EMBL-PKU/BASALT

Issues

• Almost 1/3 of the obtained bins from BASALT were removed by dRep dereplicate -sa 0.99.

  #49 opened 4 months ago by zzz199125
  1

• how to make a binning with these samples?

  #59 opened a month ago by guangingmai
  0

• The test data I ran myself was different from the data provided

  #58 opened a month ago by guangingmai
  0

• Date of update to v1.1.0 in conda?

  #43 opened 6 months ago by zhaoze2020
  3

• Running without binning

  #57 opened 2 months ago by AprilJauhal
  0

• If I follow the tutorial, v1.0.1 is installed, not v1.1.0.

  #55 opened 2 months ago by HirokiK0
  3

• results different from yours

  #56 opened 2 months ago by dsfchina
  0

• Abnormal Exit in step 8

  #52 opened 3 months ago by f12345zxcvbnm2
  1

• BASALT is stuck in the middle

  #53 opened 3 months ago by shashank-KU
  1

• The error while BASALT installed with "conda env create -n BASALT --file basalt_env.yml"

  #40 opened 6 months ago by ggezwp123
  3

• "1_DRRcontigs.fasta" does not exist or is not a Bowtie 2 index

  #51 opened 3 months ago by Juzishh
  2

• UnboundLocalError: local variable 'bam_sorted2' referenced before assignment

  #25 opened 8 months ago by Aveglia
  2

• UnboundLocalError: local variable 'level_num' referenced before assignment

  #54 opened 3 months ago by haihao999
  0

• Question: Any plans to make the tool available at Biocontainers?

  #48 opened 5 months ago by erikrikarddaniel
  2

• Didn‘t Get The Binning Result

  #50 opened 4 months ago by Flooooooooooooower
  1

• sh: Cytoscapeviz.pl: command not found

  #47 opened 5 months ago by jiangyoufeng
  1

• UnboundLocalError: local variable 'level_num' referenced before assignment

  #32 opened 7 months ago by liaohu1231
  3

• FileNotFoundError: [Errno 2] No such file or directory: 'Predicted_potential_outlier.txt'

  #42 opened 6 months ago by Songq-20
  2

• empty fasta file:'Remapping.fasta'; local variable 'bam_sorted' referenced before assignment

  #46 opened 5 months ago by FengqingWang0712
  4

• Bug shows "FileNotFoundError: [Errno 2] No such file or directory: 'BestBinset_outlier_refined_filtrated_retrieved_checkm/storage/'"

  #39 opened 7 months ago by 1023011930
  7

• FileNotFoundError: [Errno 2] No such file or directory: 'clustering_gt1000.csv'

  #45 opened 5 months ago by tenguzame
  0

• VAMB and BASALT

  #41 opened 6 months ago by vicru93
  2

• Issue about LRS binning

  #44 opened 6 months ago by AlenaYoung
  1

• Error finding "quality_report.tsv" and "*vamb/clusters.tsv'

  #19 opened 9 months ago by pthieringer
  6

• Incorporating previous binning attempts

  #10 opened 10 months ago by hrwaik
  3

• Error when running with test dataset：ModuleNotFoundError: No module named 'torch'

  #33 opened 7 months ago by 1023011930
  3

• Is it normal to stay at this step for a long time?

  #36 opened 7 months ago by 1023011930
  6

• 3rd bin selection did not perform, because there is only one assembly!

  #37 opened 7 months ago by Enewmoon
  5

• Output Basalt

  #38 opened 7 months ago by vicru93
  2

• UnboundLocalError: local variable 'target_bin_folder' referenced before assignment

  #30 opened 7 months ago by Songq-20
  3

• BASALT stopped running

  #31 opened 7 months ago by Songq-20
  4

• AttributeError: 'NoneType' object has no attribute 'split'

  #35 opened 7 months ago by Enewmoon
  0

• Redundant output

  #34 opened 7 months ago by Wang0293
  1

• FileNotFoundError: [Errno 2] No such file or directory: '/work/home/songbing/.cache/BASALT'

  #27 opened 8 months ago by B1991ing
  2

• UnboundLocalError: local variable 'seq len' referenced before assignment

  #29 opened 8 months ago by mijiandui
  0

• FileNotFoundError: [Errno 2] No such file or directory: '/work/home/songbing/.cache/BASALT' or ModuleNotFoundError: No module named 'Bio'

  #28 opened 8 months ago by B1991ing
  0

• command not found

  #18 opened 9 months ago by WUD2018
  12

• a question about dRep and the source of MAGs

  #26 opened 8 months ago by liupfskygre
  1

• ModuleNotFoundError: No module named 'symbol'

  #24 opened 8 months ago by haihao999
  0

• BASALT create some file named core.123xxx after running.

  #22 opened 8 months ago by Songq-20
  2

• bowtie2每次只运行一个，太慢了，是否可以设置平行几个？

  #23 opened 8 months ago by JiayinZhangfdu
  2

• Running error: UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

  #21 opened 9 months ago by wangyujie000
  1

• Only use contig

  #20 opened 9 months ago by wangyujie000
  1

• run BASALT with multiple assemblies and short reads from several samples

  #15 opened 9 months ago by liupfskygre
  3

• how will BASALT set the min length contigs for each binner

  #16 opened 9 months ago by liupfskygre
  2

• the threads setting is not applied for all implemented tools

  #17 opened 9 months ago by liupfskygre
  1

• BASALT env does not contain BASALT command

  #11 opened 9 months ago by bowmanjeffs
  1

• don't hard-code model location

  #12 opened 9 months ago by xvazquezc
  2

• where is the 'Bin merging program"

  #14 opened 9 months ago by zoubohao
  1

• checkm2 database not found

  #13 opened 9 months ago by Caiyulu-818
  2