[2023-03-17 23:43:20,528] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:43:20,529] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:43:20,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ad8d0cb-5bc7-4da6-ac03-b2fc56f9909f/dqc_reference
[2023-03-17 23:43:21,600] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:43:21,601] [INFO] Task started: Prodigal
[2023-03-17 23:43:21,601] [INFO] Running command: cat /var/lib/cwl/stgdfbf3490-8e04-45b6-b472-b18dc59abfc5/OceanDNA-b10587.fa | prodigal -d OceanDNA-b10587/cds.fna -a OceanDNA-b10587/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:43:34,246] [INFO] Task succeeded: Prodigal
[2023-03-17 23:43:34,246] [INFO] Task started: HMMsearch
[2023-03-17 23:43:34,246] [INFO] Running command: hmmsearch --tblout OceanDNA-b10587/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ad8d0cb-5bc7-4da6-ac03-b2fc56f9909f/dqc_reference/reference_markers.hmm OceanDNA-b10587/protein.faa > /dev/null
[2023-03-17 23:43:34,420] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:43:34,421] [INFO] Found 6/6 markers.
[2023-03-17 23:43:34,433] [INFO] Query marker FASTA was written to OceanDNA-b10587/markers.fasta
[2023-03-17 23:43:34,435] [INFO] Task started: Blastn
[2023-03-17 23:43:34,435] [INFO] Running command: blastn -query OceanDNA-b10587/markers.fasta -db /var/lib/cwl/stg6ad8d0cb-5bc7-4da6-ac03-b2fc56f9909f/dqc_reference/reference_markers.fasta -out OceanDNA-b10587/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:43:35,088] [INFO] Task succeeded: Blastn
[2023-03-17 23:43:35,089] [INFO] Selected 31 target genomes.
[2023-03-17 23:43:35,089] [INFO] Target genome list was writen to OceanDNA-b10587/target_genomes.txt
[2023-03-17 23:43:35,157] [INFO] Task started: fastANI
[2023-03-17 23:43:35,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfbf3490-8e04-45b6-b472-b18dc59abfc5/OceanDNA-b10587.fa --refList OceanDNA-b10587/target_genomes.txt --output OceanDNA-b10587/fastani_result.tsv --threads 1
[2023-03-17 23:43:52,266] [INFO] Task succeeded: fastANI
[2023-03-17 23:43:52,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ad8d0cb-5bc7-4da6-ac03-b2fc56f9909f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:43:52,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ad8d0cb-5bc7-4da6-ac03-b2fc56f9909f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:43:52,281] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:43:52,282] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:43:52,282] [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
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.998	91	578	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.8713	65	578	95	below_threshold
Mangrovimonas yunxiaonensis	strain=CGMCC 1.12280	GCA_014636995.1	1197477	1197477	type	True	76.7719	51	578	95	below_threshold
Mangrovimonas yunxiaonensis	strain=LY01	GCA_000733475.1	1197477	1197477	type	True	76.7648	50	578	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.7628	66	578	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.7441	67	578	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.6621	90	578	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.568	81	578	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.5646	60	578	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.5607	69	578	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	76.5198	82	578	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.4917	85	578	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.43	69	578	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.3859	82	578	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.3317	80	578	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.308	75	578	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	76.3034	76	578	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.2844	67	578	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.209	72	578	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.1861	71	578	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	76.1812	70	578	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	76.1581	82	578	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.1458	59	578	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	76.1146	87	578	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.0176	76	578	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	75.9289	69	578	95	below_threshold
Paucihalobacter ruber	strain=CWB-1	GCA_006494535.1	2567861	2567861	type	True	75.9045	65	578	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:43:52,288] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10587/tc_result.tsv
[2023-03-17 23:43:52,300] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:43:52,300] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:43:52,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ad8d0cb-5bc7-4da6-ac03-b2fc56f9909f/dqc_reference/checkm_data
[2023-03-17 23:43:52,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:43:52,303] [INFO] Task started: CheckM
[2023-03-17 23:43:52,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10587/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10587/checkm_input OceanDNA-b10587/checkm_result
[2023-03-17 23:44:28,188] [INFO] Task succeeded: CheckM
[2023-03-17 23:44:28,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:44:28,245] [INFO] ===== Completeness check finished =====
[2023-03-17 23:44:28,245] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:44:28,246] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10587/markers.fasta)
[2023-03-17 23:44:28,247] [INFO] Task started: Blastn
[2023-03-17 23:44:28,247] [INFO] Running command: blastn -query OceanDNA-b10587/markers.fasta -db /var/lib/cwl/stg6ad8d0cb-5bc7-4da6-ac03-b2fc56f9909f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10587/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:44:29,052] [INFO] Task succeeded: Blastn
[2023-03-17 23:44:29,053] [INFO] Selected 25 target genomes.
[2023-03-17 23:44:29,053] [INFO] Target genome list was writen to OceanDNA-b10587/target_genomes_gtdb.txt
[2023-03-17 23:44:29,089] [INFO] Task started: fastANI
[2023-03-17 23:44:29,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfbf3490-8e04-45b6-b472-b18dc59abfc5/OceanDNA-b10587.fa --refList OceanDNA-b10587/target_genomes_gtdb.txt --output OceanDNA-b10587/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:44:38,499] [INFO] Task succeeded: fastANI
[2023-03-17 23:44:38,512] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:44:38,513] [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
GCF_001735715.1	s__GCA001735715 sp001735715	79.3493	308	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
GCA_002709185.1	s__UBA3537 sp002709185	77.577	105	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCA_002684355.1	s__UBA3537 sp002684355	77.4557	151	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	-
GCA_002690085.1	s__UBA3537 sp002690085	77.3087	118	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	77.1306	111	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	77.0692	87	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	76.998	91	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	76.9507	154	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725015.1	s__UBA3537 sp002725015	76.8776	108	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	76.8349	128	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	76.796	128	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202195.1	s__Oceanihabitans iliipiscarium	76.5775	85	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698705.1	s__UBA3537 sp002698705	76.5696	129	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003650305.1	s__PRS1 sp003650305	76.5615	91	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335675.1	s__Winogradskyella sp003335675	76.5554	69	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	76.4515	84	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018608705.1	s__Hel1-33-131 sp018608705	76.4166	96	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.44	99.44	0.94	0.94	2	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	76.4163	81	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	76.322	108	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCF_000828715.1	s__Winogradskyella sp000828715	76.3117	77	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163855.1	s__Winogradskyella sp002163855	76.2875	88	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCA_002784145.1	s__Yeosuana sp002784145	76.1725	75	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCF_009741275.1	s__Winogradskyella endarachnes	76.0176	76	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	75.9867	93	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:44:38,515] [INFO] GTDB search result was written to OceanDNA-b10587/result_gtdb.tsv
[2023-03-17 23:44:38,519] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:44:38,522] [INFO] DFAST_QC result json was written to OceanDNA-b10587/dqc_result.json
[2023-03-17 23:44:38,522] [INFO] DFAST_QC completed!
[2023-03-17 23:44:38,522] [INFO] Total running time: 0h1m18s