[2023-03-18 01:41:20,934] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:20,934] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:20,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a4b75c8-663b-4d8d-a6b6-aa3d59cec96d/dqc_reference
[2023-03-18 01:41:22,088] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:22,088] [INFO] Task started: Prodigal
[2023-03-18 01:41:22,088] [INFO] Running command: cat /var/lib/cwl/stgd33f0d74-542c-47c9-b5d5-7487be12579f/OceanDNA-b6794.fa | prodigal -d OceanDNA-b6794/cds.fna -a OceanDNA-b6794/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:37,622] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:37,622] [INFO] Task started: HMMsearch
[2023-03-18 01:41:37,622] [INFO] Running command: hmmsearch --tblout OceanDNA-b6794/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a4b75c8-663b-4d8d-a6b6-aa3d59cec96d/dqc_reference/reference_markers.hmm OceanDNA-b6794/protein.faa > /dev/null
[2023-03-18 01:41:37,813] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:37,814] [INFO] Found 6/6 markers.
[2023-03-18 01:41:37,830] [INFO] Query marker FASTA was written to OceanDNA-b6794/markers.fasta
[2023-03-18 01:41:37,831] [INFO] Task started: Blastn
[2023-03-18 01:41:37,831] [INFO] Running command: blastn -query OceanDNA-b6794/markers.fasta -db /var/lib/cwl/stg9a4b75c8-663b-4d8d-a6b6-aa3d59cec96d/dqc_reference/reference_markers.fasta -out OceanDNA-b6794/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:38,543] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:38,544] [INFO] Selected 22 target genomes.
[2023-03-18 01:41:38,544] [INFO] Target genome list was writen to OceanDNA-b6794/target_genomes.txt
[2023-03-18 01:41:38,558] [INFO] Task started: fastANI
[2023-03-18 01:41:38,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgd33f0d74-542c-47c9-b5d5-7487be12579f/OceanDNA-b6794.fa --refList OceanDNA-b6794/target_genomes.txt --output OceanDNA-b6794/fastani_result.tsv --threads 1
[2023-03-18 01:41:52,981] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:52,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a4b75c8-663b-4d8d-a6b6-aa3d59cec96d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:52,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a4b75c8-663b-4d8d-a6b6-aa3d59cec96d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:52,994] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:41:52,994] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:41:52,994] [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 jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	79.1519	430	847	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	79.1201	385	847	95	below_threshold
Flavobacterium haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	79.1105	382	847	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	79.093	445	847	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	79.0293	426	847	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	78.9622	365	847	95	below_threshold
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	78.9611	422	847	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.7509	417	847	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	78.7509	417	847	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.7203	413	847	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	78.6373	385	847	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.5689	380	847	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.5489	396	847	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	78.5323	369	847	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	77.7825	264	847	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	77.7565	264	847	95	below_threshold
Flavobacterium aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	77.7248	264	847	95	below_threshold
Flavobacterium hydatis	strain=DSM 2063	GCA_000737695.1	991	991	type	True	77.5459	218	847	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.3879	220	847	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	77.3654	169	847	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.352	234	847	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.3802	105	847	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:41:52,994] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6794/tc_result.tsv
[2023-03-18 01:41:52,994] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:52,994] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:52,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a4b75c8-663b-4d8d-a6b6-aa3d59cec96d/dqc_reference/checkm_data
[2023-03-18 01:41:52,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:52,999] [INFO] Task started: CheckM
[2023-03-18 01:41:52,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6794/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6794/checkm_input OceanDNA-b6794/checkm_result
[2023-03-18 01:42:34,276] [INFO] Task succeeded: CheckM
[2023-03-18 01:42:34,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:42:34,605] [INFO] ===== Completeness check finished =====
[2023-03-18 01:42:34,605] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:42:34,605] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6794/markers.fasta)
[2023-03-18 01:42:34,605] [INFO] Task started: Blastn
[2023-03-18 01:42:34,605] [INFO] Running command: blastn -query OceanDNA-b6794/markers.fasta -db /var/lib/cwl/stg9a4b75c8-663b-4d8d-a6b6-aa3d59cec96d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6794/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:42:35,513] [INFO] Task succeeded: Blastn
[2023-03-18 01:42:35,514] [INFO] Selected 19 target genomes.
[2023-03-18 01:42:35,514] [INFO] Target genome list was writen to OceanDNA-b6794/target_genomes_gtdb.txt
[2023-03-18 01:42:35,529] [INFO] Task started: fastANI
[2023-03-18 01:42:35,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgd33f0d74-542c-47c9-b5d5-7487be12579f/OceanDNA-b6794.fa --refList OceanDNA-b6794/target_genomes_gtdb.txt --output OceanDNA-b6794/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:42:46,498] [INFO] Task succeeded: fastANI
[2023-03-18 01:42:46,509] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:42:46,509] [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_002862805.1	s__Flavobacterium sp002862805	86.1511	608	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	79.0301	450	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491595.2	s__Flavobacterium jejuense	79.0247	426	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422685.1	s__Flavobacterium gelidilacus	78.9813	420	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293845.1	s__Flavobacterium tibetense	78.9622	365	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363695.1	s__Flavobacterium cheniae	78.8657	392	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009495755.1	s__Flavobacterium sp009495755	78.8656	396	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	78.7666	415	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003497625.1	s__Flavobacterium sp003497625	78.7455	379	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_012032075.1	s__Flavobacterium sp012032075	78.717	342	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401995.1	s__Flavobacterium sp018401995	78.6248	290	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	78.5687	379	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004303025.1	s__Flavobacterium sp004303025	78.5398	396	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686885.1	s__Flavobacterium sasangense	78.5171	371	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506265.1	s__Flavobacterium sp902506265	78.455	383	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983975.1	s__Flavobacterium sp017983975	78.4048	228	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862755.1	s__Flavobacterium sp002862755	78.3773	380	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889745.1	s__Flavobacterium sp903889745	78.0608	251	847	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	77.7656	264	847	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-18 01:42:46,509] [INFO] GTDB search result was written to OceanDNA-b6794/result_gtdb.tsv
[2023-03-18 01:42:46,509] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:42:46,512] [INFO] DFAST_QC result json was written to OceanDNA-b6794/dqc_result.json
[2023-03-18 01:42:46,512] [INFO] DFAST_QC completed!
[2023-03-18 01:42:46,512] [INFO] Total running time: 0h1m26s