedwrair15380 FVM00003]$ ls /tmp/FVM00003_AndesZYDTDDrunsample/qualdepth/
(ngs_mapper) [melanie.melendrez@amedwrair15380 FVM00003]$ ls /tmp/FVM00003_AndesZYDTDDrunsample/qualdepth/
Can you post the contents of flagstats.txt, I highly suspect that you are right that maybe no reads actually mapped or something. Once we figure out the issue, i'll make a bug report because the pipeline needs to check for these things
ok - ya I looked in flagstats but couldn't figure what was going on with it: flagstats
81329 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
0 + 0 mapped (0.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Haha, well basically there were 81,329 reads and 0 of them mapped
81329 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
0 + 0 mapped (0.00%:-nan%)
ahhhh
ok - ya i figured. but at least we know an area of the pipeline we can improve for clarity.
So I'm testing your pipeline on some new stuff. I got it to run successfully with Chik a full genome virus like Dengue. I am trying to run it against another segmented virus and it failed:
my command and screen output:
FVM00003_Andes.log
pipeline.log
bwa.log
std.log
graphsample.log
All output is currently located on my computer under /tmp/FVM00003_AndesZYDTDDrunsample/
I wouldn't be too surprised if it failed because nothing matched to this virus I just wanted to make sure it wasn't a pipeline issue. They told me this virus serology matched Andes virus, so I pulled the segmented genome - formatted the reference to look like our flu genomes and ran the pipeline on it. Pathogen discovery said this was Chikungunya - so I also ran Chik and that seemed to finish succesffully. Just didn't know what this error meant.