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VDBWRAIR / ngs_mapper

Genome Mapping Pipeline
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Error version 1.4.0 - index issue? Error needs to be more informative? #224

Closed mmelendrez closed 8 years ago

mmelendrez commented 8 years ago

I am using a custom config file - config_quasi.yaml.txt

Used runsample and this was the output:

[melanie.melendrez@amedwrair015380 SubjCHD10_034_044]$ runsample -od Day1_10672 -c config_quasi.yaml /media/VD_Research/NGSData/ReadsBySample/10672/ KDH0053A_Thailand_NC_2010.fasta Day1_10672
2016-03-28 13:28:02,892 -- INFO -- runsample       --- Starting Day1_10672 --- 
2016-03-28 13:28:02,892 -- INFO -- runsample       --- Using custom config from config_quasi.yaml ---

2016-03-28 13:41:45,839 -- ERROR -- runsample

Only 1 log file generated - pipeline.log: This log isn't too informative as to what might have happened. No other logs were generated.

2016-03-28 13:28:04,809 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq
2016-03-28 13:28:04,863 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I2_001_2015_11_20.fastq
2016-03-28 13:28:04,886 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq
2016-03-28 13:28:04,940 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq
2016-03-28 13:28:04,972 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq
2016-03-28 13:28:04,973 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I2_001_2015_11_20.fastq
2016-03-28 13:28:04,974 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq
2016-03-28 13:28:04,975 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq
2016-03-28 13:28:04,976 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq
2016-03-28 13:28:04,977 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I2_001_2015_11_20.fastq
2016-03-28 13:28:04,978 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq
2016-03-28 13:28:04,979 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq
2016-03-28 13:28:04,980 -- DEBUG -- ngs_mapper.data Attempting to pair readlist ['/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq', '/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I2_001_2015_11_20.fastq', '/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq', '/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq']
2016-03-28 13:28:04,980 -- INFO -- ngs_mapper.data paired_reads: []                  
2016-03-28 13:28:04,980 -- DEBUG -- ngs_mapper.data i: 0                             
2016-03-28 13:28:04,980 -- DEBUG -- ngs_mapper.data Cannot find _R1_ or _R2_ in /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq
2016-03-28 13:28:04,980 -- DEBUG -- ngs_mapper.data Index in readlist for /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq is -1
2016-03-28 13:28:04,981 -- DEBUG -- ngs_mapper.data Index was -1 so appending readfile
2016-03-28 13:28:04,981 -- INFO -- ngs_mapper.data paired_reads: ['/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq']
2016-03-28 13:28:04,981 -- DEBUG -- ngs_mapper.data i: 1                             
2016-03-28 13:28:04,981 -- DEBUG -- ngs_mapper.data Cannot find _R1_ or _R2_ in /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I2_001_2015_11_20.fastq
2016-03-28 13:28:04,981 -- DEBUG -- ngs_mapper.data Index in readlist for /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I2_001_2015_11_20.fastq is -1
2016-03-28 13:28:04,981 -- DEBUG -- ngs_mapper.data Index was -1 so appending readfile
2016-03-28 13:28:04,982 -- INFO -- ngs_mapper.data paired_reads: ['/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq', '/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I2_001_2015_11_20.fastq']
2016-03-28 13:28:04,982 -- DEBUG -- ngs_mapper.data i: 2                             
2016-03-28 13:28:04,982 -- DEBUG -- ngs_mapper.data 1 found in /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq and will search for /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq
2016-03-28 13:28:04,982 -- DEBUG -- ngs_mapper.data Index in readlist for /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq is 3
2016-03-28 13:28:04,982 -- DEBUG -- ngs_mapper.data Appending mated pairs (/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq,/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq)
2016-03-28 13:28:04,982 -- DEBUG -- ngs_mapper.data Mate list ['/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq']
2016-03-28 13:28:04,982 -- INFO -- ngs_mapper.data paired_reads: ['/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq', '/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I2_001_2015_11_20.fastq', ('/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq', '/media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq')]
2016-03-28 13:28:04,983 -- DEBUG -- ngs_mapper.data i: 3                             
2016-03-28 13:28:04,983 -- DEBUG -- ngs_mapper.data Ignoring /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq because it has already been added to the mate list
2016-03-28 13:28:04,984 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I1_001_2015_11_20.fastq
2016-03-28 13:28:04,985 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_I2_001_2015_11_20.fastq
2016-03-28 13:28:04,985 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq
2016-03-28 13:28:04,987 -- DEBUG -- ngs_mapper.data Reading first read from /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R2_001_2015_11_20.fastq

I think it might have something to do with the usage of filtering by index using ngs_filter (see config file).

mmelendrez commented 8 years ago

just found another log file...

mmelendrez commented 8 years ago

std.log = empty .log file:

2016-03-28 13:28:02,892 -- INFO -- runsample       --- Starting Day1_10672 ---                                                              
2016-03-28 13:28:02,892 -- INFO -- runsample       --- Using custom config from config_quasi.yaml ---
2016-03-28 13:28:02,893 -- DEBUG -- runsample       Copying reference file KDH0053A_Thailand_NC_2010.fasta to Day1_10672/Day1_10672wHyL59runsample/KDH0053A_Thailand_NC_2010.fasta
2016-03-28 13:28:02,909 -- DEBUG -- runsample       {'minth': 0.95, 'flagstats': 'Day1_10672/Day1_10672wHyL59runsample/flagstats.txt', 'readsdir': '/media/VD_Research/NGSData/ReadsBySample/10672/', 'vcf': 'Day1_10672/Day1_10672wHyL59runsample/Day1_10672.bam.vcf', 'reference': 'Day1_10672/Day1_10672wHyL59runsample/KDH0053A_Thailand_NC_2010.fasta', 'primer_info': (None, 2, 30, 20), 'samplename': 'Day1_10672', 'drop_ns': True, 'bamfile': 'Day1_10672/Day1_10672wHyL59runsample/Day1_10672.bam', 'filtered_dir': 'Day1_10672/Day1_10672wHyL59runsample/filtered', 'consensus': 'Day1_10672/Day1_10672wHyL59runsample/Day1_10672.bam.consensus.fasta', 'platforms': ['MiSeq', 'Sanger', 'Roche454', 'IonTorrent'], 'tdir': 'Day1_10672/Day1_10672wHyL59runsample', 'head_crop': 0, 'trim_qual': 20, 'index_min': 25, 'config': 'config_quasi.yaml', 'trim_outdir': 'Day1_10672/Day1_10672wHyL59runsample/trimmed_reads', 'CN': None}
2016-03-28 13:41:45,839 -- ERROR -- runsample

Within the filtered file - was the following stats:

ngs_filter found 3809635 reads in file /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq, and filtered out 71259 reads.                                                                                                                                  
In file /media/VD_Research/NGSData/ReadsBySample/10672/10672_S6_L001_R1_001_2015_11_20.fastq, 70783 reads were filtered for poor quality index below 25. 476 reads had Ns and were filtered.

A couple things:

  1. Top one says 71259 were filtered but due to what? Quality?
  2. Next line says 70783 reads were filtered for poor quality index below 25 and 476 reads had Ns and were filtered out.
  3. So does this mean out of 3809635 reads - 71259+70783+476 were filtered out? That would leave 3667117 - still plenty.

So did the error occur due to pairing problems? Does the pipeline try to pair and by filtering out all those reads, it now cannot pair? Just thinking out loud.

averagehat commented 8 years ago

The top line is the total number of reads that were filtered out (71259). The second line breaks it down into which had Ns and which had poor quality. So 70783 (quality) + 476 (Ns) = 71259 total.

It's difficult to tell what went wrong here. (This is a good demonstration that the error reporting needs to be consolidated, which we are working on in #206. This is worsened by the fact that ngs_filter doesn't log in consistent way, which is fixed in #215) Once those get resolved it will be easier to fix these kinds of issues. I will work on re-creating the problem. It's possible that one of the read files was filtered out completely, but it might be something else.

mmelendrez commented 8 years ago

Ok - well you have my command and config file - let me know if you cannot access the reference.

I don't know that it would completely filter out one of the R files because total it only filtered about 70K and there is over 3 million reads between both files.

[melanie.melendrez@amedwrair015380 SubjCHD10_015_025]$ ls -lh /media/VD_Research/NGSData/ReadData/MiSeq/151120_M02261_0033_000000000-AHKJP/10672_S6_L001_*
-rw-r--r--. 1 607 607 267M Nov 23 16:30 /media/VD_Research/NGSData/ReadData/MiSeq/151120_M02261_0033_000000000-AHKJP/10672_S6_L001_I1_001_2015_11_20.fastq
-rw-r--r--. 1 607 607 267M Nov 23 16:30 /media/VD_Research/NGSData/ReadData/MiSeq/151120_M02261_0033_000000000-AHKJP/10672_S6_L001_I2_001_2015_11_20.fastq
-rw-r--r--. 1 607 607 2.2G Nov 23 16:31 /media/VD_Research/NGSData/ReadData/MiSeq/151120_M02261_0033_000000000-AHKJP/10672_S6_L001_R1_001_2015_11_20.fastq
-rw-r--r--. 1 607 607 2.3G Nov 23 16:33 /media/VD_Research/NGSData/ReadData/MiSeq/151120_M02261_0033_000000000-AHKJP/10672_S6_L001_R2_001_2015_11_20.fast

They both have equal amounts of data so with 3 million total - it's unlikely 2.2 or 2.3G represents only 70K reads which is what would have to be if one of the files was completely filtered out.

I am also running this a couple different ways. I have it running on a different sample and it's still going and I have it running on the same sample I just did but without the index filtering by Q25 (just pulling Ns out).

mmelendrez commented 8 years ago

Version updated - ngs_filter fixed - reloading and running

mmelendrez commented 8 years ago

Hmmm...run results:

[melanie.melendrez@amedwrair015380 SubjCHD10_015_025]$ RUNSAMPLEOPTIONS="-c config_quasi.yaml" runsamplesheet.sh /media/VD_Research/NGSData/ReadsBySample/ samplesheet_SubjCHD10_015_025
Using 12 cpus
2016-03-29 14:04:44,877 -- INFO -- runsample       --- Starting 10669 --- 
2016-03-29 14:04:44,877 -- INFO -- runsample       --- Using custom config from config_quasi.yaml ---
2016-03-29 14:04:44,879 -- INFO -- runsample       --- Starting 10668 --- 
2016-03-29 14:04:44,879 -- INFO -- runsample       --- Using custom config from config_quasi.yaml ---
2016-03-29 14:04:44,880 -- INFO -- runsample       --- Starting 10670 --- 
2016-03-29 14:04:44,880 -- INFO -- runsample       --- Using custom config from config_quasi.yaml ---
2016-03-29 14:04:44,880 -- INFO -- runsample       --- Starting 10671 --- 
2016-03-29 14:04:44,880 -- INFO -- runsample       --- Using custom config from config_quasi.yaml ---
2016-03-29 14:04:44,881 -- INFO -- runsample       --- Starting 10667 --- 
2016-03-29 14:04:44,881 -- INFO -- runsample       --- Using custom config from config_quasi.yaml ---

2016-03-29 14:04:47,435 -- ERROR -- runsample       Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/ngs_filter", line 9, in <module>
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'ngs_filter')()
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 236, in main
    run_from_config(args['<readdir>'], args['--outdir'], args['--config'])
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 218, in run_from_config
    outdir, defaults['threads']['default'])
KeyError: 'threads'

2016-03-29 14:04:47,435 -- ERROR -- runsample       Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/ngs_filter", line 9, in <module>
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'ngs_filter')()
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 236, in main
    run_from_config(args['<readdir>'], args['--outdir'], args['--config'])
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 218, in run_from_config
    outdir, defaults['threads']['default'])
KeyError: 'threads'

2016-03-29 14:04:47,436 -- ERROR -- runsample       Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/ngs_filter", line 9, in <module>
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'ngs_filter')()
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 236, in main
    run_from_config(args['<readdir>'], args['--outdir'], args['--config'])
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 218, in run_from_config
    outdir, defaults['threads']['default'])
KeyError: 'threads'

2016-03-29 14:04:47,437 -- ERROR -- runsample       Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/ngs_filter", line 9, in <module>
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'ngs_filter')()
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 236, in main
    run_from_config(args['<readdir>'], args['--outdir'], args['--config'])
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 218, in run_from_config
    outdir, defaults['threads']['default'])
KeyError: 'threads'

2016-03-29 14:04:47,438 -- ERROR -- runsample       Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/ngs_filter", line 9, in <module>
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'ngs_filter')()
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 236, in main
    run_from_config(args['<readdir>'], args['--outdir'], args['--config'])
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/nfilter.py", line 218, in run_from_config
    outdir, defaults['threads']['default'])
KeyError: 'threads'

Using 12 cpus
Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/graphsample", line 9, in <module>
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'graphsample')()
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 23, in main
Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/graphsample", line 9, in <module>
Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/graphsample", line 9, in <module>
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'graphsample')()
Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/graphsample", line 9, in <module>
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 23, in main
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'graphsample')()
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 23, in main
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'graphsample')()
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 23, in main
Traceback (most recent call last):
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/bin/graphsample", line 9, in <module>
    load_entry_point('ngs-mapper==1.4.2', 'console_scripts', 'graphsample')()
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 23, in main
        pngfile = make_image( jfile, args.outpath )
pngfile = make_image( jfile, args.outpath )
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 41, in make_image
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 41, in make_image
    pngfile = make_image( jfile, args.outpath )
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 41, in make_image
    pngfile = make_image( jfile, args.outpath )
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 41, in make_image
    pngfile = make_image( jfile, args.outpath )
  File "/media/VD_Research/Admin/PBS/Software/ngs_mapper/miniconda/lib/python2.7/site-packages/ngs_mapper-1.4.2-py2.7.egg/ngs_mapper/graphsample.py", line 41, in make_image
    j = json.load( open(jfile) )
    j = json.load( open(jfile) )
IOError: [Errno 2] No such file or directory: 'Projects/10670/10670.bam.qualdepth.json'
        j = json.load( open(jfile) )
j = json.load( open(jfile) )
IOError: IOError[Errno 2] No such file or directory: 'Projects/10667/10667.bam.qualdepth.json'IOError
: : [Errno 2] No such file or directory: 'Projects/10668/10668.bam.qualdepth.json'    [Errno 2] No such file or directory: 'Projects/10671/10671.bam.qualdepth.json'
j = json.load( open(jfile) )

IOError: [Errno 2] No such file or directory: 'Projects/10669/10669.bam.qualdepth.json'

real    0m6.854s
user    0m0.250s
sys 0m0.146s

real    0m6.842s
user    0m0.249s
sys 0m0.151s

real    0m6.860s
real    0m6.851s
user    0m0.269s
user    0m0.255s
sys 0m0.138s
sys 0m0.135s

real    0m6.847s
user    0m0.269s
sys 0m0.140s
mmelendrez commented 8 years ago

making a new config file

mmelendrez commented 8 years ago

now it seems to be running...

averagehat commented 8 years ago

215 changed the required config file; ngs_filter now requires a threads option, rather than a parallel option.

So, that was fixed and that worked properly.