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UCSC-LoweLab / tRAX

tRNA Analysis of eXpression
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Unable to align with bowtie2 - choosemappings.py error #7

Closed divyanandu closed 3 years ago

divyanandu commented 4 years ago

Hi Andrew,

I was able to generate the tRNAdb files, but am facing a problem when trying to run the process samples command. my input command was

python tRAX/threadprocesssamples.py --experimentname=smallRNAs --databasename=mm10 --samplefile=TestSamples.txt --ensemblgtf=mm10-genes.gtf

but i get the following error:

Mapping Reads
cores: 8
logging to smallRNAs/smallRNAs-mapstats.txt
bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446506_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446506_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/inf_R1temp - -o ./inf_R1.bam
bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446507_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446507_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/inf_R2temp - -o ./inf_R2.bam
bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446509_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446509_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/mock_R1temp - -o ./mock_R1.bam
bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446508_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446508_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/inf_R3temp - -o ./inf_R3.bam
bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446510_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446510_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/mock_R2temp - -o ./mock_R2.bam
Could not map SRR446509_trimmed.fastq, check mapstats file
Exiting...
Traceback (most recent call last):
  File "/clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py", line 291, in <module>
    getbesttrnamappings(args.trnaname, progname = args.progname, fqname = args.fqname, libname = args.expname, setcountfile = args.trnasetcounts)
  File "/clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py", line 76, in getbesttrnamappings
    newheader = bamfile.header.to_dict()
AttributeError: 'dict' object has no attribute 'to_dict'
Error outputting data
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) 

Failure to Bowtie2 map

The map-stats file shows:

bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446509_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446509_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/mock_R1temp - -o ./mock_R1.bam
Traceback (most recent call last):
  File "/clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py", line 291, in <module>
    getbesttrnamappings(args.trnaname, progname = args.progname, fqname = args.fqname, libname = args.expname, setcountfile = args.trnasetcounts)
  File "/clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py", line 76, in getbesttrnamappings
    newheader = bamfile.header.to_dict()
AttributeError: 'dict' object has no attribute 'to_dict'
Error outputting data
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT)

Not sure what I am doing incorrectly here..

andrewdholmes commented 4 years ago

That looks like an issue where the pysam version you have is out of date. Make sure you using the latest version of pysam.

On Fri, Mar 27, 2020 at 3:40 PM divyanandu notifications@github.com wrote:

Hi Andrew,

I was able to generate the tRNAdb files, but am facing a problem when trying to run the process samples command. my input command was

python tRAX/threadprocesssamples.py --experimentname=smallRNAs --databasename=mm10 --samplefile=TestSamples.txt --ensemblgtf=mm10-genes.gtf

but i get the following error:

Mapping Reads cores: 8 logging to smallRNAs/smallRNAs-mapstats.txt bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446506_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446506_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/inf_R1temp - -o ./inf_R1.bam bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446507_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446507_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/inf_R2temp - -o ./inf_R2.bam bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446509_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446509_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/mock_R1temp - -o ./mock_R1.bam bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446508_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446508_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/inf_R3temp - -o ./inf_R3.bam bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446510_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446510_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/mock_R2temp - -o ./mock_R2.bam Could not map SRR446509_trimmed.fastq, check mapstats file Exiting... Traceback (most recent call last): File "/clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py", line 291, in getbesttrnamappings(args.trnaname, progname = args.progname, fqname = args.fqname, libname = args.expname, setcountfile = args.trnasetcounts) File "/clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py", line 76, in getbesttrnamappings newheader = bamfile.header.to_dict() AttributeError: 'dict' object has no attribute 'to_dict' Error outputting data terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT)

Failure to Bowtie2 map

The map-stats file shows:

bowtie2 -x mm10-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 4 -U SRR446509_trimmed.fastq | /clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py mm10-trnatable.txt --progname=TRAX --fqname=SRR446509_trimmed.fastq --expname=TestSamples.txt | samtools sort -T /tmp/mock_R1temp - -o ./mock_R1.bam Traceback (most recent call last): File "/clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py", line 291, in getbesttrnamappings(args.trnaname, progname = args.progname, fqname = args.fqname, libname = args.expname, setcountfile = args.trnasetcounts) File "/clusterfs/vector/scratch/dnandaku/tRAX/choosemappings.py", line 76, in getbesttrnamappings newheader = bamfile.header.to_dict() AttributeError: 'dict' object has no attribute 'to_dict' Error outputting data terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT)

Not sure what I am doing incorrectly here..

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