[2023-03-15 04:00:14,042] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:00:14,042] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:00:14,042] [INFO] DQC Reference Directory: /var/lib/cwl/stg765a3a3f-c4a9-410e-8ed0-84b72e14fa8f/dqc_reference
[2023-03-15 04:00:15,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:00:15,166] [INFO] Task started: Prodigal
[2023-03-15 04:00:15,167] [INFO] Running command: cat /var/lib/cwl/stg1336884b-c79e-4afd-938a-005694101e61/OceanDNA-b6345.fa | prodigal -d OceanDNA-b6345/cds.fna -a OceanDNA-b6345/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:00:23,544] [INFO] Task succeeded: Prodigal
[2023-03-15 04:00:23,544] [INFO] Task started: HMMsearch
[2023-03-15 04:00:23,544] [INFO] Running command: hmmsearch --tblout OceanDNA-b6345/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg765a3a3f-c4a9-410e-8ed0-84b72e14fa8f/dqc_reference/reference_markers.hmm OceanDNA-b6345/protein.faa > /dev/null
[2023-03-15 04:00:23,734] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:00:23,735] [INFO] Found 6/6 markers.
[2023-03-15 04:00:23,751] [INFO] Query marker FASTA was written to OceanDNA-b6345/markers.fasta
[2023-03-15 04:00:23,752] [INFO] Task started: Blastn
[2023-03-15 04:00:23,753] [INFO] Running command: blastn -query OceanDNA-b6345/markers.fasta -db /var/lib/cwl/stg765a3a3f-c4a9-410e-8ed0-84b72e14fa8f/dqc_reference/reference_markers.fasta -out OceanDNA-b6345/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:00:24,342] [INFO] Task succeeded: Blastn
[2023-03-15 04:00:24,346] [INFO] Selected 28 target genomes.
[2023-03-15 04:00:24,346] [INFO] Target genome list was writen to OceanDNA-b6345/target_genomes.txt
[2023-03-15 04:00:24,362] [INFO] Task started: fastANI
[2023-03-15 04:00:24,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg1336884b-c79e-4afd-938a-005694101e61/OceanDNA-b6345.fa --refList OceanDNA-b6345/target_genomes.txt --output OceanDNA-b6345/fastani_result.tsv --threads 1
[2023-03-15 04:00:40,035] [INFO] Task succeeded: fastANI
[2023-03-15 04:00:40,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg765a3a3f-c4a9-410e-8ed0-84b72e14fa8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:00:40,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg765a3a3f-c4a9-410e-8ed0-84b72e14fa8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:00:40,044] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:00:40,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:00:40,044] [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
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.4429	57	462	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.2737	65	462	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.1399	52	462	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.0801	52	462	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	75.9584	56	462	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	75.9038	60	462	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.8827	51	462	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	75.7241	56	462	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	75.7151	63	462	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	75.6951	64	462	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.6723	53	462	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	75.6623	50	462	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	75.6215	55	462	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:00:40,046] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6345/tc_result.tsv
[2023-03-15 04:00:40,046] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:00:40,046] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:00:40,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg765a3a3f-c4a9-410e-8ed0-84b72e14fa8f/dqc_reference/checkm_data
[2023-03-15 04:00:40,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:00:40,051] [INFO] Task started: CheckM
[2023-03-15 04:00:40,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6345/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6345/checkm_input OceanDNA-b6345/checkm_result
[2023-03-15 04:01:05,673] [INFO] Task succeeded: CheckM
[2023-03-15 04:01:05,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:01:05,676] [INFO] ===== Completeness check finished =====
[2023-03-15 04:01:05,676] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:01:05,676] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6345/markers.fasta)
[2023-03-15 04:01:05,677] [INFO] Task started: Blastn
[2023-03-15 04:01:05,677] [INFO] Running command: blastn -query OceanDNA-b6345/markers.fasta -db /var/lib/cwl/stg765a3a3f-c4a9-410e-8ed0-84b72e14fa8f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6345/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:01:06,496] [INFO] Task succeeded: Blastn
[2023-03-15 04:01:06,497] [INFO] Selected 16 target genomes.
[2023-03-15 04:01:06,497] [INFO] Target genome list was writen to OceanDNA-b6345/target_genomes_gtdb.txt
[2023-03-15 04:01:06,511] [INFO] Task started: fastANI
[2023-03-15 04:01:06,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg1336884b-c79e-4afd-938a-005694101e61/OceanDNA-b6345.fa --refList OceanDNA-b6345/target_genomes_gtdb.txt --output OceanDNA-b6345/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:01:13,736] [INFO] Task succeeded: fastANI
[2023-03-15 04:01:13,743] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:01:13,743] [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_004213995.1	s__SGZJ01 sp004213995	95.4879	328	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	95.83	95.53	0.71	0.69	3	conclusive
GCA_018674025.1	s__SGZJ01 sp018674025	90.4319	296	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515565.1	s__SGZJ01 sp902515565	90.2137	294	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182835.1	s__SGZJ01 sp905182835	79.8867	280	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	76.6595	56	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510415.1	s__MED-G13 sp902510415	76.5101	63	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_003443635.1	s__AU392 sp003443635	76.3347	70	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902626365.1	s__MED-G13 sp902626365	76.2742	53	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.07	96.07	0.74	0.74	2	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.0394	63	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	75.9046	63	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337215.1	s__Oceanihabitans sediminis	75.6951	64	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014239895.1	s__GCA-2700405 sp014239895	75.6473	58	462	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:01:13,744] [INFO] GTDB search result was written to OceanDNA-b6345/result_gtdb.tsv
[2023-03-15 04:01:13,744] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:01:13,745] [INFO] DFAST_QC result json was written to OceanDNA-b6345/dqc_result.json
[2023-03-15 04:01:13,745] [INFO] DFAST_QC completed!
[2023-03-15 04:01:13,745] [INFO] Total running time: 0h0m60s