[2023-03-18 20:40:39,436] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg9017c139-268d-4f70-910d-8f1a052015a2/dqc_reference
[2023-03-18 20:40:41,213] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,213] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,213] [INFO] Running command: cat /var/lib/cwl/stg36a85c92-57c3-4673-bcbf-d76c36a9d897/OceanDNA-b34724.fa | prodigal -d OceanDNA-b34724/cds.fna -a OceanDNA-b34724/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:41:06,552] [INFO] Task succeeded: Prodigal
[2023-03-18 20:41:06,552] [INFO] Task started: HMMsearch
[2023-03-18 20:41:06,552] [INFO] Running command: hmmsearch --tblout OceanDNA-b34724/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9017c139-268d-4f70-910d-8f1a052015a2/dqc_reference/reference_markers.hmm OceanDNA-b34724/protein.faa > /dev/null
[2023-03-18 20:41:06,846] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:41:06,847] [INFO] Found 6/6 markers.
[2023-03-18 20:41:06,876] [INFO] Query marker FASTA was written to OceanDNA-b34724/markers.fasta
[2023-03-18 20:41:06,877] [INFO] Task started: Blastn
[2023-03-18 20:41:06,877] [INFO] Running command: blastn -query OceanDNA-b34724/markers.fasta -db /var/lib/cwl/stg9017c139-268d-4f70-910d-8f1a052015a2/dqc_reference/reference_markers.fasta -out OceanDNA-b34724/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:07,526] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:07,527] [INFO] Selected 18 target genomes.
[2023-03-18 20:41:07,527] [INFO] Target genome list was writen to OceanDNA-b34724/target_genomes.txt
[2023-03-18 20:41:07,534] [INFO] Task started: fastANI
[2023-03-18 20:41:07,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg36a85c92-57c3-4673-bcbf-d76c36a9d897/OceanDNA-b34724.fa --refList OceanDNA-b34724/target_genomes.txt --output OceanDNA-b34724/fastani_result.tsv --threads 1
[2023-03-18 20:41:21,679] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:21,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9017c139-268d-4f70-910d-8f1a052015a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:21,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9017c139-268d-4f70-910d-8f1a052015a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:21,690] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:21,690] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:21,690] [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
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	80.255	664	1605	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.518	252	1605	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.3553	261	1605	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.0006	251	1605	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.8504	297	1605	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.7234	202	1605	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.674	217	1605	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.6735	244	1605	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.527	190	1605	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.3238	199	1605	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.1681	201	1605	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.0151	208	1605	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.003	214	1605	95	below_threshold
Thalassomonas actiniarum	strain=A5K-106	GCA_000948975.1	485447	485447	type	True	76.6084	115	1605	95	below_threshold
Moritella dasanensis	strain=ArB 0140	GCA_000276805.1	428031	428031	type	True	75.9415	55	1605	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	75.9342	58	1605	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:21,690] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34724/tc_result.tsv
[2023-03-18 20:41:21,691] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:21,691] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:21,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9017c139-268d-4f70-910d-8f1a052015a2/dqc_reference/checkm_data
[2023-03-18 20:41:21,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:21,700] [INFO] Task started: CheckM
[2023-03-18 20:41:21,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34724/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34724/checkm_input OceanDNA-b34724/checkm_result
[2023-03-18 20:42:23,486] [INFO] Task succeeded: CheckM
[2023-03-18 20:42:23,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:42:23,490] [INFO] ===== Completeness check finished =====
[2023-03-18 20:42:23,490] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:42:23,490] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34724/markers.fasta)
[2023-03-18 20:42:23,490] [INFO] Task started: Blastn
[2023-03-18 20:42:23,490] [INFO] Running command: blastn -query OceanDNA-b34724/markers.fasta -db /var/lib/cwl/stg9017c139-268d-4f70-910d-8f1a052015a2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34724/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:42:24,491] [INFO] Task succeeded: Blastn
[2023-03-18 20:42:24,492] [INFO] Selected 11 target genomes.
[2023-03-18 20:42:24,492] [INFO] Target genome list was writen to OceanDNA-b34724/target_genomes_gtdb.txt
[2023-03-18 20:42:24,517] [INFO] Task started: fastANI
[2023-03-18 20:42:24,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg36a85c92-57c3-4673-bcbf-d76c36a9d897/OceanDNA-b34724.fa --refList OceanDNA-b34724/target_genomes_gtdb.txt --output OceanDNA-b34724/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:33,693] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:33,700] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:42:33,700] [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_013215385.1	s__Colwellia_A sp013215385	99.9648	1578	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215295.1	s__Colwellia_A sp013215295	82.4002	819	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014076845.1	s__Colwellia_A sp014076845	80.3254	662	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCF_007954355.1	s__Colwellia_A hornerae	80.2414	667	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	-
GCF_001767295.1	s__Colwellia_A sp001767295	80.0943	632	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	78.4525	297	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	78.0047	190	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162675.1	s__Colwellia sp002162675	77.6371	237	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401725.1	s__GCA-2401725 sp002401725	77.5591	171	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765685.1	s__Colwellia sp016765685	77.4721	153	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765535.1	s__GCA-2401725 sp016765535	77.4478	165	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:33,701] [INFO] GTDB search result was written to OceanDNA-b34724/result_gtdb.tsv
[2023-03-18 20:42:33,701] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:33,702] [INFO] DFAST_QC result json was written to OceanDNA-b34724/dqc_result.json
[2023-03-18 20:42:33,702] [INFO] DFAST_QC completed!
[2023-03-18 20:42:33,702] [INFO] Total running time: 0h1m54s