Test works but binsanity-profile fails

[biotemon]

Binsanity-profile -i contigs_v2.fa -s /Volumes/Red_4TB/scratch_BK/CS_BACKUP/p31_anvio_metagenomes/OC26_EXPERIMENT/binsanity_bins/bam_files/ -c binsanity.profile

/Users/tito_miniconda/opt/miniconda3/bin/Binsanity-profile:152: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if args.outDirectory is not ".":

        ******************************************************
                    Contigs formated to generate counts
        ******************************************************
        
Traceback (most recent call last):
  File "/Users/tito_miniconda/opt/miniconda3/bin/Binsanity-profile", line 164, in <module>
    feature_counts(args.inputMapLoc, args.outDirectory, args.Threads)
  File "/Users/tito_miniconda/opt/miniconda3/bin/Binsanity-profile", line 31, in feature_counts
    subprocess.call(["featureCounts", "-M", "-O", "-F", "SAF", "-T", str(threads), "-a", os.path.join(outputdir, str(
  File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/subprocess.py", line 340, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/subprocess.py", line 858, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/subprocess.py", line 1704, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'featureCounts'

[edgraham]

Hello Tito, I'm sorry you're having issues. This looks like a python related syntax error. I'll look into it ASAP and send out a repair. In the meantime try these things: 1. Try running the test dataset and see if that will run. 2. Try dropping your conda env to python 3.6 and re-running this command.

…

-Elaina

On Mon, Jan 17, 2022 at 7:16 PM Tito Montenegro ***@***.***> wrote: Binsanity-profile -i contigs_v2.fa -s /Volumes/Red_4TB/scratch_BK/CS_BACKUP/p31_anvio_metagenomes/OC26_EXPERIMENT/binsanity_bins/bam_files/ -c binsanity.profile /Users/tito_miniconda/opt/miniconda3/bin/Binsanity-profile:152: SyntaxWarning: "is not" with a literal. Did you mean "!="? if args.outDirectory is not ".": ****************************************************** Contigs formated to generate counts ****************************************************** Traceback (most recent call last): File "/Users/tito_miniconda/opt/miniconda3/bin/Binsanity-profile", line 164, in <module> feature_counts(args.inputMapLoc, args.outDirectory, args.Threads) File "/Users/tito_miniconda/opt/miniconda3/bin/Binsanity-profile", line 31, in feature_counts subprocess.call(["featureCounts", "-M", "-O", "-F", "SAF", "-T", str(threads), "-a", os.path.join(outputdir, str( File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/subprocess.py", line 340, in call with Popen(*popenargs, **kwargs) as p: File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/subprocess.py", line 858, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/subprocess.py", line 1704, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'featureCounts' — Reply to this email directly, view it on GitHub <#59>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEC7DI44R2E635BNO2YMMBDUWTLRHANCNFSM5MGCDK3Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[saras224]

Hi @edgraham
I also got an error while running binsanity_profile command.
Command: Binsanity-profile -i A1.fa -s /home/saraswati/MAPPED_SORTED/SORTED/BINSANITY_TRIAL/ -c binsanity_coverage

error message:
/lustre/saraswati/anaconda3/bin/Binsanity-profile:152: SyntaxWarning: "is not" with a literal. Did you mean "!="?
if args.outDirectory is not ".":

    ==========     _____ _    _ ____  _____  ______          _____  
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
  v2.0.3

//========================== featureCounts setting ===========================\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| A1.sorted.bam ||
|| ||
|| Output file : A1.sorted.bam.readcounts ||
|| Summary : A1.sorted.bam.readcounts.summary ||
|| Paired-end : no ||
|| Count read pairs : no ||
|| Annotation : A1.sorted.bam.saf (SAF) ||
|| Dir for temp files : . ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\============================================================================//

//================================= Running ==================================\
|| ||
|| Load annotation file A1.sorted.bam.saf ... ||
|| Features : 35630 ||
|| Meta-features : 35630 ||
|| Chromosomes/contigs : 35630 ||
|| ||
|| Process BAM file A1.sorted.bam... ||
ERROR: Paired-end reads were detected in single-end read library : /home/saraswati/MAPPED_SORTED/SORTED/BINSANITY_TRIAL/A1.sorted.bam

    ******************************************************
                Contigs formated to generate counts
    ******************************************************

Traceback (most recent call last):
File "/lustre/saraswati/anaconda3/bin/Binsanity-profile", line 166, in
make_coverage(args.inputFasta, args.outCov, args.outDirectory)
File "/lustre/saraswati/anaconda3/bin/Binsanity-profile", line 54, in make_coverage
contig_length = cov_data[k].pop(0)
IndexError: pop from empty list

real 1m37.531s
user 0m54.310s
sys 0m1.387s

Kindly help me resolve the error!

Thanks in Advance!