[12/09/2022 01:57:32 PM INFO] autometa.common.metagenome: Getting contigs greater than or equal to 2,500 bp
[12/09/2022 01:57:39 PM INFO] autometa.common.utilities: length_filter took 7.27 seconds
[12/09/2022 01:57:43 PM INFO] autometa.common.utilities: gc_content took 4.28 seconds
/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/external/bedtools.py:107: FutureWarning: Indexing with multiple keys (implicitly converted to a tuple of keys) will be deprecated, use a list instead.
  dff = df.groupby("contig")["depth_product", "bases"].sum()
[12/09/2022 02:09:05 PM DEBUG] autometa.common.external.hmmscan: hmmscan --seed 42 --cpu 4 --tblout /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.bacteria.hmmscan.tsv /GWSPH/home/ecastron/Databases/autometa_db/bacteria.single_copy.hmm /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa/metagneome.orfs.faa
[12/09/2022 02:09:05 PM WARNING] autometa.common.external.hmmscan: Make sure your hmm profiles are pressed! hmmpress -f /GWSPH/home/ecastron/Databases/autometa_db/bacteria.single_copy.hmm
Traceback (most recent call last):
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/bin/autometa-markers", line 10, in <module>
    sys.exit(main())
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/markers.py", line 266, in main
    get(
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/markers.py", line 162, in get
    scans = hmmscan.run(
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/external/hmmscan.py", line 170, in run
    annotate_sequential(
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/external/hmmscan.py", line 106, in annotate_sequential
    raise err
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/external/hmmscan.py", line 101, in annotate_sequential
    subprocess.run(
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['hmmscan', '--seed', '42', '--cpu', '4', '--tblout', '/lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.bacteria.hmmscan.tsv', '/GWSPH/home/ecastron/Databases/autometa_db/bacteria.single_copy.hmm', '/lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa/metagneome.orfs.faa']' returned non-zero exit status 1.
[12/09/2022 02:09:05 PM DEBUG] autometa.common.external.hmmscan: hmmscan --seed 42 --cpu 4 --tblout /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.archaea.hmmscan.tsv /GWSPH/home/ecastron/Databases/autometa_db/archaea.single_copy.hmm /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa/metagneome.orfs.faa
[12/09/2022 02:09:05 PM WARNING] autometa.common.external.hmmscan: Make sure your hmm profiles are pressed! hmmpress -f /GWSPH/home/ecastron/Databases/autometa_db/archaea.single_copy.hmm
Traceback (most recent call last):
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/bin/autometa-markers", line 10, in <module>
    sys.exit(main())
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/markers.py", line 266, in main
    get(
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/markers.py", line 162, in get
    scans = hmmscan.run(
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/external/hmmscan.py", line 170, in run
    annotate_sequential(
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/external/hmmscan.py", line 106, in annotate_sequential
    raise err
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/external/hmmscan.py", line 101, in annotate_sequential
    subprocess.run(
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['hmmscan', '--seed', '42', '--cpu', '4', '--tblout', '/lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.archaea.hmmscan.tsv', '/GWSPH/home/ecastron/Databases/autometa_db/archaea.single_copy.hmm', '/lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa/metagneome.orfs.faa']' returned non-zero exit status 1.
[12/09/2022 02:09:06 PM WARNING] autometa.taxonomy.ncbi: DatabaseWarning: /GWSPH/home/ecastron/Databases/autometa_db/nr.gz needs to be formatted for diamond!
[12/09/2022 02:09:13 PM DEBUG] autometa.taxonomy.lca: Retrieving taxids from /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa/blastp.tsv
[12/09/2022 02:09:32 PM WARNING] autometa.taxonomy.lca: Skipping taxid conversion from /GWSPH/home/ecastron/Databases/autometa_db/dead_prot.accession2taxid
[12/09/2022 02:09:32 PM WARNING] autometa.taxonomy.ncbi: prot.accession2taxid.FULL.gz was not found. Reverting to prot.accession2taxid.gz
[12/09/2022 02:09:32 PM WARNING] autometa.taxonomy.ncbi: To achieve greater resolution of your metagenome taxonomy, considering downloading the prot.accession2taxid.FULL.gz database file
[12/09/2022 02:09:32 PM DEBUG] autometa.taxonomy.ncbi: Searching for 3,721,388 accessions in prot.accession2taxid.gz. This may take a while...
[12/09/2022 02:25:34 PM DEBUG] autometa.taxonomy.ncbi: sseqids converted from prot.accession2taxid.gz: 2,637,415
[12/09/2022 02:25:35 PM WARNING] autometa.taxonomy.lca: sseqids without corresponding taxid: 1,083,973
[12/09/2022 02:26:26 PM INFO] autometa.taxonomy.lca: Wrote 9,186,460 qseqids to /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.orfs.sseqid2taxid.tsv
[12/09/2022 02:26:26 PM DEBUG] autometa.taxonomy.lca: Assigning LCAs to 760,697 ORFs
[12/09/2022 02:26:34 PM DEBUG] autometa.taxonomy.lca: Precomputing LCAs
[12/09/2022 02:28:55 PM DEBUG] autometa.taxonomy.lca: LCA data structures prepared
[12/09/2022 02:35:14 PM INFO] autometa.taxonomy.lca: Assigned LCA to 760,697 ORFs: /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.orfs.lca.tsv
DatabaseWarning: /GWSPH/home/ecastron/Databases/autometa_db/nr.gz needs to be formatted for diamond!
[12/09/2022 02:35:40 PM WARNING] autometa.taxonomy.ncbi: DatabaseWarning: /GWSPH/home/ecastron/Databases/autometa_db/nr.gz needs to be formatted for diamond!
[12/09/2022 02:35:48 PM DEBUG] root: Wrote 377,644 contigs canonical rank names to /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.taxonomy.tsv
[12/09/2022 02:35:55 PM DEBUG] autometa.taxonomy.vote: Wrote 54 records to /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.archaea.fna
[12/09/2022 02:35:57 PM DEBUG] autometa.taxonomy.vote: Wrote 147,493 records to /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.bacteria.fna
[12/09/2022 02:35:57 PM DEBUG] autometa.taxonomy.vote: Wrote 7,761 records to /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.eukaryota.fna
[12/09/2022 02:35:59 PM DEBUG] autometa.taxonomy.vote: Wrote 216,539 records to /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.unclassified.fna
[12/09/2022 02:36:00 PM DEBUG] autometa.taxonomy.vote: Wrote 5,797 records to /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.viruses.fna
[12/09/2022 02:36:00 PM INFO] root: Wrote 5 ranks to files.
[12/09/2022 02:36:34 PM INFO] autometa.common.kmers: Counting 5-mers.
[12/09/2022 02:36:38 PM DEBUG] autometa.common.kmers: Pool counter (cpus=32): counting 147,493 records k-mer frequencies
[12/09/2022 02:37:51 PM DEBUG] autometa.common.kmers: Wrote 147493 contigs 5-mers frequencies to /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.bacteria.5mers.tsv.
[12/09/2022 02:37:51 PM INFO] autometa.common.utilities: count took 76.89 seconds
[12/09/2022 02:37:51 PM DEBUG] autometa.common.kmers: Transforming k-mer counts using am_clr
[12/09/2022 02:40:40 PM DEBUG] autometa.common.kmers: Performing decomposition with PCA (seed 42): 512 to 50 dims
[12/09/2022 02:40:44 PM DEBUG] autometa.common.kmers: bhsne: 147493 data points and 50 dimensions
[12/09/2022 02:40:44 PM DEBUG] autometa.common.kmers: Performing embedding with bhsne (seed 42)
[12/09/2022 02:59:29 PM DEBUG] autometa.common.kmers: embedded.shape (147493, 2) : Written /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.bacteria.5mers.am_clr.bhsne.tsv
[12/09/2022 02:59:45 PM INFO] autometa.common.kmers: Counting 5-mers.
[12/09/2022 02:59:45 PM DEBUG] autometa.common.kmers: Pool counter (cpus=32): counting 54 records k-mer frequencies
[12/09/2022 02:59:45 PM DEBUG] autometa.common.kmers: Wrote 54 contigs 5-mers frequencies to /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.archaea.5mers.tsv.
[12/09/2022 02:59:45 PM INFO] autometa.common.utilities: count took 0.30 seconds
[12/09/2022 02:59:45 PM DEBUG] autometa.common.kmers: Transforming k-mer counts using am_clr
[12/09/2022 02:59:45 PM DEBUG] autometa.common.kmers: Performing decomposition with PCA (seed 42): 512 to 50 dims
[12/09/2022 02:59:45 PM DEBUG] autometa.common.kmers: bhsne: 54 data points and 50 dimensions
[12/09/2022 02:59:45 PM DEBUG] autometa.common.kmers: Performing embedding with bhsne (seed 42)
[12/09/2022 02:59:46 PM DEBUG] autometa.common.kmers: embedded.shape (54, 2) : Written /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.archaea.5mers.am_clr.bhsne.tsv
[12/09/2022 02:59:48 PM DEBUG] autometa.binning.utilities: Reading/merging 4 contig annotation files
[12/09/2022 02:59:49 PM DEBUG] autometa.binning.utilities: merged annotations shape: (24054, 15)
[12/09/2022 02:59:49 PM DEBUG] autometa.binning.utilities: superkingdom filtered to bacteria taxonomy. shape: (24054, 15)
Traceback (most recent call last):
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/bin/autometa-binning", line 10, in <module>
    sys.exit(main())
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/binning/recursive_dbscan.py", line 870, in main
    markers_df = load_markers(args.markers, format="wide")
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/markers.py", line 61, in load
    raise FileNotFoundError(fpath)
FileNotFoundError: /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.bacteria.markers.tsv
[12/09/2022 02:59:50 PM DEBUG] autometa.binning.utilities: Reading/merging 4 contig annotation files
[12/09/2022 02:59:51 PM DEBUG] autometa.binning.utilities: merged annotations shape: (6, 15)
[12/09/2022 02:59:51 PM DEBUG] autometa.binning.utilities: superkingdom filtered to archaea taxonomy. shape: (6, 15)
Traceback (most recent call last):
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/bin/autometa-binning", line 10, in <module>
    sys.exit(main())
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/binning/recursive_dbscan.py", line 870, in main
    markers_df = load_markers(args.markers, format="wide")
  File "/GWSPH/home/ecastron/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/markers.py", line 61, in load
    raise FileNotFoundError(fpath)
FileNotFoundError: /lustre/groups/cbi/Users/ecastron/valentin/sea_lions/filtered/no_host/cluster2/autometa_output/SLF_CL2.archaea.markers.tsv