In a python script I gave a call in this way:
do.call([cfg.tool_cmd("cuffdiff"),
"-p", str(cfg.project["analysis"]["threads"]),
"-b", str(cfg.project["genome"]["fasta"]),
"-u", cfg.project["experiment"]["merged"],
"-L", str(cfg.project["phenotype"][0])[2:8],str(cfg.project["phenotype"][1])[2:7],
"-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"] + ' ' + cfg.project["samples"][1]["files"]["bam"]], cfg.project["analysis"]["log_file"])
And this gives an Error: number of labels must match number of conditions
subprocess.CalledProcessError: Command '['/usr/local/bin/cuffdiff', '-p', '5', '-b', '/scratchsan/venkatesh/TuxedoProject/data/genome/ce10.fa', '-u', 'pipeline/merging/merged.gtf', '-L', 'embryo', 'larva', '-o', 'pipeline/degenes', 'pipeline/SAMN00990702-1/mappings/accepted_hits.bam pipeline/SAMN00990702-2/mappings/accepted_hits.bam']' returned non-zero exit status 1
do.call([cfg.tool_cmd("cuffdiff"),
"-p", str(cfg.project["analysis"]["threads"]),
"-b", str(cfg.project["genome"]["fasta"]),
"-u", cfg.project["experiment"]["merged"],
"-L", str(cfg.project["phenotype"][0])[2:8],str(cfg.project["phenotype"][1])[2:7],
"-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"] + ' ' + cfg.project["samples"][1]["files"]["bam"]], cfg.project["analysis"]["log_file"])
And this gives an Error: number of labels must match number of conditions
subprocess.CalledProcessError: Command '['/usr/local/bin/cuffdiff', '-p', '5', '-b', '/scratchsan/venkatesh/TuxedoProject/data/genome/ce10.fa', '-u', 'pipeline/merging/merged.gtf', '-L', 'embryo', 'larva', '-o', 'pipeline/degenes', 'pipeline/SAMN00990702-1/mappings/accepted_hits.bam pipeline/SAMN00990702-2/mappings/accepted_hits.bam']' returned non-zero exit status 1
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