[2023-03-15 05:56:37,367] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:56:37,374] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:56:37,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgab9a9094-8c2b-4f41-ad0c-2b89758054e6/dqc_reference
[2023-03-15 05:56:39,400] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:56:39,401] [INFO] Task started: Prodigal
[2023-03-15 05:56:39,401] [INFO] Running command: cat /var/lib/cwl/stg5756eec6-e274-4a99-82c5-6c2e1c202a93/OceanDNA-a2926.fa | prodigal -d OceanDNA-a2926/cds.fna -a OceanDNA-a2926/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:56:49,124] [INFO] Task succeeded: Prodigal
[2023-03-15 05:56:49,124] [INFO] Task started: HMMsearch
[2023-03-15 05:56:49,124] [INFO] Running command: hmmsearch --tblout OceanDNA-a2926/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab9a9094-8c2b-4f41-ad0c-2b89758054e6/dqc_reference/reference_markers.hmm OceanDNA-a2926/protein.faa > /dev/null
[2023-03-15 05:56:49,272] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:56:49,273] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5756eec6-e274-4a99-82c5-6c2e1c202a93/OceanDNA-a2926.fa]
[2023-03-15 05:56:49,403] [INFO] Query marker FASTA was written to OceanDNA-a2926/markers.fasta
[2023-03-15 05:56:49,404] [INFO] Task started: Blastn
[2023-03-15 05:56:49,404] [INFO] Running command: blastn -query OceanDNA-a2926/markers.fasta -db /var/lib/cwl/stgab9a9094-8c2b-4f41-ad0c-2b89758054e6/dqc_reference/reference_markers.fasta -out OceanDNA-a2926/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:56:49,862] [INFO] Task succeeded: Blastn
[2023-03-15 05:56:49,915] [INFO] Selected 1 target genomes.
[2023-03-15 05:56:49,916] [INFO] Target genome list was writen to OceanDNA-a2926/target_genomes.txt
[2023-03-15 05:56:49,917] [INFO] Task started: fastANI
[2023-03-15 05:56:49,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg5756eec6-e274-4a99-82c5-6c2e1c202a93/OceanDNA-a2926.fa --refList OceanDNA-a2926/target_genomes.txt --output OceanDNA-a2926/fastani_result.tsv --threads 1
[2023-03-15 05:56:50,388] [INFO] Task succeeded: fastANI
[2023-03-15 05:56:50,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab9a9094-8c2b-4f41-ad0c-2b89758054e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:56:50,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab9a9094-8c2b-4f41-ad0c-2b89758054e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:56:50,388] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:56:50,388] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:56:50,389] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-15 05:56:50,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2926/tc_result.tsv
[2023-03-15 05:56:50,442] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:56:50,442] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:56:50,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab9a9094-8c2b-4f41-ad0c-2b89758054e6/dqc_reference/checkm_data
[2023-03-15 05:56:50,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:56:50,484] [INFO] Task started: CheckM
[2023-03-15 05:56:50,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2926/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2926/checkm_input OceanDNA-a2926/checkm_result
[2023-03-15 05:57:23,035] [INFO] Task succeeded: CheckM
[2023-03-15 05:57:23,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:57:23,303] [INFO] ===== Completeness check finished =====
[2023-03-15 05:57:23,303] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:57:23,303] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2926/markers.fasta)
[2023-03-15 05:57:23,304] [INFO] Task started: Blastn
[2023-03-15 05:57:23,304] [INFO] Running command: blastn -query OceanDNA-a2926/markers.fasta -db /var/lib/cwl/stgab9a9094-8c2b-4f41-ad0c-2b89758054e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2926/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:57:23,795] [INFO] Task succeeded: Blastn
[2023-03-15 05:57:23,849] [INFO] Selected 6 target genomes.
[2023-03-15 05:57:23,850] [INFO] Target genome list was writen to OceanDNA-a2926/target_genomes_gtdb.txt
[2023-03-15 05:57:23,856] [INFO] Task started: fastANI
[2023-03-15 05:57:23,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg5756eec6-e274-4a99-82c5-6c2e1c202a93/OceanDNA-a2926.fa --refList OceanDNA-a2926/target_genomes_gtdb.txt --output OceanDNA-a2926/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:57:25,404] [INFO] Task succeeded: fastANI
[2023-03-15 05:57:25,406] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:57:25,406] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002495645.1	s__Poseidonia sp002495645	76.9582	65	498	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002728035.1	s__Poseidonia sp002728035	76.4922	78	498	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.50	96.50	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:57:25,429] [INFO] GTDB search result was written to OceanDNA-a2926/result_gtdb.tsv
[2023-03-15 05:57:25,467] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:57:25,488] [INFO] DFAST_QC result json was written to OceanDNA-a2926/dqc_result.json
[2023-03-15 05:57:25,489] [INFO] DFAST_QC completed!
[2023-03-15 05:57:25,489] [INFO] Total running time: 0h0m48s