after omitting blacklist arguments, phaser ran for a long time but then ...
completed chromosome 16...
completed chromosome 17...
completed chromosome 22...
completed chromosome 19...
completed chromosome 6...
processing mapped reads...
Traceback (most recent call last):
File "REDO/phaser/phaser/phaser.py", line 2358, in
main();
File "REDO/phaser/phaser/phaser.py", line 170, in main
parse_sample(sample_name, map_sample_column, args.bam, args.o, contig_ban)
File "REDO/phaser/phaser/phaser.py", line 262, in parse_sample
start_time, vcf_out, sample_out_path, last_chr=True, pi_block_value = 0)
File "REDO/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'
vjcitn
commented
5 years ago
after omitting blacklist arguments, phaser ran for a long time but then ... completed chromosome 16... completed chromosome 17... completed chromosome 22... completed chromosome 19... completed chromosome 6... processing mapped reads... Traceback (most recent call last): File "REDO/phaser/phaser/phaser.py", line 2358, in
main();
File "REDO/phaser/phaser/phaser.py", line 170, in main
parse_sample(sample_name, map_sample_column, args.bam, args.o, contig_ban)
File "REDO/phaser/phaser/phaser.py", line 262, in parse_sample
start_time, vcf_out, sample_out_path, last_chr=True, pi_block_value = 0)
File "REDO/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'