[2024-01-24 14:12:46,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:46,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:46,049] [INFO] DQC Reference Directory: /var/lib/cwl/stgead62ffb-a54c-4374-9603-f800fd0e8ba6/dqc_reference
[2024-01-24 14:12:47,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:47,320] [INFO] Task started: Prodigal
[2024-01-24 14:12:47,321] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bdf0867-f338-41ac-8e7b-18911ee40f69/GCF_000255455.1_ASM25545v1_genomic.fna.gz | prodigal -d GCF_000255455.1_ASM25545v1_genomic.fna/cds.fna -a GCF_000255455.1_ASM25545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:00,280] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:00,280] [INFO] Task started: HMMsearch
[2024-01-24 14:13:00,280] [INFO] Running command: hmmsearch --tblout GCF_000255455.1_ASM25545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgead62ffb-a54c-4374-9603-f800fd0e8ba6/dqc_reference/reference_markers.hmm GCF_000255455.1_ASM25545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:00,592] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:00,593] [INFO] Found 6/6 markers.
[2024-01-24 14:13:00,629] [INFO] Query marker FASTA was written to GCF_000255455.1_ASM25545v1_genomic.fna/markers.fasta
[2024-01-24 14:13:00,629] [INFO] Task started: Blastn
[2024-01-24 14:13:00,629] [INFO] Running command: blastn -query GCF_000255455.1_ASM25545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgead62ffb-a54c-4374-9603-f800fd0e8ba6/dqc_reference/reference_markers.fasta -out GCF_000255455.1_ASM25545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:01,354] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:01,358] [INFO] Selected 26 target genomes.
[2024-01-24 14:13:01,358] [INFO] Target genome list was writen to GCF_000255455.1_ASM25545v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:01,370] [INFO] Task started: fastANI
[2024-01-24 14:13:01,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bdf0867-f338-41ac-8e7b-18911ee40f69/GCF_000255455.1_ASM25545v1_genomic.fna.gz --refList GCF_000255455.1_ASM25545v1_genomic.fna/target_genomes.txt --output GCF_000255455.1_ASM25545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:19,417] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:19,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgead62ffb-a54c-4374-9603-f800fd0e8ba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:19,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgead62ffb-a54c-4374-9603-f800fd0e8ba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:19,441] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:19,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:19,442] [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
Aquimarina agarilytica	strain=ZC1	GCA_000255455.1	1087449	1087449	type	True	100.0	1369	1374	95	conclusive
Aquimarina agarivorans	strain=HQM9	GCA_000218485.2	980584	980584	type	True	81.3285	652	1374	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	77.4079	151	1374	95	below_threshold
Aquimarina brevivitae	strain=DSM 17196	GCA_004216895.1	323412	323412	type	True	77.0995	65	1374	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.8895	60	1374	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.8495	104	1374	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	76.754	144	1374	95	below_threshold
Aquimarina algicola	strain=M625	GCA_006443095.1	2589995	2589995	type	True	76.6558	127	1374	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.6428	79	1374	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	76.6281	162	1374	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6082	91	1374	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.5789	55	1374	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.5729	87	1374	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	76.5177	136	1374	95	below_threshold
Flavobacterium terrigena	strain=DSM 17934	GCA_900108955.1	402734	402734	type	True	76.5044	71	1374	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	76.4791	106	1374	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.4619	110	1374	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	76.4536	140	1374	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	76.4392	102	1374	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.4334	110	1374	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	76.4143	135	1374	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.334	124	1374	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	76.3118	107	1374	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	76.218	94	1374	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.2016	109	1374	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	76.0878	82	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:19,445] [INFO] DFAST Taxonomy check result was written to GCF_000255455.1_ASM25545v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:19,446] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:19,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:19,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgead62ffb-a54c-4374-9603-f800fd0e8ba6/dqc_reference/checkm_data
[2024-01-24 14:13:19,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:19,493] [INFO] Task started: CheckM
[2024-01-24 14:13:19,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000255455.1_ASM25545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000255455.1_ASM25545v1_genomic.fna/checkm_input GCF_000255455.1_ASM25545v1_genomic.fna/checkm_result
[2024-01-24 14:14:01,117] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:01,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:01,148] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:01,148] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:01,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000255455.1_ASM25545v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:01,149] [INFO] Task started: Blastn
[2024-01-24 14:14:01,150] [INFO] Running command: blastn -query GCF_000255455.1_ASM25545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgead62ffb-a54c-4374-9603-f800fd0e8ba6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000255455.1_ASM25545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:02,315] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:02,320] [INFO] Selected 24 target genomes.
[2024-01-24 14:14:02,320] [INFO] Target genome list was writen to GCF_000255455.1_ASM25545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:02,342] [INFO] Task started: fastANI
[2024-01-24 14:14:02,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bdf0867-f338-41ac-8e7b-18911ee40f69/GCF_000255455.1_ASM25545v1_genomic.fna.gz --refList GCF_000255455.1_ASM25545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000255455.1_ASM25545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:25,582] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:25,606] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:25,606] [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_000255455.1	s__Aquimarina agarilytica	100.0	1369	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000218485.1	s__Aquimarina agarivorans	81.3323	652	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430645.1	s__Aquimarina latercula	77.4658	150	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.44	98.41	0.94	0.92	4	-
GCF_004216895.1	s__Aquimarina brevivitae	77.0579	66	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299505.1	s__Aquimarina sp900299505	76.8988	140	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100805.1	s__Aquimarina sp018100805	76.7841	114	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109375.1	s__Aquimarina amphilecti	76.7701	143	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299535.1	s__Aquimarina sp900299535	76.7545	127	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_000211855.2	s__Lacinutrix sp000211855	76.75	111	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	76.746	156	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943565.1	s__Tamlana_B sedimentorum	76.7053	109	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001401755.1	s__Aquimarina longa	76.6855	158	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	76.5789	55	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCF_000430665.1	s__Aquimarina muelleri	76.5027	137	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.98	99.98	0.99	0.99	2	-
GCF_007997385.1	s__Seonamhaeicola algicola	76.334	124	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	76.3282	106	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054895.1	s__Lutibacter sp018054895	76.2917	73	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007489275.1	s__Aquimarina algiphila	76.2881	178	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.78	98.78	0.88	0.88	2	-
GCF_003610735.1	s__Tenacibaculum lutimaris	76.2348	93	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCA_001800945.1	s__Flavobacterium sp001800945	76.1909	51	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015594725.1	s__Flavobacterium sp015594725	76.1256	72	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543325.1	s__Lutibacter profundi	76.0542	84	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524575.1	s__Aquimarina sp011524575	75.9234	84	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	75.8533	67	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:25,617] [INFO] GTDB search result was written to GCF_000255455.1_ASM25545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:25,618] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:25,625] [INFO] DFAST_QC result json was written to GCF_000255455.1_ASM25545v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:25,625] [INFO] DFAST_QC completed!
[2024-01-24 14:14:25,625] [INFO] Total running time: 0h1m40s