Great! Hope you are able to use it to identify interesting plasmids. Let us know if you run into any other problems
(scapp-new) hsv709@pallas:/mibi/Wanli/benchmark$ scapp -g assembly-out/assembly_graph.fastg -k 99 -r1 R1.fq.gz -r2 R2.fq.gz -o scapp-out -p 20
Creating BAM file of read mappings with BWA
Traceback (most recent call last):
File "/mibi/Wanli/anaconda/envs/scapp-new/bin/scapp", line 10, in
sys.exit(main())
File "/mibi/Wanli/anaconda/envs/scapp-new/lib/python3.7/site-packages/scapp/scapp.py", line 234, in main
subprocess.check_call(cmd,stderr=subprocess.STDOUT, stdout=bwa_outfile, shell=True)
File "/mibi/Wanli/anaconda/envs/scapp-new/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'bwa mem -t 20 scapp-out/intermediate_files/assembly_graph.nodes.fasta R1.fq.gz R2.fq.gz | samtools view -buS -@ 19 - > scapp-out/intermediate_files/reads_pe.bam' returned non-zero exit status 1.
today, i run another data, but raise error again, like this. the fastg file is output from spades, and the assembly k-mer are 21,33,55,77,99, so the k is scapp is 99. before this, the assembler i used is megahit. so i don`t know whether this is the problem
Originally posted by @aaa-meituo-aaa in #14 (comment)
(scapp-new) hsv709@pallas:/mibi/Wanli/benchmark$ scapp -g assembly-out/assembly_graph.fastg -k 99 -r1 R1.fq.gz -r2 R2.fq.gz -o scapp-out -p 20
Creating BAM file of read mappings with BWA
Traceback (most recent call last):
File "/mibi/Wanli/anaconda/envs/scapp-new/bin/scapp", line 10, in
sys.exit(main())
File "/mibi/Wanli/anaconda/envs/scapp-new/lib/python3.7/site-packages/scapp/scapp.py", line 234, in main
subprocess.check_call(cmd,stderr=subprocess.STDOUT, stdout=bwa_outfile, shell=True)
File "/mibi/Wanli/anaconda/envs/scapp-new/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'bwa mem -t 20 scapp-out/intermediate_files/assembly_graph.nodes.fasta R1.fq.gz R2.fq.gz | samtools view -buS -@ 19 - > scapp-out/intermediate_files/reads_pe.bam' returned non-zero exit status 1.
today, i run another data, but raise error again, like this. the fastg file is output from spades, and the assembly k-mer are 21,33,55,77,99, so the k is scapp is 99. before this, the assembler i used is megahit. so i don`t know whether this is the problem
Originally posted by @aaa-meituo-aaa in #14 (comment)