[2023-03-17 08:11:32,509] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,509] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c9f122b-6d60-44bb-9d67-2fc9b098a8fb/dqc_reference
[2023-03-17 08:11:33,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:33,598] [INFO] Task started: Prodigal
[2023-03-17 08:11:33,598] [INFO] Running command: cat /var/lib/cwl/stg538b3527-15a1-48c2-bd54-0c8210852af1/OceanDNA-b7018.fa | prodigal -d OceanDNA-b7018/cds.fna -a OceanDNA-b7018/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:44,498] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:44,499] [INFO] Task started: HMMsearch
[2023-03-17 08:11:44,499] [INFO] Running command: hmmsearch --tblout OceanDNA-b7018/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c9f122b-6d60-44bb-9d67-2fc9b098a8fb/dqc_reference/reference_markers.hmm OceanDNA-b7018/protein.faa > /dev/null
[2023-03-17 08:11:44,694] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:44,694] [INFO] Found 6/6 markers.
[2023-03-17 08:11:44,710] [INFO] Query marker FASTA was written to OceanDNA-b7018/markers.fasta
[2023-03-17 08:11:44,710] [INFO] Task started: Blastn
[2023-03-17 08:11:44,710] [INFO] Running command: blastn -query OceanDNA-b7018/markers.fasta -db /var/lib/cwl/stg2c9f122b-6d60-44bb-9d67-2fc9b098a8fb/dqc_reference/reference_markers.fasta -out OceanDNA-b7018/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:45,271] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:45,272] [INFO] Selected 37 target genomes.
[2023-03-17 08:11:45,272] [INFO] Target genome list was writen to OceanDNA-b7018/target_genomes.txt
[2023-03-17 08:11:45,294] [INFO] Task started: fastANI
[2023-03-17 08:11:45,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg538b3527-15a1-48c2-bd54-0c8210852af1/OceanDNA-b7018.fa --refList OceanDNA-b7018/target_genomes.txt --output OceanDNA-b7018/fastani_result.tsv --threads 1
[2023-03-17 08:12:06,507] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:06,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c9f122b-6d60-44bb-9d67-2fc9b098a8fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:12:06,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c9f122b-6d60-44bb-9d67-2fc9b098a8fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:12:06,526] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:12:06,526] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:12:06,526] [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
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.4828	75	572	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.478	76	572	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.4233	89	572	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.418	53	572	95	below_threshold
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	76.3729	75	572	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.352	72	572	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	76.3444	76	572	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.3422	112	572	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.3335	68	572	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.3161	99	572	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	76.2912	73	572	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.285	61	572	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.2753	75	572	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.2559	74	572	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.254	73	572	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	76.2392	60	572	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	76.1991	85	572	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.1959	84	572	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.1932	89	572	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.1651	70	572	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.1583	77	572	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.1558	87	572	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.1338	74	572	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.1118	103	572	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.0612	77	572	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.0146	73	572	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	75.956	73	572	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	75.9358	54	572	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.764	89	572	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	75.7331	75	572	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	75.599	69	572	95	below_threshold
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	75.5542	60	572	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	75.5542	60	572	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:12:06,526] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7018/tc_result.tsv
[2023-03-17 08:12:06,527] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:12:06,527] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:12:06,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c9f122b-6d60-44bb-9d67-2fc9b098a8fb/dqc_reference/checkm_data
[2023-03-17 08:12:06,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:12:06,645] [INFO] Task started: CheckM
[2023-03-17 08:12:06,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7018/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7018/checkm_input OceanDNA-b7018/checkm_result
[2023-03-17 08:12:38,165] [INFO] Task succeeded: CheckM
[2023-03-17 08:12:38,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:12:38,168] [INFO] ===== Completeness check finished =====
[2023-03-17 08:12:38,168] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:12:38,168] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7018/markers.fasta)
[2023-03-17 08:12:38,170] [INFO] Task started: Blastn
[2023-03-17 08:12:38,170] [INFO] Running command: blastn -query OceanDNA-b7018/markers.fasta -db /var/lib/cwl/stg2c9f122b-6d60-44bb-9d67-2fc9b098a8fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7018/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:12:38,986] [INFO] Task succeeded: Blastn
[2023-03-17 08:12:38,987] [INFO] Selected 14 target genomes.
[2023-03-17 08:12:38,987] [INFO] Target genome list was writen to OceanDNA-b7018/target_genomes_gtdb.txt
[2023-03-17 08:12:39,097] [INFO] Task started: fastANI
[2023-03-17 08:12:39,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg538b3527-15a1-48c2-bd54-0c8210852af1/OceanDNA-b7018.fa --refList OceanDNA-b7018/target_genomes_gtdb.txt --output OceanDNA-b7018/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:12:46,191] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:46,200] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:12:46,200] [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_018669795.1	s__GCA-002733185 sp018669795	99.8882	553	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	conclusive
GCA_002713705.1	s__GCA-002733185 sp002713705	89.4657	491	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCA_905181835.1	s__GCA-002733185 sp905181835	78.6537	278	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	78.6005	245	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213605.1	s__GCA-002733185 sp004213605	78.3356	167	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	95.79	95.79	0.89	0.89	2	-
GCA_004214175.1	s__GCA-002733185 sp004214175	77.7642	172	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366675.1	s__Xanthomarina sp002366675	76.6773	75	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	76.3834	77	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_003008425.1	s__Aurantibacter aestuarii	76.3729	75	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	76.361	101	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	76.3161	99	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	76.1745	90	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	76.1651	70	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014651495.1	s__Algibacter_E mikhailovii	75.9358	54	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:12:46,200] [INFO] GTDB search result was written to OceanDNA-b7018/result_gtdb.tsv
[2023-03-17 08:12:46,200] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:12:46,203] [INFO] DFAST_QC result json was written to OceanDNA-b7018/dqc_result.json
[2023-03-17 08:12:46,203] [INFO] DFAST_QC completed!
[2023-03-17 08:12:46,203] [INFO] Total running time: 0h1m14s