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secastel / phaser

phasing and Allele Specific Expression from RNA-seq
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RSLVD?: Invalid literal during cutoff: " " #51

Closed LillianZ closed 5 years ago

LillianZ commented 5 years ago

Error: ... completed chromosome X... processing mapped reads... using alignment score cutoff of 122 Traceback (most recent call last): File "tools/phaser-v1.1.0/phaser/phaser.py", line 2359, in main(); File "tools/phaser-v1.1.0/phaser/phaser.py", line 170, in main parse_sample(sample_name, map_sample_column, args.bam, args.o, contig_ban) File "tools/phaser-v1.1.0/phaser/phaser.py", line 262, in parse_sample start_time, vcf_out, sample_out_path, last_chr=True, pi_block_value = 0) File "tools/phaser-v1.1.0/phaser/phaser.py", line 555, in process_vcf pool_output = parallelize(process_mapping_result, result_files); File "tools/phaser-v1.1.0/phaser/phaser.py", line 2090, in parallelize pool_output.append(function(input)); File "tools/phaser-v1.1.0/phaser/phaser.py", line 1303, in process_mapping_result if use_as_cutoff == False or int(fields[4]) >= as_cutoff: ValueError: invalid literal for int() with base 10: '' Command exited with non-zero status 1

LillianZ commented 5 years ago

Occurred while trying to run on a merged RNA and DNA BAM file; but realized that phaser can run on multiple bam files, which avoided the issue.

My bams: successfully phased! The reason for error: still unknown.

secastel commented 5 years ago

Sorry for the delayed response. The reason for this is that one of your BAMs had an alignment score tag (AS), while the other did not. phASER has problems if the alignment score is found in some, but not all alignments in a single bam. The correct way to solve this is what you've done already, which is to provide the BAMs separately. Thanks!