pdf - MissingOutputException using python 3 and ReportLab -


i experiencing problem using snakemake. wrote python code generate pdf report using reportlab python package , want integrate code in snakemake pipeline. job failed because missingoutputexception if first file processed created. suggested error message tried use option --latency-wait different values. high values doesn't work...

here example of code 

import os  samples = ["17-1206_s11","17-1198_s12", "17-1286_s10"]  rule all:     input:         expand("reports/{s}.pdf",s=samples)  rule patientmetricsreport:     input:         "hs_metrics/{s}",     output:          "reports/{s}.pdf"     params:         ptfilename = "{s}",         = "170809_nb501855_0029_ah7tk7bgx3",         o = "tsone_170809-54054"     shell:         "python3 report.py -pt {input} -id {params.ptfilename} -sr {params.i} -ar {params.o}"

and here error

snakemake --snakefile report.test --latency-wait 30 provided cores: 1 rules claiming more threads scaled down. job counts:         count   jobs         3       patientmetricsreport         1               4  rule patientmetricsreport:     input: hs_metrics/17-1206_s11     output: reports/17-1206_s11.pdf     jobid: 1     wildcards: s=17-1206_s11  waiting @ 30 seconds missing files. error in job patientmetricsreport while creating output file reports/17-1206_s11.pdf. missingoutputexception in line 9 of report.test: missing files after 30 seconds: reports/17-1206_s11.pdf might due filesystem latency. if case, consider increase wait time --latency-wait. exit after finishing running jobs. exiting because job execution failed. above error message

python libraries reportlab installed on python 3 while default python version 2.6.6.


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