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Old 09-10-2021, 01:13 AM   #685
mewu3
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Join Date: Sep 2021
Posts: 4
Question [help]

Hello,

I am using bbmap on HPC and I get the fallowing message :

Quote:
Aligning C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001 reads to fasta file ...
java -Djava.library.path=/opt/apps/bbtools-37.97/jni/ -ea -Xmx50G -cp /opt/apps/bbtools-37.97/current/ align2.BBWrap build=1 overwrite=true fastareadlen=500 build=1 in1=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_R1_trim.fastq.gz,C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_se_trim.fastq.gz in2=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_R2_trim.fastq.gz,null trimreaddescriptions=t outm=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_aligned.sam outu1=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_R1.sam,C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_se.sam outu2=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_R2.sam threads=8 pairlen=1000 pairedonly=t minid=0.9 mdtag=t xstag=fs nmtag=t sam=1.3 ambiguous=best secondary=t saa=f maxsites=10 -Xmx50G
Executing align2.BBWrap [build=1, overwrite=true, fastareadlen=500, build=1, in1=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_R1_trim.fastq.gz,C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_se_trim.fastq.gz, in2=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_R2_trim.fastq.gz,null, trimreaddescriptions=t, outm=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_aligned.sam, outu1=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_R1.sam,C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_se.sam, outu2=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_R2.sam, threads=8, pairlen=1000, pairedonly=t, minid=0.9, mdtag=t, xstag=fs, nmtag=t, sam=1.3, ambiguous=best, secondary=t, saa=f, maxsites=10, -Xmx50G]

Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, build=1, trimreaddescriptions=t, threads=8, pairlen=1000, pairedonly=t, minid=0.9, mdtag=t, xstag=fs, nmtag=t, sam=1.3, ambiguous=best, secondary=t, saa=f, maxsites=10, in=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_R1_trim.fastq.gz, outu=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_R1.sam, outm=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_aligned.sam, in2=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_R2_trim.fastq.gz, outu2=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_R2.sam]
Version 37.97 [build=1, overwrite=true, fastareadlen=500, build=1, trimreaddescriptions=t, threads=8, pairlen=1000, pairedonly=t, minid=0.9, mdtag=t, xstag=fs, nmtag=t, sam=1.3, ambiguous=best, secondary=t, saa=f, maxsites=10, in=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_R1_trim.fastq.gz, outu=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_R1.sam, outm=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_aligned.sam, in2=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_R2_trim.fastq.gz, outu2=C_CGTCTGCG-ATTGTGAA-AHGKC2BBXY_L001_unaligned_R2.sam]

Set threads to 8
Retaining first best site only for ambiguous mappings.
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.816
Set genome to 1

Loaded Reference: 3.463 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 2.556 seconds.
Analyzed Index: 7.028 seconds.
Started output stream: 0.043 seconds.
Exception in thread "main" java.lang.AssertionError: Attempting to output paired reads to different sam files.
at stream.ReadStreamWriter.<init>(ReadStreamWriter.java:51)
at stream.ReadStreamByteWriter.<init>(ReadStreamByteWriter.java:17)
at stream.ConcurrentGenericReadOutputStream.<init>(ConcurrentGenericReadOutputStream.java:40)
at stream.ConcurrentReadOutputStream.getStream(ConcurrentReadOutputStream.java:52)
at stream.ConcurrentReadOutputStream.getStream(ConcurrentReadOutputStream.java:29)
at align2.AbstractMapper.openStreams(AbstractMapper.java:873)
at align2.BBMap.testSpeed(BBMap.java:437)
at align2.BBMap.main(BBMap.java:34)
at align2.BBWrap.execute(BBWrap.java:144)
at align2.BBWrap.main(BBWrap.java:22)
I get the impression that bbmap is stuck on something and i don't know what's wrong with it. Please help !

mewu3
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