Skip to content

Problems with illumina reads #36

@diaz13

Description

@diaz13

Hi
I use the illumina reads. I run this command
python3.7 ismap.py --reads *.fastq --queries IS.fasta --reference .sequence.gbk --output_dir test1

And I have this error

[main] CMD: bwa mem -t 1 ../../../test1/1_S1_L001/IS-LL6_IS3_IS3/tmp/CP000803.1.fasta ../../../test1/1_S1_L001/IS-LL6_IS3_IS3/1_S1_L001_IS-LL6_IS3_IS3_right_final.fastq
[main] Real time: 0.007 sec; CPU: 0.005 sec
[samopen] SAM header is present: 1 sequences.
[sam_read1] reference 'ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem -t 1 ../../../test1/1_S1_L001/IS-LL6_IS3_IS3/tmp/CP000803.1.fasta ../../../test1/1_S1_L001/IS-LL6_IS3_IS3/1_S1_L001_IS-LL6_IS3_IS3_left_final.fastq
' is recognized as '*'.
[main_samview] truncated file.
Traceback (most recent call last):
File "ismap.py", line 244, in
main()
File "ismap.py", line 222, in main
tmp_output_folder, is_output_folder, args.t, args.a)
File "/home/user/Tools/IS_mapper/build/lib/ismap/mapping_to_ref.py", line 77, in map_to_ref_seq
run_command(samtools_runner.view(filenames['left_bam'], filenames['left_sam']), shell=True)
File "/home/user/Tools/IS_mapper/build/lib/ismap/run_commands.py", line 29, in run_command
raise CommandError({"message": message})
run_commands.CommandError: {'message': "Command 'samtools view -Sb -o ../../../test1/1_S1_L001/IS-LL6_IS3_IS3/tmp/1_S1_L001_left_CP000803.1.bam ../../../test1/1_S1_L001/IS-LL6_IS3_IS3/tmp/1_S1_L001_left_CP000803.1.sam' failed with non-zero exit status: 1"}

I don't understand why ??

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions