SPAdes-MaxBin2 bins with renamed contigs about graphbin

[nvpatin]

Some more information: below is (1) the exact error message I see when I try to run GraphBin, (2) the first 10 lines of the contigs.paths file, (3) the first 10 headers of the contigs file, and (4) the first 10 lines of the assembly graph file. The assembly graph is the only file that was constructed with the original fasta deflines, but it doesn't look like they are part of the file content anyway.

(1)
2021-12-16 10:50:52,790 - INFO - Welcome to GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs.
2021-12-16 10:50:52,790 - INFO - This version of GraphBin makes use of the assembly graph produced by SPAdes which is based on the de Bruijn graph approach.
2021-12-16 10:50:52,790 - INFO - Input arguments:
2021-12-16 10:50:52,790 - INFO - Assembly graph file: assembly_graph_with_scaffolds.gfa
2021-12-16 10:50:52,790 - INFO - Contig paths file: contigs-v3.paths
2021-12-16 10:50:52,790 - INFO - Existing binning output file: MaxBin2_graphbin_map.csv
2021-12-16 10:50:52,790 - INFO - Final binning output file: graphbin/
2021-12-16 10:50:52,790 - INFO - Maximum number of iterations: 100
2021-12-16 10:50:52,790 - INFO - Difference threshold: 0.1
2021-12-16 10:50:52,790 - INFO - GraphBin started
2021-12-16 10:50:52,801 - INFO - Number of bins available in the initial binning result: 23
2021-12-16 10:50:52,801 - INFO - Constructing the assembly graph
2021-12-16 10:50:52,801 - ERROR - Please make sure that the correct path to the contig paths file is provided.
2021-12-16 10:50:52,802 - INFO - Exiting GraphBin... Bye...!

(2) contigs.paths
c_000000000001
93572836-,92654567+,92654571+,92654567+,92654573+,93571458-
c_000000000001'
93571458+,92654573-,92654567-,92654571-,92654567-,93572836+
c_000000000002
91213823-,93572872-,93549998-,93054327-,25436494-,93565676-,93574710-,93461762-,84512918+,93553746-,93560474+,93464329+,92657131+,92657087+
c_000000000002'
92657087-,92657131-,93464329-,93560474-,93553746+,84512918-,93461762+,93574710+,93565676+,25436494+,93054327+,93549998+,93572872+,91213823+
c_000000000003
84786808+,93050927-;

(3) contigs file

c_000000000001
c_000000000002
c_000000000003
c_000000000004
c_000000000005
c_000000000006
c_000000000007
c_000000000008
c_000000000009
c_000000000010

(4) assembly graph
S 1562096 GACAAGAGCTCATGTCTGTGCTGCAATACTGGCGGGGCCAGGATGTGACGCTCATCGGCGCCACTACACTATGTGATCATTATTCCAAAGCGCTCGCCCTCGCTGGTGCCGCTGCATCAATCCTTGATGTGACCGCAATGACCCTAGCCGGGCTTGCGGCGGCACATCAGCAAGGGCAGCATGCCGATGCATAGAGAAATCATCGCAATTCTGCGGGGCGT KC:i:938
S 43432 CAGTTGTCCAGAGGCCTGCAACATATTTTGAACCAGCAACAAAAACATTGCCCAGAACAGCCATAAAAATACCAATTATGGTGCTGAACAGAATGACCATTACTGACGAAAAGATTAAACCAAACATTCACATTACCTTCTTCGAAGGTCACTTGTTTACAATACATTAACTTAAAGCATAAACATTATAAATTGCGGATCTTTGCTCTTTTCCCCCTTTCATTTCTT KC:i:848
S 85384538 GCCTCCTCCTCCTCCGCCGTCGCCTCCGCAGCTCGTCGGGCGGTCCGCGAATGGCGGTCGGCCGCGAGACATCGAGGCGTCTGCGTCCACGCGCGCCGCTCGGGACCACGCCGTACGGAGCTCCCCCATCTGCGCCCGGCTCTGGGGCACCAGCTGGTGGATGTGCAGCCCGTTGGTGCCGAGGGTTGCGAAGGAAGGTTGCTGCCAGCCGGAGGCCACCCCCCCCGCTCCACCAGAAGGGGTCGCGG KC:i:836
S 92795225 TTATTGATTGATGATGGATCAATATCAATATGTACTTTTTTTGACTTTGGAGAGAACTCATCAATTTTACCAGTTATACGATCATCAAATCTTGCACCAATATTAATTAGTAAATCACAATCGTGCATGGCATTATTGGCTTCATAAGTTCCATGCATTCCAAGCATTCCTAAAAATTGATTATCATCACCAGGATAAGAGCCAAGACCTTGCAGTGTTGAAGTAATTGGAAATCCAGTTAATGCAACTAGCCCTCTCAAGAGTTCACTTGCTTTTGGCCCAGAATTTACAACACCACCACCTGTATAAAAAATTGGTTTAGAAGCTTTATTCATTAACTCAATCAATTGATCAATATCTTTTTGATTAAATTTATTTTTGTTTTTAATTTCAATTTTTTTTTCTTTTTTAAAAGAAGCATATTTTGTTTTTGCAAACTGGATATCTTTTGGAATATCTACAAGCACTGGCCCCGGTCTTCCTGTGGTTGCAACCTCAAATGCTTCATTCATAATTCTTTGGAGATCATTAATATTTTTCACTAACCAATTGTGTTTTGTGCATGGTCTTGTAATTCCAGTTGTGTCACATTCCTGAAAAGCATCTGTTCCTATTAAATGAGTGGGTACTTGTCCTGAAATACAAACTAATGGTACCGAGTCCATGTAAGCATCTGTTAATGCAGTAACAACATTAGTTGCTCCCGGCCCAGAAGTAACTAAAACAACTCCTGGTTTACCAGAAGATCTTGCATAACCCTCTGCTGCATGACCTGCGCCCTGTTCATGTCTAACTAAAATATGTTTAATCGAAGTGTGATTTTTAAGTTCATCATAAATCGGAAGAACTGCTCCTCCTGGGTAACCAAAAATATGATTTACTTTTTGGTCTTCTAGACACTTAAATACTATCTCTGCTCCAGTATAT KC:i:4363
S 952260 GGGCCGTCTTCGACCCCGCGGACATGCCGCAGGGGCTCGAACAGATAGAGCCACATCTTTGCCAACCAAATCGCGTTTCACGCTCTCCTTTTTCCGGTCGGAGGGGCATTTGATTATCTTGGGAAGTGATAAACTTGTTGAGAAAGTTGAAACTGATATTCAATCAGAACCACTGCGAGTTTTTTTGGATCTAGGCTCGACCTCCTCGGCCGCCGTATACGCC KC:i:384
S 777246 GCCCAGCGCTCCCCCTCCGCCGTTCATATGTGCCCCCAAATACGCCGGTCACAGGGACGGCATGGTCTTCAAAAATGACCACAGTGGCCTGGGCTACTACCGCGATGTTGGGCATCAAGTCGCGAGCGTGCTGGCTGACGCCGCCGCCGTCAGCCAGTACATGCCGGTGGTGCAAATCCCTCTGCACCAGCTTCTTCTTGAGCAGCTCCGCCTTGAGGGCAGAGCTGAGGACCTGTCT KC:i:192
S 739802 GCGGCGCCCGGAACCCGGACGAGGTGAGTTTATATTTTATTTCTCGTACGGGCAATTGAACTGACGGCGTGTTTTATTTACTGTATAGATTCCGTTTGACGATCAAGCCGCCTTTGCCAAAGATTTAGCCGCGCTCTTCGAAGAGCCCGGCGCGTTCGCGGACATCGTCATCACCGCGGAGGTGATCCAGACGGTGCTCGCGCTCGGCGTGGTCACCGCCGTCGC KC:i:761
S 81177015 CTTCGACGCCGGCTCGATCGGTGGAGGAGGGCTGCTCGACCTCGGACCCCAGCCCGCGGACGAGCCGGCCCAGCTGCGTGCTAGTGGCGGCGGAGGCGGGGGCGTGCCAGAAAGCGTGCGAGACGCCGCCCGCGCCTCGAGGGAGCGACGGAGCGGCGAGCGGGTGCGCATGAGCAACGATCGCTCGGTCGACTCGCTGACGCCGCGGGGCGACGGCGCGGACGAGGCGTTCCTGACAGC KC:i:384
S 85844838 GTCAATACCAGCAGAATATTCATCAAAGCTCTTAACTTCTGGTGGGAATGACGAAATACGGGGCTGTACCCGCAACATTGGGAGAAAAACAGAACGAGCAAACCGGGCAAAACGTTCGTTAATCATACGAAGCGCATAGTAGTCACCAAGTAGCGAAAGATCATCCGAACCAAACTTGAATGGACGAACATCTGCCATATCACCAACATCTAGAGATGCAACTGATTCGGAAGTTTCTGACCCAAGCCCTTCAATAAGGGCATTAACTTCATCACTACTTAATTTGCGGGTGGATGCCAAAATAACACCTATTATGTTCTAAAAGTTTATTGTAGTACAAAAGATGTGAAATGTACTTCTGCCACACCACCAAAGTCTTCAAGAGATATAAGTTTAGCATTCATGGCATCTTTCATTGTAGTAGCAAGCTTCTCACGTCCTGCAATACCCTTAATATCCTCTTCACCAAACTCACTTAAAACTCCAAGGACGATTGAACGAAGCGCAAGCTGATGAGACTCAACCATTTCCATTATGCTTTCATCATATTGCGTTGATACACCAACACCAACCTGAAGCATTTTACGTGATCCCATTAGGTTTGCCGTAAATGTGCCTGGAAATTCATAATAGATGGTCACAAAGTTCTCAACTTCAGGTGTTTCTTTGGAA KC:i:2253
S 1347984 CTTCTAAAGCAGGCAGTACTTTAGGAAGGACACAAGATCTACTAGAGCAGGCAGTTCTCTAGCAGAGGCTTAGGCAGCAGTAATGGATAACTTGGTATACTGTAAGGTTGATTCCTTTATTTCAGAATAAGTTTTAACATAATATAAAATGATTATACCTAAGGTTCACCACTATAACCACTGTCAGAATGTCTAGGAGCAAGTAATCACTTATGAGT KC:i:861

[Vini2]

Hello @nvpatin,

Thanks for the issue. All the versions of GraphBin were originally designed to make use of the standard contig-naming conventions of the respective assemblers (e.g., NODE_* for SPAdes) to keep track of the contig numbers. This is why you are getting the above error. I would suggest using the original naming convention of SPAdes and giving it a try.

If you need to run GraphBin with custom naming formats, it might take a really long time to implement and test it for all the assemblers. Let me know how it goes.

Thank you!

Best regards,
Vijini