ncbi/fcs

Issues

• Fatal error: fasta.cpp:594 in ApplyActionReport(...): Assertion failed: row.size() == 8 || old_style

  #96 opened a month ago by polchan
  2

• Understanding clean.fasta and contam.fasta

  #99 opened a month ago by katiecdillon
  2

• Screening for mitochondrion

  #65 opened 10 months ago by wharvey31
  5

• Action report AssertionError

  #98 opened 2 months ago by mneitzey
  3

• [BUG]: Long runtime with excess RAM/Memory and cores

  #97 opened 2 months ago by Artifice120
  12

• [FEATURE REQUEST]: disable generation of cleaned sequences

  #95 opened 3 months ago by fgvieira
  4

• subprocess.CalledProcessError

  #94 opened 3 months ago by zilaijuand
  1

• Request for Conda Installation Option for fcs-gx on GitHub

  #92 opened 3 months ago by wangshuangyi
  1

• Can FCS-GX be used to batch process a large number of genomes with different taxid?

  #93 opened 3 months ago by ShenMJ99
  2

• Issue with source code compilation “make"

  #89 opened 4 months ago by ShenMJ99
  2

• gzip: stdin: No data available

  #80 opened 4 months ago by eeaunin
  17

• [BUG]: /bin/sh does not exist in container

  #90 opened 4 months ago by fgvieira
  5

• [FEATURE REQUEST]: clean up temp when finishes

  #91 opened 4 months ago by fgvieira
  0

• Issue with using get-fasta command

  #87 opened 4 months ago by ShenMJ99
  3

• [FEATURE REQUEST]: Single action to trim contaminant ends and mask internal contamination

  #88 opened 4 months ago by dmacguigan
  10

• AssertionError: Integrity check failed

  #79 opened 4 months ago by eeaunin
  5

• FCS-GX bypasses memory limits set in the bsub command on the LSF platform

  #81 opened 4 months ago by eeaunin
  4

• translate score to bit-score for FCS-gx output tax-id matches?

  #83 opened 4 months ago by blemmond
  3

• Question regarding assembly

  #84 opened 4 months ago by abacigalupo
  1

• Problems with downloading all.gxi and all.gxs files

  #85 opened 4 months ago by qb-lyu
  2

• [FEATURE REQUEST]: remove prefix to sequence names

  #73 opened 4 months ago by fgvieira
  4

• Using FCS-GX to split/mask internal adaptor sequences

  #67 opened 4 months ago by bndaniel
  13

• [FEATURE REQUEST]: shebang for `fcs.py`

  #60 opened 4 months ago by schellt
  2

• [BUG]: Contam file is empty but output shows taxonomy of contaminates

  #82 opened 6 months ago by brysonab
  4

• [BUG]: fcsadaptor gives errors related to psutil library

  #61 opened 6 months ago by LiaOb21
  4

• Fatal error trying to clean genome using fcs.py

  #66 opened 6 months ago by hugh0335
  5

• FCS-GX runtime on SGE cluster

  #68 opened 6 months ago by YanisChrys
  4

• Command terminated by signal 9

  #69 opened 6 months ago by eeaunin
  7

• Error: Process failed with retcode -13

  #71 opened 6 months ago by eeaunin
  1

• [FEATURE REQUEST]: <title>How to shorten the processing time?

  #75 opened 6 months ago by zhaoxuetong
  1

• [BUG]: <title>Download database failed, please help me to see what went wrong, thank you.

  #76 opened 6 months ago by zhaoxuetong
  3

• [BUG]: <title>subprocess.CalledProcessError

  #77 opened 6 months ago by zhaoxuetong
  4

• Is it possible to keep the FCS-GX database always loaded?

  #78 opened 6 months ago by eeaunin
  2

• [FEATURE REQUEST]: Add FCS-adaptor and FCS-GX "clean genome" option in the bioconda recipe & make executable names consistent

  #74 opened 8 months ago by LiaOb21
  3

• [FEATURE REQUEST]: accept gz input for `clean genome`

  #72 opened 9 months ago by schellt
  2

• segment.cpp:506 in sort_and_merge(...): Assertion failed: (prev->pos < 0) == (ivl.pos < 0)

  #70 opened 9 months ago by eeaunin
  2

• [FEATURE REQUEST]: skip over/ignore short sequences

  #62 opened 10 months ago by ptrebert
  3

• [BUG]: fix log output destination

  #63 opened 10 months ago by ptrebert
  2

• [FEATURE REQUEST]: Support on FASTQ/FASTQ.gz as an input and output

  #64 opened 10 months ago by mingyanisa
  1

• [FEATURE REQUEST]: Using FCS-GX to filter long-read contaminations?

  #58 opened a year ago by BitaoQiu
  2

• Running FCS-GX on genomes of unidentified prokaryotic organisms

  #56 opened a year ago by d-golzato
  4

• Incorrect identification and exclusion of valid contigs using fcs-genome/0.4.0

  #59 opened a year ago by Macrobrachium
  9

• FATAL: could not open image fcs-adaptor.sif: SIF imagefcs-adaptor.sif is corrupted: wrong partition size

  #57 opened a year ago by Catherine9826
  2

• Can run fcs.py interactively, but in a batch job keep getting: "No such file or directory: 'docker'"

  #55 opened a year ago by SchwarzEM
  2

• Which manufacturers' sequencing adapters are included in the reference database of FCS-adaptor?

  #54 opened a year ago by maruiqi0710
  2

• What's the effect of "--allow-same-species" option in the "fcs gx screen genome"？

  #53 opened a year ago by maruiqi0710
  2

• [BUG]: fcs.py fails to download database

  #51 opened a year ago by h836472
  5

• Can I provide a tax-id at a level higher than species?

  #52 opened a year ago by maruiqi0710
  2

• Making singularity the default engine

  #50 opened a year ago by Jokendo-collab
  11

• [BUG]: v0.4.0 fcs.py help is broken

  #48 opened a year ago by ptrebert
  2