Open biotemon opened 2 years ago
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:
-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
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 https://github.com/edgraham/BinSanity/issues/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.
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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
real 1m37.531s user 0m54.310s sys 0m1.387s
Kindly help me resolve the error!
Thanks in Advance!
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