[2024-01-25 20:00:50,811] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:50,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:50,824] [INFO] DQC Reference Directory: /var/lib/cwl/stgacb05e41-28ad-4903-88eb-d15ecd0f266d/dqc_reference
[2024-01-25 20:00:52,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:52,008] [INFO] Task started: Prodigal
[2024-01-25 20:00:52,009] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a5acee7-a43b-459b-a2e1-8dd6469309a2/GCF_014638095.1_ASM1463809v1_genomic.fna.gz | prodigal -d GCF_014638095.1_ASM1463809v1_genomic.fna/cds.fna -a GCF_014638095.1_ASM1463809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:04,527] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:04,527] [INFO] Task started: HMMsearch
[2024-01-25 20:01:04,527] [INFO] Running command: hmmsearch --tblout GCF_014638095.1_ASM1463809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacb05e41-28ad-4903-88eb-d15ecd0f266d/dqc_reference/reference_markers.hmm GCF_014638095.1_ASM1463809v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:04,816] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:04,817] [INFO] Found 6/6 markers.
[2024-01-25 20:01:04,848] [INFO] Query marker FASTA was written to GCF_014638095.1_ASM1463809v1_genomic.fna/markers.fasta
[2024-01-25 20:01:04,849] [INFO] Task started: Blastn
[2024-01-25 20:01:04,849] [INFO] Running command: blastn -query GCF_014638095.1_ASM1463809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacb05e41-28ad-4903-88eb-d15ecd0f266d/dqc_reference/reference_markers.fasta -out GCF_014638095.1_ASM1463809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:05,423] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:05,430] [INFO] Selected 17 target genomes.
[2024-01-25 20:01:05,430] [INFO] Target genome list was writen to GCF_014638095.1_ASM1463809v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:05,439] [INFO] Task started: fastANI
[2024-01-25 20:01:05,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a5acee7-a43b-459b-a2e1-8dd6469309a2/GCF_014638095.1_ASM1463809v1_genomic.fna.gz --refList GCF_014638095.1_ASM1463809v1_genomic.fna/target_genomes.txt --output GCF_014638095.1_ASM1463809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:17,185] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:17,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacb05e41-28ad-4903-88eb-d15ecd0f266d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:17,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacb05e41-28ad-4903-88eb-d15ecd0f266d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:17,196] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:01:17,196] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:17,196] [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
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	100.0	1007	1007	95	conclusive
Muriicola jejuensis	strain=KCTC 22299	GCA_010671595.1	504488	504488	type	True	80.4158	648	1007	95	below_threshold
Muriicola soli	strain=MMS17-SY002	GCA_004139715.1	2507538	2507538	type	True	77.7571	297	1007	95	below_threshold
Zeaxanthinibacter enoshimensis	strain=DSM 18435	GCA_004362865.1	392009	392009	type	True	77.154	132	1007	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.9879	119	1007	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	76.8	59	1007	95	below_threshold
Robiginitalea biformata	strain=HTCC2501	GCA_000024125.1	252307	252307	type	True	76.7491	136	1007	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	76.7462	74	1007	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.7376	89	1007	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.7372	50	1007	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	76.7201	80	1007	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	76.6603	60	1007	95	below_threshold
Robiginitalea sediminis	strain=O458	GCA_002198115.1	1982593	1982593	type	True	76.6526	129	1007	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.6299	69	1007	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	76.0933	63	1007	95	below_threshold
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	76.0867	64	1007	95	below_threshold
Pricia antarctica	strain=DSM 23421	GCA_900101815.1	641691	641691	type	True	76.06	53	1007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:17,198] [INFO] DFAST Taxonomy check result was written to GCF_014638095.1_ASM1463809v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:17,198] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:17,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:17,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacb05e41-28ad-4903-88eb-d15ecd0f266d/dqc_reference/checkm_data
[2024-01-25 20:01:17,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:17,234] [INFO] Task started: CheckM
[2024-01-25 20:01:17,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014638095.1_ASM1463809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014638095.1_ASM1463809v1_genomic.fna/checkm_input GCF_014638095.1_ASM1463809v1_genomic.fna/checkm_result
[2024-01-25 20:01:55,298] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:55,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:55,315] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:55,315] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:55,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014638095.1_ASM1463809v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:55,316] [INFO] Task started: Blastn
[2024-01-25 20:01:55,316] [INFO] Running command: blastn -query GCF_014638095.1_ASM1463809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacb05e41-28ad-4903-88eb-d15ecd0f266d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014638095.1_ASM1463809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:56,091] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:56,094] [INFO] Selected 17 target genomes.
[2024-01-25 20:01:56,095] [INFO] Target genome list was writen to GCF_014638095.1_ASM1463809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:56,109] [INFO] Task started: fastANI
[2024-01-25 20:01:56,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a5acee7-a43b-459b-a2e1-8dd6469309a2/GCF_014638095.1_ASM1463809v1_genomic.fna.gz --refList GCF_014638095.1_ASM1463809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014638095.1_ASM1463809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:07,738] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:07,748] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:07,748] [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_014638095.1	s__Muriicola marianensis	100.0	1007	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010671595.1	s__Muriicola jejuensis	80.4158	648	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004139715.1	s__Muriicola sp004139715	77.7392	297	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042315.1	s__Muriicola sp013042315	77.3906	248	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	99.31	99.31	0.85	0.85	2	-
GCA_013042255.1	s__Muriicola sp013042255	77.1176	184	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	98.63	98.55	0.78	0.75	6	-
GCA_009901585.1	s__R33 sp009901585	76.9879	119	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243345.1	s__Robiginitalea sp014243345	76.7967	141	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	76.7934	58	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_000024125.1	s__Robiginitalea biformata	76.7491	136	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	76.7417	73	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010500845.1	s__Muricauda sediminis	76.7156	79	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198115.1	s__Robiginitalea sediminis	76.6373	128	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009371985.2	s__TP-CH-4 sp009371985	76.6233	68	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TP-CH-4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426735.1	s__Arenibacter sp003426735	76.285	56	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227965.1	s__Robiginitalea sp006227965	76.1891	75	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101815.1	s__Pricia antarctica	76.06	53	1007	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:07,750] [INFO] GTDB search result was written to GCF_014638095.1_ASM1463809v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:07,750] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:07,753] [INFO] DFAST_QC result json was written to GCF_014638095.1_ASM1463809v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:07,754] [INFO] DFAST_QC completed!
[2024-01-25 20:02:07,754] [INFO] Total running time: 0h1m17s