[2023-03-16 06:31:19,231] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:31:19,231] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:31:19,231] [INFO] DQC Reference Directory: /var/lib/cwl/stg51fa960e-2475-4c79-b780-74ecf786a768/dqc_reference
[2023-03-16 06:31:20,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:31:20,405] [INFO] Task started: Prodigal
[2023-03-16 06:31:20,405] [INFO] Running command: cat /var/lib/cwl/stg8c84e891-b409-4e45-a386-3c05c4dd653a/OceanDNA-b6784.fa | prodigal -d OceanDNA-b6784/cds.fna -a OceanDNA-b6784/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:31:42,053] [INFO] Task succeeded: Prodigal
[2023-03-16 06:31:42,053] [INFO] Task started: HMMsearch
[2023-03-16 06:31:42,054] [INFO] Running command: hmmsearch --tblout OceanDNA-b6784/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51fa960e-2475-4c79-b780-74ecf786a768/dqc_reference/reference_markers.hmm OceanDNA-b6784/protein.faa > /dev/null
[2023-03-16 06:31:42,247] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:31:42,248] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8c84e891-b409-4e45-a386-3c05c4dd653a/OceanDNA-b6784.fa]
[2023-03-16 06:31:42,271] [INFO] Query marker FASTA was written to OceanDNA-b6784/markers.fasta
[2023-03-16 06:31:42,272] [INFO] Task started: Blastn
[2023-03-16 06:31:42,272] [INFO] Running command: blastn -query OceanDNA-b6784/markers.fasta -db /var/lib/cwl/stg51fa960e-2475-4c79-b780-74ecf786a768/dqc_reference/reference_markers.fasta -out OceanDNA-b6784/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:31:42,889] [INFO] Task succeeded: Blastn
[2023-03-16 06:31:42,891] [INFO] Selected 20 target genomes.
[2023-03-16 06:31:42,891] [INFO] Target genome list was writen to OceanDNA-b6784/target_genomes.txt
[2023-03-16 06:31:42,907] [INFO] Task started: fastANI
[2023-03-16 06:31:42,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c84e891-b409-4e45-a386-3c05c4dd653a/OceanDNA-b6784.fa --refList OceanDNA-b6784/target_genomes.txt --output OceanDNA-b6784/fastani_result.tsv --threads 1
[2023-03-16 06:31:57,065] [INFO] Task succeeded: fastANI
[2023-03-16 06:31:57,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51fa960e-2475-4c79-b780-74ecf786a768/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:31:57,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51fa960e-2475-4c79-b780-74ecf786a768/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:31:57,077] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:31:57,077] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:31:57,077] [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
Flavobacterium antarcticum	strain=DSM 19726	GCA_000419685.1	271155	271155	type	True	81.8253	585	1015	95	below_threshold
Flavobacterium tegetincola	strain=DSM 22377	GCA_000425485.1	150172	150172	type	True	81.1292	587	1015	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	77.7539	191	1015	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	77.7447	168	1015	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	77.7379	200	1015	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	77.6654	191	1015	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	77.64	230	1015	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	77.6051	228	1015	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	77.591	224	1015	95	below_threshold
Flavobacterium geliluteum	strain=P7388	GCA_017948595.1	2816120	2816120	type	True	77.5693	213	1015	95	below_threshold
Flavobacterium flevense	strain=DSM 1076	GCA_900142775.1	983	983	type	True	77.5655	196	1015	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	77.5235	216	1015	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	77.441	194	1015	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.3143	198	1015	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	77.1829	172	1015	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.1785	213	1015	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.1702	197	1015	95	below_threshold
Flavobacterium chungbukense	strain=CS100	GCA_020805785.1	877464	877464	type	True	77.1694	236	1015	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.6777	166	1015	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.6442	136	1015	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:31:57,091] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6784/tc_result.tsv
[2023-03-16 06:31:57,117] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:31:57,117] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:31:57,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51fa960e-2475-4c79-b780-74ecf786a768/dqc_reference/checkm_data
[2023-03-16 06:31:57,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:31:57,125] [INFO] Task started: CheckM
[2023-03-16 06:31:57,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6784/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6784/checkm_input OceanDNA-b6784/checkm_result
[2023-03-16 06:32:50,936] [INFO] Task succeeded: CheckM
[2023-03-16 06:32:50,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:32:50,973] [INFO] ===== Completeness check finished =====
[2023-03-16 06:32:50,973] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:32:50,974] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6784/markers.fasta)
[2023-03-16 06:32:50,974] [INFO] Task started: Blastn
[2023-03-16 06:32:50,974] [INFO] Running command: blastn -query OceanDNA-b6784/markers.fasta -db /var/lib/cwl/stg51fa960e-2475-4c79-b780-74ecf786a768/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6784/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:32:51,879] [INFO] Task succeeded: Blastn
[2023-03-16 06:32:51,912] [INFO] Selected 19 target genomes.
[2023-03-16 06:32:51,912] [INFO] Target genome list was writen to OceanDNA-b6784/target_genomes_gtdb.txt
[2023-03-16 06:32:51,927] [INFO] Task started: fastANI
[2023-03-16 06:32:51,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c84e891-b409-4e45-a386-3c05c4dd653a/OceanDNA-b6784.fa --refList OceanDNA-b6784/target_genomes_gtdb.txt --output OceanDNA-b6784/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:33:04,739] [INFO] Task succeeded: fastANI
[2023-03-16 06:33:04,749] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:33:04,749] [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_000419685.1	s__Flavobacterium antarcticum	81.8131	586	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425485.1	s__Flavobacterium tegetincola	81.1292	587	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001529295.1	s__Flavobacterium sp001529295	77.9403	220	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349145.1	s__Flavobacterium hiemivividum	77.7405	191	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	-
GCF_003076455.1	s__Flavobacterium faecale	77.7324	168	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106645.1	s__Flavobacterium degerlachei	77.6694	192	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014844035.1	s__Flavobacterium sp014844035	77.5994	208	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948595.1	s__Flavobacterium sp017948595	77.5756	213	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832125.1	s__Flavobacterium hibernum	77.5602	231	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001975985.1	s__Flavobacterium sp001975985	77.5406	216	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142885.1	s__Flavobacterium xinjiangense	77.5402	214	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142775.1	s__Flavobacterium flevense	77.534	198	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900129705.1	s__Flavobacterium granuli	77.4741	184	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013298525.1	s__Flavobacterium sp013298525	77.4606	207	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	77.4234	264	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_002813295.1	s__Flavobacterium sp002813295	77.347	215	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839195.1	s__Flavobacterium sp903839195	77.0651	181	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
GCF_014486675.1	s__Flavobacterium macrobrachii	77.013	224	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCA_010365135.1	s__Flavobacterium sp010365135	76.9402	195	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:33:04,762] [INFO] GTDB search result was written to OceanDNA-b6784/result_gtdb.tsv
[2023-03-16 06:33:04,782] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:33:04,797] [INFO] DFAST_QC result json was written to OceanDNA-b6784/dqc_result.json
[2023-03-16 06:33:04,797] [INFO] DFAST_QC completed!
[2023-03-16 06:33:04,797] [INFO] Total running time: 0h1m46s