[2023-03-18 22:53:23,464] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:53:23,464] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:53:23,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a4a004c-e9fc-4fc1-a087-595138f59377/dqc_reference
[2023-03-18 22:53:25,710] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:53:25,710] [INFO] Task started: Prodigal
[2023-03-18 22:53:25,711] [INFO] Running command: cat /var/lib/cwl/stg8643912e-ce9d-4df0-b5aa-3ca32e2534f9/OceanDNA-b34767.fa | prodigal -d OceanDNA-b34767/cds.fna -a OceanDNA-b34767/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:53:52,602] [INFO] Task succeeded: Prodigal
[2023-03-18 22:53:52,603] [INFO] Task started: HMMsearch
[2023-03-18 22:53:52,603] [INFO] Running command: hmmsearch --tblout OceanDNA-b34767/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a4a004c-e9fc-4fc1-a087-595138f59377/dqc_reference/reference_markers.hmm OceanDNA-b34767/protein.faa > /dev/null
[2023-03-18 22:53:52,848] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:53:52,849] [INFO] Found 6/6 markers.
[2023-03-18 22:53:52,877] [INFO] Query marker FASTA was written to OceanDNA-b34767/markers.fasta
[2023-03-18 22:53:52,878] [INFO] Task started: Blastn
[2023-03-18 22:53:52,878] [INFO] Running command: blastn -query OceanDNA-b34767/markers.fasta -db /var/lib/cwl/stg1a4a004c-e9fc-4fc1-a087-595138f59377/dqc_reference/reference_markers.fasta -out OceanDNA-b34767/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:53:53,515] [INFO] Task succeeded: Blastn
[2023-03-18 22:53:53,516] [INFO] Selected 22 target genomes.
[2023-03-18 22:53:53,516] [INFO] Target genome list was writen to OceanDNA-b34767/target_genomes.txt
[2023-03-18 22:53:53,524] [INFO] Task started: fastANI
[2023-03-18 22:53:53,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg8643912e-ce9d-4df0-b5aa-3ca32e2534f9/OceanDNA-b34767.fa --refList OceanDNA-b34767/target_genomes.txt --output OceanDNA-b34767/fastani_result.tsv --threads 1
[2023-03-18 22:54:08,514] [INFO] Task succeeded: fastANI
[2023-03-18 22:54:08,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a4a004c-e9fc-4fc1-a087-595138f59377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:54:08,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a4a004c-e9fc-4fc1-a087-595138f59377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:54:08,523] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:54:08,523] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:54:08,523] [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
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.7484	159	1710	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.5054	182	1710	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.4989	123	1710	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.3989	202	1710	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	77.3939	182	1710	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.3727	194	1710	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.3513	176	1710	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.344	149	1710	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.303	208	1710	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.2863	175	1710	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.1433	214	1710	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.0025	158	1710	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	76.9563	147	1710	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:54:08,523] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34767/tc_result.tsv
[2023-03-18 22:54:08,523] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:54:08,523] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:54:08,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a4a004c-e9fc-4fc1-a087-595138f59377/dqc_reference/checkm_data
[2023-03-18 22:54:08,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:54:08,531] [INFO] Task started: CheckM
[2023-03-18 22:54:08,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34767/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34767/checkm_input OceanDNA-b34767/checkm_result
[2023-03-18 22:55:14,245] [INFO] Task succeeded: CheckM
[2023-03-18 22:55:14,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:55:14,252] [INFO] ===== Completeness check finished =====
[2023-03-18 22:55:14,253] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:55:14,253] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34767/markers.fasta)
[2023-03-18 22:55:14,254] [INFO] Task started: Blastn
[2023-03-18 22:55:14,254] [INFO] Running command: blastn -query OceanDNA-b34767/markers.fasta -db /var/lib/cwl/stg1a4a004c-e9fc-4fc1-a087-595138f59377/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34767/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:55:15,259] [INFO] Task succeeded: Blastn
[2023-03-18 22:55:15,262] [INFO] Selected 20 target genomes.
[2023-03-18 22:55:15,262] [INFO] Target genome list was writen to OceanDNA-b34767/target_genomes_gtdb.txt
[2023-03-18 22:55:15,281] [INFO] Task started: fastANI
[2023-03-18 22:55:15,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg8643912e-ce9d-4df0-b5aa-3ca32e2534f9/OceanDNA-b34767.fa --refList OceanDNA-b34767/target_genomes_gtdb.txt --output OceanDNA-b34767/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:55:33,147] [INFO] Task succeeded: fastANI
[2023-03-18 22:55:33,166] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:55:33,166] [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_013216015.1	s__JABSOI01 sp013216015	98.8618	1525	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013216005.1	s__JABSOI01 sp013216005	85.5137	794	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	77.64	199	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_003333305.1	s__Colwellia aromaticivorans	77.6111	209	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440345.1	s__Colwellia sp001440345	77.5427	188	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764225.1	s__Colwellia psychrerythraea_D	77.5128	177	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	77.4874	205	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215465.1	s__Colwellia sp013215465	77.4574	215	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_007954275.1	s__Colwellia demingiae	77.428	190	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	77.4135	210	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCF_002207865.1	s__Colwellia marinimaniae	77.4124	181	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.40	98.81	0.97	0.94	3	-
GCF_001767295.1	s__Colwellia_A sp001767295	77.3891	212	1710	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_004295665.1	s__Litorilituus sediminis	77.3257	150	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	77.2145	179	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	77.194	197	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	77.1554	189	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	77.1319	186	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCA_015491935.1	s__GCA-2401725 sp015491935	77.0431	183	1710	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_015487235.1	s__GCA-2401725 sp015487235	77.0308	164	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653195.1	s__Thalassotalea_B profundi	76.9728	160	1710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:55:33,168] [INFO] GTDB search result was written to OceanDNA-b34767/result_gtdb.tsv
[2023-03-18 22:55:33,170] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:55:33,175] [INFO] DFAST_QC result json was written to OceanDNA-b34767/dqc_result.json
[2023-03-18 22:55:33,175] [INFO] DFAST_QC completed!
[2023-03-18 22:55:33,175] [INFO] Total running time: 0h2m10s