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- EXITING: FATAL INPUT ERROR: duplicate parameter "outSAMtype" in input "Command-Line"
- SOLUTION: keep only one definition of input parameters in each input source
- Nov 15 09:46:07 ...... FATAL ERROR, exiting
- logs/star/se/UY2_S7.log (END)
- __author__ = "Johannes Köster"
- __copyright__ = "Copyright 2016, Johannes Köster"
- __email__ = "koester@jimmy.harvard.edu"
- __license__ = "MIT"
- import os
- from snakemake.shell import shell
- extra = snakemake.params.get("extra", "")
- log = snakemake.log_fmt_shell(stdout=True, stderr=True)
- fq1 = snakemake.input.get("fq1")
- assert fq1 is not None, "input-> fq1 is a required input parameter"
- fq1 = [snakemake.input.fq1] if isinstance(snakemake.input.fq1, str) else snakemake.input.fq1
- fq2 = snakemake.input.get("fq2")
- if fq2:
- fq2 = [snakemake.input.fq2] if isinstance(snakemake.input.fq2, str) else snakemake.input.fq2
- assert len(fq1) == len(fq2), "input-> equal number of files required for fq1 and fq2"
- input_str_fq1 = ",".join(fq1)
- input_str_fq2 = ",".join(fq2) if fq2 is not None else ""
- input_str = " ".join([input_str_fq1, input_str_fq2])
- if fq1[0].endswith(".gz"):
- readcmd = "--readFilesCommand zcat"
- else:
- readcmd = ""
- outprefix = os.path.dirname(snakemake.output[0]) + "/"
- shell(
- "STAR "
- "{extra} "
- "--runThreadN {snakemake.threads} "
- "--genomeDir {snakemake.params.index} "
- "--readFilesIn {input_str} "
- "{readcmd} "
- "--outSAMtype BAM Unsorted "
- "--outFileNamePrefix {outprefix} "
- "--outStd Log "
- "{log}")
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