[2023-03-14 12:10:30,354] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:10:30,354] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:10:30,354] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf720d4a-69be-49de-b7ff-0ce306eebc0d/dqc_reference
[2023-03-14 12:10:31,465] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:10:31,466] [INFO] Task started: Prodigal
[2023-03-14 12:10:31,466] [INFO] Running command: cat /var/lib/cwl/stg63e518b2-66c3-45bf-8699-c2de758ab22b/OceanDNA-b7448.fa | prodigal -d OceanDNA-b7448/cds.fna -a OceanDNA-b7448/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:10:54,799] [INFO] Task succeeded: Prodigal
[2023-03-14 12:10:54,799] [INFO] Task started: HMMsearch
[2023-03-14 12:10:54,799] [INFO] Running command: hmmsearch --tblout OceanDNA-b7448/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf720d4a-69be-49de-b7ff-0ce306eebc0d/dqc_reference/reference_markers.hmm OceanDNA-b7448/protein.faa > /dev/null
[2023-03-14 12:10:55,032] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:10:55,033] [INFO] Found 6/6 markers.
[2023-03-14 12:10:55,054] [INFO] Query marker FASTA was written to OceanDNA-b7448/markers.fasta
[2023-03-14 12:10:55,056] [INFO] Task started: Blastn
[2023-03-14 12:10:55,056] [INFO] Running command: blastn -query OceanDNA-b7448/markers.fasta -db /var/lib/cwl/stgdf720d4a-69be-49de-b7ff-0ce306eebc0d/dqc_reference/reference_markers.fasta -out OceanDNA-b7448/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:10:55,851] [INFO] Task succeeded: Blastn
[2023-03-14 12:10:55,851] [INFO] Selected 21 target genomes.
[2023-03-14 12:10:55,852] [INFO] Target genome list was writen to OceanDNA-b7448/target_genomes.txt
[2023-03-14 12:10:55,865] [INFO] Task started: fastANI
[2023-03-14 12:10:55,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e518b2-66c3-45bf-8699-c2de758ab22b/OceanDNA-b7448.fa --refList OceanDNA-b7448/target_genomes.txt --output OceanDNA-b7448/fastani_result.tsv --threads 1
[2023-03-14 12:11:10,792] [INFO] Task succeeded: fastANI
[2023-03-14 12:11:10,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf720d4a-69be-49de-b7ff-0ce306eebc0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:11:10,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf720d4a-69be-49de-b7ff-0ce306eebc0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:11:10,851] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 12:11:10,851] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 12:11:10,851] [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
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	98.7605	1139	1270	95	conclusive
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	81.176	697	1270	95	below_threshold
Galbibacter marinus	strain=ck-I2-15	GCA_000300875.1	555500	555500	type	True	77.573	228	1270	95	below_threshold
Robertkochia solimangrovi	strain=CL23	GCA_007279655.1	2213046	2213046	type	True	77.4095	110	1270	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.9959	163	1270	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	76.7555	116	1270	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.6535	131	1270	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.5738	110	1270	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.5074	116	1270	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.4914	146	1270	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.482	92	1270	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.4252	162	1270	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.3966	96	1270	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.3894	143	1270	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.3614	138	1270	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	76.3568	134	1270	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	76.3367	127	1270	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.2888	103	1270	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	76.2286	97	1270	95	below_threshold
Spongiivirga citrea	strain=KCTC 32990	GCA_010671565.1	1481457	1481457	type	True	76.174	81	1270	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.0626	130	1270	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:11:10,852] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7448/tc_result.tsv
[2023-03-14 12:11:10,852] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:11:10,852] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:11:10,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf720d4a-69be-49de-b7ff-0ce306eebc0d/dqc_reference/checkm_data
[2023-03-14 12:11:10,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:11:10,860] [INFO] Task started: CheckM
[2023-03-14 12:11:10,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7448/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7448/checkm_input OceanDNA-b7448/checkm_result
[2023-03-14 12:12:11,373] [INFO] Task succeeded: CheckM
[2023-03-14 12:12:11,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:12:11,384] [INFO] ===== Completeness check finished =====
[2023-03-14 12:12:11,384] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:12:11,384] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7448/markers.fasta)
[2023-03-14 12:12:11,386] [INFO] Task started: Blastn
[2023-03-14 12:12:11,386] [INFO] Running command: blastn -query OceanDNA-b7448/markers.fasta -db /var/lib/cwl/stgdf720d4a-69be-49de-b7ff-0ce306eebc0d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7448/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:12:12,663] [INFO] Task succeeded: Blastn
[2023-03-14 12:12:12,663] [INFO] Selected 20 target genomes.
[2023-03-14 12:12:12,664] [INFO] Target genome list was writen to OceanDNA-b7448/target_genomes_gtdb.txt
[2023-03-14 12:12:12,679] [INFO] Task started: fastANI
[2023-03-14 12:12:12,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e518b2-66c3-45bf-8699-c2de758ab22b/OceanDNA-b7448.fa --refList OceanDNA-b7448/target_genomes_gtdb.txt --output OceanDNA-b7448/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:12:26,109] [INFO] Task succeeded: fastANI
[2023-03-14 12:12:26,121] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:12:26,121] [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_000260115.1	s__Joostella marina	98.7605	1139	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013391805.1	s__Galbibacter_A sp013391805	79.1632	464	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	78.8708	434	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300875.1	s__Galbibacter_B marinus	77.573	228	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007279655.1	s__Robertkochia solimangrovi	77.4358	109	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116665.1	s__Pustulibacterium marinum	77.0427	160	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pustulibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.6664	164	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	76.628	146	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403955.1	s__Winogradskyella vidalii	76.555	111	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	76.5074	116	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013285155.1	s__Winogradskyella undariae	76.4914	146	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_014641635.1	s__Aquaticitalea lipolytica	76.4692	150	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900112395.1	s__Algibacter lectus	76.4105	162	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_900102165.1	s__Cellulophaga baltica	76.3989	141	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_002973595.1	s__Jejuia pallidilutea	76.3943	113	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_017814435.1	s__Mariniflexile gromovii	76.3392	134	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	76.2019	128	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983975.1	s__Flavobacterium sp017983975	76.1316	56	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524075.1	s__Lutibacter sp012524075	76.0436	110	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889745.1	s__Flavobacterium sp903889745	75.707	78	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:12:26,121] [INFO] GTDB search result was written to OceanDNA-b7448/result_gtdb.tsv
[2023-03-14 12:12:26,121] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:12:26,124] [INFO] DFAST_QC result json was written to OceanDNA-b7448/dqc_result.json
[2023-03-14 12:12:26,124] [INFO] DFAST_QC completed!
[2023-03-14 12:12:26,124] [INFO] Total running time: 0h1m56s