An error was found that was difficult to resolve after manually reroot

[Five296]

graftM create --sequences bglX_all_rename_dup.fasta --taxtastic_taxonomy graftm_create_taxonomy.bglX_all_rename_dup.csv --taxtastic_seqinfo graftm_create_seqinfo.bglX_all_rename_dup.csv --alignment graftm_create_alignment.bglX_all_rename_dup.faa --rerooted_tree 1.tree

                         GraftM 0.15.0

01/17/2024 11:57:12 PM WARNING: Program found with multiple commands: taxit FastTreeMP hmmalign mafft. Arbitrarily selecting FastTreeMP

                        CREATE

               Joel Boyd, Ben Woodcroft

                                                /
          >a                                   /
          -------------                       /
          >b                        |        |
          --------          >>>     |  GPKG  |
          >c                        |________|
          ----------

01/17/2024 11:57:12 PM INFO: Building gpkg for bglX_all_rename_dup.gpkg 01/17/2024 11:57:12 PM INFO: Reading taxonomy from taxtastic taxonomy and seqinfo files 01/17/2024 11:57:12 PM INFO: Checking for duplicate sequence names 01/17/2024 11:57:12 PM INFO: Building HMM from alignment 01/17/2024 11:57:13 PM INFO: Filtered 0 short sequences from the alignment 01/17/2024 11:57:13 PM INFO: 320 sequences remaining 01/17/2024 11:57:13 PM INFO: Checking for incorrect or fragmented reads 01/17/2024 11:57:59 PM INFO: Building HMM from alignment 01/17/2024 11:58:00 PM INFO: Filtered 0 short sequences from the alignment 01/17/2024 11:58:00 PM INFO: 320 sequences remaining 01/17/2024 11:58:00 PM INFO: Deduplicating sequences 01/17/2024 11:58:00 PM INFO: Removed 0 sequences as duplicates, leaving 320 non-identical sequences 01/17/2024 11:58:00 PM INFO: Removing duplicates from tree 01/17/2024 11:58:00 PM INFO: Generating log file 01/17/2024 11:58:14 PM INFO: Creating reference package 01/17/2024 11:58:15 PM INFO: Creating diamond database 01/17/2024 11:58:15 PM INFO: Compiling gpkg 01/17/2024 11:58:15 PM INFO: Cleaning up 01/17/2024 11:58:15 PM INFO: Testing gpkg package works Traceback (most recent call last): File "/data/home/wuzy/miniconda3/envs/mNGS/bin/graftM", line 420, in Run(args).main() File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/graftm/run.py", line 672, in main self.create.main( File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/graftm/create.py", line 889, in main self._test_package(output_gpkg_path) File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/graftm/create.py", line 546, in _test_package extern.run(cmd) File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/extern/init.py", line 41, in run raise ExternCalledProcessError(process, command) extern.ExternCalledProcessError: Command graftM graft --forward /tmp/tmpq6zrcmo4.fa --graftm_package bglX_all_rename_dup.gpkg --output_directory /tmp/tmpppt30s5u --force returned non-zero exit status 1. STDERR was: b'01/17/2024 11:58:15 PM INFO: Working on tmpq6zrcmo4\n01/17/2024 11:58:17 PM INFO: 10 read(s) detected\n01/17/2024 11:58:17 PM INFO: aligning reads to reference package database\n01/17/2024 11:58:20 PM INFO: Filtered 0 short sequences from the alignment\n01/17/2024 11:58:20 PM INFO: 10 sequences remaining\n01/17/2024 11:58:20 PM INFO: Placing reads into phylogenetic tree\nTraceback (most recent call last):\n File "/data/home/wuzy/miniconda3/envs/mNGS/bin/graftM", line 420, in \n Run(args).main()\n File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/graftm/run.py", line 620, in main\n self.graft()\n File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/graftm/run.py", line 509, in graft\n taxonomic_assignment_time, assignments=self.p.place(REVERSE_PIPE,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/graftm/timeit.py", line 10, in timed\n result = method(*args, **kw)\n ^^^^^^^^^^^^^^^^^^^\n File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/graftm/pplacer.py", line 189, in place\n jplace = self.pplacer(files.jplace_output_path(), args.output_directory, files.comb_aln_fa(), args.threads)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/graftm/pplacer.py", line 28, in pplacer\n extern.run(cmd)\n File "/data/home/wuzy/miniconda3/envs/mNGS/lib/python3.11/site-packages/extern/init.py", line 41, in run\n raise ExternCalledProcessError(process, command)\nextern.ExternCalledProcessError: Command pplacer -j 5 --verbosity 0 --out-dir /tmp/tmpppt30s5u -c bglX_all_rename_dup.gpkg/bglX_all_rename_dup.gpkg.refpkg /tmp/tmpppt30s5u/combined_alignment.aln.fa returned non-zero exit status -6.\nSTDERR was: b"pplacer: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))\' failed.\n"STDOUT was: b\'\'\n'STDOUT was: b'\n GraftM 0.15.0\n\n GRAFT\n\n Joel Boyd, Ben Woodcroft\n\n /\n __|\n - - ____| |/\n - - - | |____/\n - >>>> - >>>> ____|\n - - - - | __\n - |____|\n - |__\n \n'

[Five296]

bglX.zip Here's my file

[wwood]

Hi,

This appaears to be a problem with your pplacer installation, not graftM directly.

[Five296]

Thank you for your response. I used 'mamba create -n graftM graftM' to download graftM and its dependencies, such as pplacer (latest version v1.1.alpha19-0-g807f6f3). I then extracted 20 sequences from the dataset successfully creating a gpkg subset, but the original dataset consistently failed. After trying various methods, I discovered that using '--rerooted' caused such issues, while switching to '--no-tree' resolved the problem. Does '--no-tree' compromise the reliability of the results?

[Five296]

I solved it ! The problem is caused by the compiler

[wwood]

Ah good, glad you managed to solve.