[2023-03-16 00:05:33,649] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:05:33,650] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:05:33,650] [INFO] DQC Reference Directory: /var/lib/cwl/stge19d3a59-2c61-40c8-980e-67472632e5b3/dqc_reference
[2023-03-16 00:05:34,771] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:05:34,771] [INFO] Task started: Prodigal
[2023-03-16 00:05:34,771] [INFO] Running command: cat /var/lib/cwl/stgc7cc2c7b-3297-47e7-9b9d-969caca135f4/OceanDNA-b11726.fa | prodigal -d OceanDNA-b11726/cds.fna -a OceanDNA-b11726/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:05:57,394] [INFO] Task succeeded: Prodigal
[2023-03-16 00:05:57,395] [INFO] Task started: HMMsearch
[2023-03-16 00:05:57,395] [INFO] Running command: hmmsearch --tblout OceanDNA-b11726/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge19d3a59-2c61-40c8-980e-67472632e5b3/dqc_reference/reference_markers.hmm OceanDNA-b11726/protein.faa > /dev/null
[2023-03-16 00:05:57,560] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:05:57,561] [INFO] Found 6/6 markers.
[2023-03-16 00:05:57,576] [INFO] Query marker FASTA was written to OceanDNA-b11726/markers.fasta
[2023-03-16 00:05:57,578] [INFO] Task started: Blastn
[2023-03-16 00:05:57,578] [INFO] Running command: blastn -query OceanDNA-b11726/markers.fasta -db /var/lib/cwl/stge19d3a59-2c61-40c8-980e-67472632e5b3/dqc_reference/reference_markers.fasta -out OceanDNA-b11726/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:05:58,139] [INFO] Task succeeded: Blastn
[2023-03-16 00:05:58,140] [INFO] Selected 18 target genomes.
[2023-03-16 00:05:58,140] [INFO] Target genome list was writen to OceanDNA-b11726/target_genomes.txt
[2023-03-16 00:05:58,152] [INFO] Task started: fastANI
[2023-03-16 00:05:58,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7cc2c7b-3297-47e7-9b9d-969caca135f4/OceanDNA-b11726.fa --refList OceanDNA-b11726/target_genomes.txt --output OceanDNA-b11726/fastani_result.tsv --threads 1
[2023-03-16 00:06:11,110] [INFO] Task succeeded: fastANI
[2023-03-16 00:06:11,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge19d3a59-2c61-40c8-980e-67472632e5b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:06:11,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge19d3a59-2c61-40c8-980e-67472632e5b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:06:11,111] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:06:11,111] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:06:11,111] [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
--------------------------------------------------------------------------------
[2023-03-16 00:06:11,111] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11726/tc_result.tsv
[2023-03-16 00:06:11,111] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:06:11,112] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:06:11,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge19d3a59-2c61-40c8-980e-67472632e5b3/dqc_reference/checkm_data
[2023-03-16 00:06:11,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:06:11,118] [INFO] Task started: CheckM
[2023-03-16 00:06:11,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11726/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11726/checkm_input OceanDNA-b11726/checkm_result
[2023-03-16 00:07:11,486] [INFO] Task succeeded: CheckM
[2023-03-16 00:07:11,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.76%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 00:07:11,498] [INFO] ===== Completeness check finished =====
[2023-03-16 00:07:11,498] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:07:11,499] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11726/markers.fasta)
[2023-03-16 00:07:11,500] [INFO] Task started: Blastn
[2023-03-16 00:07:11,500] [INFO] Running command: blastn -query OceanDNA-b11726/markers.fasta -db /var/lib/cwl/stge19d3a59-2c61-40c8-980e-67472632e5b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11726/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:07:12,459] [INFO] Task succeeded: Blastn
[2023-03-16 00:07:12,463] [INFO] Selected 15 target genomes.
[2023-03-16 00:07:12,463] [INFO] Target genome list was writen to OceanDNA-b11726/target_genomes_gtdb.txt
[2023-03-16 00:07:12,479] [INFO] Task started: fastANI
[2023-03-16 00:07:12,479] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7cc2c7b-3297-47e7-9b9d-969caca135f4/OceanDNA-b11726.fa --refList OceanDNA-b11726/target_genomes_gtdb.txt --output OceanDNA-b11726/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:07:20,710] [INFO] Task succeeded: fastANI
[2023-03-16 00:07:20,715] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:07:20,715] [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_016777435.1	s__UA16 sp016777435	91.6452	404	772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477505.1	s__UA16 sp002477505	90.7481	480	772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.58	99.42	0.88	0.80	7	-
GCA_905478895.1	s__UA16 sp905478895	90.6423	304	772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002323795.1	s__UA16 sp002323795	79.7204	283	772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.84	99.84	0.86	0.86	2	-
GCA_905479395.1	s__UA16 sp905479395	78.9285	312	772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.40	98.40	0.84	0.84	2	-
GCA_002336085.1	s__UA16 sp002336085	77.7368	222	772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863125.1	s__UA16 sp002863125	76.8609	86	772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	97.01	95.79	0.91	0.89	5	-
--------------------------------------------------------------------------------
[2023-03-16 00:07:20,715] [INFO] GTDB search result was written to OceanDNA-b11726/result_gtdb.tsv
[2023-03-16 00:07:20,715] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:07:20,716] [INFO] DFAST_QC result json was written to OceanDNA-b11726/dqc_result.json
[2023-03-16 00:07:20,716] [INFO] DFAST_QC completed!
[2023-03-16 00:07:20,716] [INFO] Total running time: 0h1m47s