I'm new to bioinformatics and I'm having an issue with BWA.
I'm using BWA (the Map with BWA for Illumina tool in Galaxy) to align some reads to the human hg19 reference. The alignment is failing with the following error:
The alignment failed.
Error generating alignments. [bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (270, 370, 464)
[infer_isize] low and high boundaries: 251 and 852 for estimating avg and std
[infer_isize] inferred external isize from 175111 pairs: 422.966 +/- 112.280
[infer_isize] skewness: 0.783; kurtosis: 0.372; ap_prior: 1.65e-05
[infer_isize] inferred maximum insert size: 1192 (6.85 sigma)
Killed
The command to run BWA was:
python /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.py --threads="${GALAXY_SLOTS:-4}" --fileSource="history" --ref="/mnt/galaxy/files/000/dataset_488.dat" --dbkey="?" --input1="/mnt/galaxy/files/000/dataset_530.dat" --input2="/mnt/galaxy/files/000/dataset_531.dat" --output="/mnt/galaxy/files/000/dataset_534.dat" --genAlignType="paired" --params="pre_set" --suppressHeader="false"
I had previously, within the same Galaxy instance, successfully aligned some bacterial reads to a bacterial reference using the same workflow. However, when I try to align some reads from a human sample to hg19 I get this error. So it must have something to do with either the reference or the reads themselves. (I should note that the human and bacterial sequence data came off the same run on the same sequencer.)
Can anyone help me figure out what the problem is?
Mike
I'm using BWA (the Map with BWA for Illumina tool in Galaxy) to align some reads to the human hg19 reference. The alignment is failing with the following error:
The alignment failed.
Error generating alignments. [bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (270, 370, 464)
[infer_isize] low and high boundaries: 251 and 852 for estimating avg and std
[infer_isize] inferred external isize from 175111 pairs: 422.966 +/- 112.280
[infer_isize] skewness: 0.783; kurtosis: 0.372; ap_prior: 1.65e-05
[infer_isize] inferred maximum insert size: 1192 (6.85 sigma)
Killed
The command to run BWA was:
python /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.py --threads="${GALAXY_SLOTS:-4}" --fileSource="history" --ref="/mnt/galaxy/files/000/dataset_488.dat" --dbkey="?" --input1="/mnt/galaxy/files/000/dataset_530.dat" --input2="/mnt/galaxy/files/000/dataset_531.dat" --output="/mnt/galaxy/files/000/dataset_534.dat" --genAlignType="paired" --params="pre_set" --suppressHeader="false"
I had previously, within the same Galaxy instance, successfully aligned some bacterial reads to a bacterial reference using the same workflow. However, when I try to align some reads from a human sample to hg19 I get this error. So it must have something to do with either the reference or the reads themselves. (I should note that the human and bacterial sequence data came off the same run on the same sequencer.)
Can anyone help me figure out what the problem is?
Mike
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