Error when running conda version

[fgvieira]

I've installed NGSCheckMate through conda but, when running it, I get these errors:

$ NCM_REF=small_genome.fasta ncm_fastq.py --depth 5 --pt small_pt.pt  --maxthread 1  --list /tmp/tmp_sdhdeky/list_file.txt  --outdir /tmp/tmp_sdhdeky -N snake_out

Traceback (most recent call last):
  File "/home/lnc113/appz/snakemake-wrappers/bio/ngscheckmate/ncm/test/.snakemake/conda/2f08aab77343104890272f54db2eac3c_/NGSCheckMate/ncm_fastq.py", line 869, in <module>
    for line in F.xreadlines():
                ^^^^^^^^^^^^
AttributeError: '_io.TextIOWrapper' object has no attribute 'xreadlines'. Did you mean: 'readlines'?

$ NCM_REF=small_genome.fasta ncm.py --nonzero --bedfile small.bed  --BAM --bedfile small.bed  --list /tmp/tmphi86f_gs/list_file.txt  --outdir /tmp/tmphi86f_gs -N snake_out

Set the path to your reference file with the NCM_REF environment variable
eg. export NCM_REF=/<path>/<to>/<reference>

Traceback (most recent call last):
  File "/home/lnc113/appz/snakemake-wrappers/bio/ngscheckmate/ncm/test/.snakemake/conda/8213eee5d2ff0fda1fa40b2051ca024e_/NGSCheckMate/ncm.py", line 1444, in <module>
    run_mpileup()
  File "/home/lnc113/appz/snakemake-wrappers/bio/ngscheckmate/ncm/test/.snakemake/conda/8213eee5d2ff0fda1fa40b2051ca024e_/NGSCheckMate/ncm.py", line 1199, in run_mpileup
    if samtool_line.find("Version") != -1:
       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: argument should be integer or bytes-like object, not 'str'

$ NCM_REF=small_genome.fasta ncm.py --nonzero --bedfile small.bed --VCF --bedfile small.bed  --list /tmp/tmpgftp5cwn/list_file.txt  --outdir /tmp/tmpgftp5cwn -N snake_out

Set the path to your reference file with the NCM_REF environment variable
eg. export NCM_REF=/<path>/<to>/<reference>

Generate Data Set from /tmp/tmpiwprad4g/list_file.txt
using this bed file : small.bed
Traceback (most recent call last):
  File "/home/lnc113/appz/snakemake-wrappers/bio/ngscheckmate/ncm/test/.snakemake/conda/8213eee5d2ff0fda1fa40b2051ca024e_/NGSCheckMate/ncm.py", line 1474, in <module>
    createDataSetFromList(base_list,bedFile)
  File "/home/lnc113/appz/snakemake-wrappers/bio/ngscheckmate/ncm/test/.snakemake/conda/8213eee5d2ff0fda1fa40b2051ca024e_/NGSCheckMate/ncm.py", line 409, in createDataSetFromList
    if glob_scores.has_key(file):
       ^^^^^^^^^^^^^^^^^^^
AttributeError: 'dict' object has no attribute 'has_key'

Is the conda recipe lacking some dependencies?
thanks,