juliema/aTRAM

Issues

• Abyss assembler issue: Missing files in temp directory

  #308 opened 3 years ago by rafelafrance
  18

• ERROR: Exception: [Errno 2] No such file or directory: '/tmp/atram_bku5sgqt/lib_des-1S_uce-5k-probes.fasta_01_owavb3if/trinity.Trinity.fasta'

  #298 opened 4 years ago by liugang9988
  10

• Could you help me figure out what causes the error?

  #320 opened a year ago by luckyvivi
  0

• [Errno 2] No such file or directory

  #314 opened 2 years ago by danielyao12
  2

• atram_preprocessor.py taking a lot of time to load .fastq.gz files

  #319 opened 2 years ago by RominaSSBatista
  1

• TypeError: 'NoneType' object is not subscriptable

  #318 opened 2 years ago by RominaSSBatista
  1

• atram_preprocessor TypeError: 'NoneType' object is not subscriptable

  #299 opened 4 years ago by n-oury
  6

• [Question] How to use aTRAM stitcher? (no tutorial available / help menu unclear)

  #317 opened 2 years ago by ClaraKoehne
  0

• ## How to continue the uncompleted tasks?

  #315 opened 2 years ago by laiqiang0728
  5

• Only using one CPU for atram_preprocessor.py

  #316 opened 2 years ago by mchaney1
  0

• using a different genetic code on stitcher

  #313 opened 2 years ago by jacksonhturner
  1

• Install in conda environment

  #307 opened 3 years ago by RvV1979
  2

• stitcher does not recognise contig file

  #312 opened 3 years ago by Upasana1991
  0

• how to merge many .fa files to one single target file containing list of amino acids

  #311 opened 3 years ago by Upasana1991
  2

• conda installation

  #310 opened 3 years ago by jacksonhturner
  0

• Missing modules

  #303 opened 3 years ago by senramvx
  6

• Dist utils is being removed in Python 3.12

  #309 opened 3 years ago by rafelafrance
  0

• meaning of node number?

  #306 opened 3 years ago by juliadupin
  0

• Spack

  #305 opened 3 years ago by rdemoya
  0

• reciprocal blast search and e-value cutoffs

  #302 opened 3 years ago by rdemoya
  0

• timeout error in atram.py

  #304 opened 3 years ago by senramvx
  2

• atram_framer.py summary stats

  #269 opened 4 years ago by HeatherKates
  0

• add --np flag to abyss to tell it how many cpus to use

  #296 opened 4 years ago by juliema
  3

• 'NoneType' object has no attribute 'debug'

  #290 opened 4 years ago by tandermann
  2

• aTRAM/2.3.0 spades and python2 compatibility issues

  #286 opened 4 years ago by HeatherKates
  1

• Open database in readonly mode for atram.py

  #300 opened 4 years ago by rafelafrance
  1

• make library shuffle and option -- not the default

  #292 opened 4 years ago by juliema
  0

• assembling large number of loci (UCEs)

  #297 opened 4 years ago by MareikeJaniak
  4

• Preprocessing step very slow after update to v2.3.3

  #295 opened 4 years ago by MareikeJaniak
  5

• sqlite3.OperationalError: disk I/O error

  #294 opened 4 years ago by nomascus
  10

• add new parameter to abyss optios

  #293 opened 4 years ago by juliema
  1

• upgrade to latest Spades version

  #291 opened 5 years ago by juliema
  0

• 'stitcher' required files are not documented

  #289 opened 5 years ago by sestaton
  29

• --timeout 0 exits immediately

  #288 opened 5 years ago by sestaton
  2

• LOGGER variable is not inherited to child processes

  #287 opened 5 years ago by Ulises-Rosas
  7

• v2.3.0 --gzip option not working

  #284 opened 5 years ago by HeatherKates
  4

• Change integer arguments to be explicit as to what is acceptable

  #285 opened 5 years ago by rafelafrance
  0

• atram.py, nothing is assembling. spades error

  #271 opened 5 years ago by HeatherKates
  3

• Abyss is erroring out

  #283 opened 5 years ago by rafelafrance
  1

• Too many files open

  #282 opened 5 years ago by rafelafrance
  1

• add in the --careful option for SPAdes

  #278 opened 5 years ago by juliema
  0

• Add more parameter options for abyss-pe

  #279 opened 5 years ago by adsweet
  4

• Look at shrinking logger output

  #277 opened 5 years ago by rafelafrance
  1

• Run --query-split jobs in parallel

  #281 opened 5 years ago by rafelafrance
  0

• Allow wildcards and lists of files in the preprocessor input files.

  #273 opened 5 years ago by rafelafrance
  0

• Find an alternative to SQLite

  #274 opened 5 years ago by rafelafrance
  0

• blast only atram not working

  #275 opened 5 years ago by juliema
  0

• incompatibility issue with python 3.7?

  #276 opened 5 years ago by juliema
  2

• atram_preprocessor.py error with multiple fastq files

  #272 opened 5 years ago by MareikeJaniak
  5

• atram_framer.py coverage cutoff option

  #270 opened 5 years ago by HeatherKates
  1