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secastel / phaser

phasing and Allele Specific Expression from RNA-seq
GNU General Public License v3.0
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TypeError: a bytes-like object is required, not 'str #63

Closed deb0612 closed 3 years ago

jegalle commented 3 years ago

Hi

I was wondering how this problem was fixed. I'm having this issue atm: Traceback (most recent call last): File "/opt/phaser/phaser/phaser.py", line 2358, in <module> main(); File "/opt/phaser/phaser/phaser.py", line 170, in main parse_sample(sample_name, map_sample_column, args.bam, args.o, contig_ban) File "/opt/phaser/phaser/phaser.py", line 262, in parse_sample start_time, vcf_out, sample_out_path, last_chr=True, pi_block_value = 0) File "/opt/phaser/phaser/phaser.py", line 546, in process_vcf alignment_scores = map(int,[x for x in subprocess.check_output("set -euo pipefail && "+"cut -f 5 "+" ".join(result_files), shell=True, executable='/bin/bash').split("\n") if x != ""]); TypeError: a bytes-like object is required, not 'str'

jegalle commented 3 years ago

Nevermind! I ran phaser in python3, running in python2.7 fixed the issue.

secastel commented 3 years ago

Great, glad you were able to sort this out!