[2023-03-17 13:01:51,477] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,477] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,477] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c9976b7-1fb7-4456-9188-5faf15312252/dqc_reference
[2023-03-17 13:01:52,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,651] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,651] [INFO] Running command: cat /var/lib/cwl/stg4473a43d-b6ef-42f6-990c-c187e606d288/OceanDNA-b10567.fa | prodigal -d OceanDNA-b10567/cds.fna -a OceanDNA-b10567/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:05,414] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:05,414] [INFO] Task started: HMMsearch
[2023-03-17 13:02:05,414] [INFO] Running command: hmmsearch --tblout OceanDNA-b10567/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c9976b7-1fb7-4456-9188-5faf15312252/dqc_reference/reference_markers.hmm OceanDNA-b10567/protein.faa > /dev/null
[2023-03-17 13:02:05,628] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:05,628] [INFO] Found 6/6 markers.
[2023-03-17 13:02:05,641] [INFO] Query marker FASTA was written to OceanDNA-b10567/markers.fasta
[2023-03-17 13:02:05,641] [INFO] Task started: Blastn
[2023-03-17 13:02:05,642] [INFO] Running command: blastn -query OceanDNA-b10567/markers.fasta -db /var/lib/cwl/stg4c9976b7-1fb7-4456-9188-5faf15312252/dqc_reference/reference_markers.fasta -out OceanDNA-b10567/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:06,247] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:06,248] [INFO] Selected 30 target genomes.
[2023-03-17 13:02:06,248] [INFO] Target genome list was writen to OceanDNA-b10567/target_genomes.txt
[2023-03-17 13:02:06,263] [INFO] Task started: fastANI
[2023-03-17 13:02:06,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg4473a43d-b6ef-42f6-990c-c187e606d288/OceanDNA-b10567.fa --refList OceanDNA-b10567/target_genomes.txt --output OceanDNA-b10567/fastani_result.tsv --threads 1
[2023-03-17 13:02:24,595] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:24,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c9976b7-1fb7-4456-9188-5faf15312252/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:24,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c9976b7-1fb7-4456-9188-5faf15312252/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:24,611] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:24,612] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:02:24,612] [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
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.7157	90	610	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.7007	97	610	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.6392	89	610	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.5796	72	610	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.5655	113	610	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.5068	91	610	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.4728	84	610	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.4652	105	610	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.4586	103	610	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.4449	86	610	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.4387	85	610	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	76.416	75	610	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	76.3681	96	610	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.3681	96	610	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	76.3357	85	610	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	76.278	69	610	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.2656	80	610	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.2013	106	610	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	76.1937	75	610	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.1377	80	610	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	76.0337	89	610	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.0255	69	610	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	76.0169	74	610	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	75.9569	72	610	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	75.944	62	610	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.9237	63	610	95	below_threshold
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	75.8987	61	610	95	below_threshold
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	75.7987	76	610	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	75.5159	62	610	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:02:24,612] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10567/tc_result.tsv
[2023-03-17 13:02:24,612] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:24,612] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:24,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c9976b7-1fb7-4456-9188-5faf15312252/dqc_reference/checkm_data
[2023-03-17 13:02:24,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:24,616] [INFO] Task started: CheckM
[2023-03-17 13:02:24,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10567/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10567/checkm_input OceanDNA-b10567/checkm_result
[2023-03-17 13:03:00,024] [INFO] Task succeeded: CheckM
[2023-03-17 13:03:00,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:03:00,026] [INFO] ===== Completeness check finished =====
[2023-03-17 13:03:00,026] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:03:00,027] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10567/markers.fasta)
[2023-03-17 13:03:00,027] [INFO] Task started: Blastn
[2023-03-17 13:03:00,027] [INFO] Running command: blastn -query OceanDNA-b10567/markers.fasta -db /var/lib/cwl/stg4c9976b7-1fb7-4456-9188-5faf15312252/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10567/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:03:00,905] [INFO] Task succeeded: Blastn
[2023-03-17 13:03:00,906] [INFO] Selected 26 target genomes.
[2023-03-17 13:03:00,906] [INFO] Target genome list was writen to OceanDNA-b10567/target_genomes_gtdb.txt
[2023-03-17 13:03:01,328] [INFO] Task started: fastANI
[2023-03-17 13:03:01,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg4473a43d-b6ef-42f6-990c-c187e606d288/OceanDNA-b10567.fa --refList OceanDNA-b10567/target_genomes_gtdb.txt --output OceanDNA-b10567/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:13,040] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:13,055] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:03:13,055] [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	79.5437	349	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
GCA_002725015.1	s__UBA3537 sp002725015	77.3218	95	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCA_002684355.1	s__UBA3537 sp002684355	77.1887	153	610	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	77.1467	128	610	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	76.987	123	610	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_002709185.1	s__UBA3537 sp002709185	76.9627	108	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	76.9433	141	610	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	76.8383	148	610	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_905181825.1	s__Hel1-33-131 sp905181825	76.7408	104	610	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_018608765.1	s__Hel1-33-131 sp018608765	76.732	125	610	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_003143755.1	s__Algibacter_B sp003143755	76.7179	98	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	76.585	113	610	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_001418105.1	s__Oceanihabitans himadriensis	76.5026	98	610	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	76.4856	106	610	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_014202225.1	s__Algibacter_B amylolyticus	76.4631	84	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	76.4622	143	610	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_900114265.1	s__Flaviramulus basaltis	76.4417	115	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	76.3954	83	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067265.1	s__Oceanihabitans sp018067265	76.2784	76	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	76.2126	102	610	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_004346845.1	s__Winogradskyella wandonensis	76.1937	75	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	76.1447	82	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114005.1	s__Olleya namhaensis	76.0276	76	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCA_905480415.1	s__Algibacter_B sp905480415	75.9625	92	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414705.1	s__Algorimicrobium sp002414705	75.8017	89	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761325.1	s__Urechidicola croceus	75.7987	76	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:13,055] [INFO] GTDB search result was written to OceanDNA-b10567/result_gtdb.tsv
[2023-03-17 13:03:13,056] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:13,058] [INFO] DFAST_QC result json was written to OceanDNA-b10567/dqc_result.json
[2023-03-17 13:03:13,059] [INFO] DFAST_QC completed!
[2023-03-17 13:03:13,059] [INFO] Total running time: 0h1m22s