[2023-03-19 05:32:22,191] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:32:22,192] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:32:22,192] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5635f86-597f-4c91-9f4f-b30847cca611/dqc_reference
[2023-03-19 05:32:23,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:32:23,274] [INFO] Task started: Prodigal
[2023-03-19 05:32:23,275] [INFO] Running command: cat /var/lib/cwl/stgc0249df6-fe0a-4944-b3a4-1908b6ef2655/OceanDNA-b30703.fa | prodigal -d OceanDNA-b30703/cds.fna -a OceanDNA-b30703/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:32:41,703] [INFO] Task succeeded: Prodigal
[2023-03-19 05:32:41,704] [INFO] Task started: HMMsearch
[2023-03-19 05:32:41,704] [INFO] Running command: hmmsearch --tblout OceanDNA-b30703/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5635f86-597f-4c91-9f4f-b30847cca611/dqc_reference/reference_markers.hmm OceanDNA-b30703/protein.faa > /dev/null
[2023-03-19 05:32:41,892] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:32:41,893] [INFO] Found 6/6 markers.
[2023-03-19 05:32:41,913] [INFO] Query marker FASTA was written to OceanDNA-b30703/markers.fasta
[2023-03-19 05:32:41,914] [INFO] Task started: Blastn
[2023-03-19 05:32:41,914] [INFO] Running command: blastn -query OceanDNA-b30703/markers.fasta -db /var/lib/cwl/stgf5635f86-597f-4c91-9f4f-b30847cca611/dqc_reference/reference_markers.fasta -out OceanDNA-b30703/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:32:42,501] [INFO] Task succeeded: Blastn
[2023-03-19 05:32:42,502] [INFO] Selected 34 target genomes.
[2023-03-19 05:32:42,502] [INFO] Target genome list was writen to OceanDNA-b30703/target_genomes.txt
[2023-03-19 05:32:42,519] [INFO] Task started: fastANI
[2023-03-19 05:32:42,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0249df6-fe0a-4944-b3a4-1908b6ef2655/OceanDNA-b30703.fa --refList OceanDNA-b30703/target_genomes.txt --output OceanDNA-b30703/fastani_result.tsv --threads 1
[2023-03-19 05:33:02,847] [INFO] Task succeeded: fastANI
[2023-03-19 05:33:02,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5635f86-597f-4c91-9f4f-b30847cca611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:33:02,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5635f86-597f-4c91-9f4f-b30847cca611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:33:02,864] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:33:02,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:33:02,865] [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
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	76.7511	124	961	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	76.7396	110	961	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.5717	162	961	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.4378	96	961	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	76.4153	147	961	95	below_threshold
Gemmobacter tilapiae	strain=KCTC 23310	GCA_014652215.1	875041	875041	type	True	76.4033	71	961	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.3984	101	961	95	below_threshold
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	76.3512	92	961	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	76.3468	87	961	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.3261	143	961	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.3055	56	961	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.2987	111	961	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.288	107	961	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	76.2471	110	961	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	76.2403	95	961	95	below_threshold
Pararhodobacter oceanensis	strain=AM505	GCA_003076755.1	2172121	2172121	type	True	76.2382	91	961	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.1724	115	961	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.1504	104	961	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.1355	87	961	95	below_threshold
Boseongicola aestuarii	strain=CECT 8489	GCA_900184815.1	1470561	1470561	type	True	76.1353	70	961	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.1205	81	961	95	below_threshold
Rhodobaca bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	76.1089	73	961	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.0914	81	961	95	below_threshold
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	76.0471	76	961	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.0412	83	961	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.0281	118	961	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.0122	60	961	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	75.9804	105	961	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	75.9407	85	961	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	75.9047	94	961	95	below_threshold
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	75.8742	85	961	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	75.8741	85	961	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	75.7961	63	961	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	75.7264	70	961	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:33:02,865] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30703/tc_result.tsv
[2023-03-19 05:33:02,865] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:33:02,865] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:33:02,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5635f86-597f-4c91-9f4f-b30847cca611/dqc_reference/checkm_data
[2023-03-19 05:33:02,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:33:02,871] [INFO] Task started: CheckM
[2023-03-19 05:33:02,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30703/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30703/checkm_input OceanDNA-b30703/checkm_result
[2023-03-19 05:33:50,453] [INFO] Task succeeded: CheckM
[2023-03-19 05:33:50,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:33:50,456] [INFO] ===== Completeness check finished =====
[2023-03-19 05:33:50,456] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:33:50,456] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30703/markers.fasta)
[2023-03-19 05:33:50,456] [INFO] Task started: Blastn
[2023-03-19 05:33:50,457] [INFO] Running command: blastn -query OceanDNA-b30703/markers.fasta -db /var/lib/cwl/stgf5635f86-597f-4c91-9f4f-b30847cca611/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30703/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:33:51,323] [INFO] Task succeeded: Blastn
[2023-03-19 05:33:51,324] [INFO] Selected 30 target genomes.
[2023-03-19 05:33:51,324] [INFO] Target genome list was writen to OceanDNA-b30703/target_genomes_gtdb.txt
[2023-03-19 05:33:51,375] [INFO] Task started: fastANI
[2023-03-19 05:33:51,375] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0249df6-fe0a-4944-b3a4-1908b6ef2655/OceanDNA-b30703.fa --refList OceanDNA-b30703/target_genomes_gtdb.txt --output OceanDNA-b30703/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:34:09,468] [INFO] Task succeeded: fastANI
[2023-03-19 05:34:09,483] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:34:09,484] [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_002430125.1	s__UBA5972 sp002430125	99.6911	727	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	99.40	99.40	0.79	0.79	2	conclusive
GCA_013151535.1	s__UBA5972 sp013151535	77.3787	228	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151335.1	s__UBA5972 sp013151335	76.7407	184	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112755.1	s__Sulfitobacter brevis	76.7396	110	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016521575.1	s__Sedimentitalea sp016521575	76.7035	101	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223125.1	s__Amylibacter sp018223125	76.6401	112	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485375.1	s__UBA3077 sp015485375	76.5443	73	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748285.1	s__Profundibacter sp002748285	76.5427	82	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487165.1	s__UBA5972 sp015487165	76.5378	142	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458355.1	s__Thalassobius gelatinovorus	76.4782	114	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	99.99	0.99	0.99	3	-
GCF_004342065.1	s__Primorskyibacter sedentarius	76.4378	96	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.3554	123	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003352045.1	s__JL08 sp003352045	76.3352	123	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019955.1	s__Shimia sp016019955	76.3297	116	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	-
GCF_900172335.1	s__Roseovarius albus	76.314	57	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.2814	128	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487255.1	s__UBA3077 sp015487255	76.2675	76	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000647975.1	s__Actibacterium mucosum	76.2471	110	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.2452	104	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760615.1	s__Puniceibacterium antarcticum	76.2153	94	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090795.1	s__Amylibacter sp019090795	76.2002	90	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719615.1	s__Amylibacter sediminis	76.1591	127	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184815.1	s__Boseongicola aestuarii	76.1353	70	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	76.1205	81	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017643305.1	s__HXMU1420-2 sp017643305	76.0923	79	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HXMU1420-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	76.0835	128	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	76.0093	96	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644125.1	s__Rhodophyticola sp017644125	75.8984	86	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCF_003646465.1	s__Chachezhania antarctica	75.6114	92	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:34:09,484] [INFO] GTDB search result was written to OceanDNA-b30703/result_gtdb.tsv
[2023-03-19 05:34:09,484] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:34:09,487] [INFO] DFAST_QC result json was written to OceanDNA-b30703/dqc_result.json
[2023-03-19 05:34:09,487] [INFO] DFAST_QC completed!
[2023-03-19 05:34:09,487] [INFO] Total running time: 0h1m47s