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Old 09-08-2014, 09:08 AM   #31
biodan
Junior Member
 
Location: NYC

Join Date: Oct 2012
Posts: 2
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Hi Brian,

Thanks for the bbduk tool, it is indeed very fast. I just downloaded bbmap today (Aug29 release), and get errors when i try to process a pair of files in 1 line:

/opt/bbmap/bbduk.sh -Xmx4g in1=clean_1g_C10_R1.fastq.gz in2=clean_1g_C10_R2.fastq.gz out1=tc_clean_1g_C10_R1.fastq.gz out2=tc_clean_1g_C10_R2.fastq.gz minlen=50 qtrim=rl trimq=20

Initial:
Memory: free=2013m, used=12m

Input is being processed as paired
Started output streams: 0.046 seconds.
Exception in thread "Thread-4" java.lang.AssertionError:
There appear to be different numbers of reads in the paired input files.
The pairing may have been corrupted by an upstream process. It may be fixable by running repair.sh.
at stream.ConcurrentGenericReadInputStream.pair(ConcurrentGenericReadInputStream.java:501)
at stream.ConcurrentGenericReadInputStream.readLists(ConcurrentGenericReadInputStream.java:367)
at stream.ConcurrentGenericReadInputStream.run(ConcurrentGenericReadInputStream.java:205)
at java.lang.Thread.run(Thread.java:744)

However, when i do 1 file at a time, it works with no errors. The input files are relatively small (about 1.5M reads from single cells).
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