Traceback (most recent call last):


 "setoolkit", line 60, in <module>

os.makedirs("src/logs/")


 "/usr/lib/python2.7/os.py", line 157, in makedirs

mkdir(name, mode)
OSError: [Errno 13] Permission denied: 'src/logs/'

Traceback (most recent call last):


 "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 50, in _setup_logging

yield config


 "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 133, in run_kallisto_rnaseq

return ipython.zip_args(apply(kallisto.run_kallisto_rnaseq, *args))


 "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/kallisto.py", line 34, in run_kallisto_rnaseq

out_file = kallisto_rnaseq(fq1, fq2, kallisto_dir, gtf_file, fasta_file, data)


 "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/kallisto.py", line 45, in kallisto_rnaseq

index = kallisto_index(gtf_file, fasta_file, data, kallisto_dir)


 "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/kallisto.py", line 114, in kallisto_index

gtf_fa = sailfish.create_combined_fasta(data)


 "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/sailfish.py", line 104, in create_combined_fasta

out_file = gtf.gtf_to_fasta(gtf_file, ref_file, out_file=out_file)


 "/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py", line 134, in gtf_to_fasta

os.remove(tmp_file)
OSError: [Errno 2] No such file or directory: '/rnaseq/low-pass-test-config1/work/inputs/transcriptome/hg38-noalt.fa.tmp'
