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 ??
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 ??