Closed karel-brinda closed 8 years ago
Error:
/Users/karel/.smbl/bin/art_illumina -sam -na -i "/Users/karel/.smbl/fa/Mycobacterium_tuberculosis.fa" -l 100 -rs 12345 -f 20 -o "mtb_reads/001/tmp.1" -p -m 500 -s 50.0 > /dev/null cat "mtb_reads/001/tmp.1.sam" | grep -v ^@ | "/Users/karel/.smbl/bin/samtools" view -h -T "/Users/karel/.smbl/fa/Mycobacterium_tuberculosis.fa" - > "mtb_reads/001/tmp.1.corrected.sam" Error in job 43 while creating output files mtb_reads/001/_final_reads.fq, mtb_reads/001/tmp.1.sam, mtb_reads/001/tmp.1.corrected.sam, mtb_reads/001/tmp.11.fq, mtb_reads/001/tmp.12.fq. RuleException: TypeError in line 52 of /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/rnftools/mishmash/mishmash.snake: _open() takes at least 1 positional argument (0 given) File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/rnftools/mishmash/ArtIllumina.py", line 153, in create_fq File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/rnftools/mishmash/Source.py", line 197, in recode_sam_reads Removing output files of failed job 43 since they might be corrupted: mtb_reads/001/_final_reads.fq, mtb_reads/001/tmp.1.sam, mtb_reads/001/tmp.1.corrected.sam, mtb_reads/001/tmp.11.fq, mtb_reads/001/tmp.12.fq Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message
Snakefile:
import rnftools import smbl # CONFIGURATION reads = "mtb_reads.fq" reference = smbl.fasta.EXAMPLE # READ SIMULATION rnftools.mishmash.sample(reads[:-3],reads_in_tuple=2) rnftools.mishmash.ArtIllumina( fasta=reference, read_length_1=100, read_length_2=100, coverage=20, distance=500, distance_deviation=50.0, rng_seed=12345, ) # SNAKEMAKE RULES include: rnftools.include() rule: input: rnftools.input()
A relevant problem: http://www.biopython.org/pipermail/biopython/2011-April/007209.html
Error:
Snakefile: