subprocess.CalledProcessError

I got the following error while using the repo phaser.

##################################################
              Welcome to phASER v1.1.1
  Author: Stephane Castel (scastel@nygenome.org)
  Updated by: Bishwa K. Giri (bkgiri@uncg.edu)
##################################################

Completed the check of dependencies and input files availability... 

STARTED "Read backed phasing and ASE/haplotype analyses" ... 
    DATE, TIME : 2019-04-24, 17:21:25
#1. Loading heterozygous variants into intervals...
Processing sample named 10780_wgs_FromBam
    using all the chromosomes ...
    processing VCF...

    Memory efficient mode is deactivated...
    If RAM is limited, activate memory efficient mode using the flag "--process_slow = 1"...

     creating variant mapping table...
          2441858 heterozygous sites being used for phasing (0 filtered, 0 indels excluded, 2268598 unphased)

#2. Retrieving reads that overlap heterozygous sites...
     file: /imppc/labs/lplab/share/marc/epimutations/processed/bam/hg38/atacBam/10780_ATAC.bam
          minimum mapq: 255
          mapping reads to variants...
Traceback (most recent call last):
  File "/imppc/labs/lplab/share/marc/repos/phaser/phaser/call_read_variant_map.py", line 2, in <module>
    import read_variant_map;
ImportError: /imppc/labs/lplab/share/marc/repos/phaser/phaser/read_variant_map.so: undefined symbol: PyUnicodeUCS2_DecodeUTF8
[main_samview] failed to write the SAM header
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Traceback (most recent call last):
  File "/imppc/labs/lplab/share/marc/repos/phaser/phaser/phaser.py", line 2358, in <module>
    main();
  File "/imppc/labs/lplab/share/marc/repos/phaser/phaser/phaser.py", line 170, in main
    parse_sample(sample_name, map_sample_column, args.bam, args.o, contig_ban)
  File "/imppc/labs/lplab/share/marc/repos/phaser/phaser/phaser.py", line 262, in parse_sample
    start_time, vcf_out, sample_out_path, last_chr=True, pi_block_value = 0)
  File "/imppc/labs/lplab/share/marc/repos/phaser/phaser/phaser.py", line 533, in process_vcf
    result_files = parallelize(call_mapping_script, pool_input);
  File "/imppc/labs/lplab/share/marc/repos/phaser/phaser/phaser.py", line 2089, in parallelize
    pool_output.append(function(input));
  File "/imppc/labs/lplab/share/marc/repos/phaser/phaser/phaser.py", line 1346, in call_mapping_script
    error_code = subprocess.check_call("set -euo pipefail && "+run_cmd, stdout=devnull, shell=True, executable='/bin/bash')
  File "/soft/general/python/lib/python2.7/subprocess.py", line 540, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail && samtools view -h /imppc/labs/lplab/share/marc/epimutations/processed/bam/hg38/atacBam/10780_ATAC.bam 'chr1': | samtools view -Sh -F 0x400  -L /tmp/tmpnWNPVv -q 255 - | python2.7 /imppc/labs/lplab/share/marc/repos/phaser/phaser/call_read_variant_map.py --baseq 10 --splice 1 --isize_cutoff 0.0 --variant_table /tmp/tmpy1yJfS --o /tmp/tmppUwFEs' returned non-zero exit status 1

Code:

python /imppc/labs/lplab/share/marc/repos/phaser/phaser/phaser.py --vcf $vcf --bam $bam --mapq 255 --baseq 10 --sample $(bcftools query -l $vcf) --o prove --paired_end 0 --id_separator "@"

I used the id_separator "@" becuase the error:

FATAL ERROR: Character '_' must not be present in contig name. Please change id separtor using --id_separator to a character not found in the contig names and try again.

Any suggestions?

secastel / phaser

subprocess.CalledProcessError #53