[2024-01-24 11:58:51,228] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:51,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:51,231] [INFO] DQC Reference Directory: /var/lib/cwl/stgf296e5ac-d97f-443c-87c5-db5900b57a58/dqc_reference
[2024-01-24 11:58:52,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:52,429] [INFO] Task started: Prodigal
[2024-01-24 11:58:52,429] [INFO] Running command: gunzip -c /var/lib/cwl/stgef584e38-113b-4595-8e32-8848b8d8d819/GCF_016827595.1_ASM1682759v1_genomic.fna.gz | prodigal -d GCF_016827595.1_ASM1682759v1_genomic.fna/cds.fna -a GCF_016827595.1_ASM1682759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:07,985] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:07,985] [INFO] Task started: HMMsearch
[2024-01-24 11:59:07,985] [INFO] Running command: hmmsearch --tblout GCF_016827595.1_ASM1682759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf296e5ac-d97f-443c-87c5-db5900b57a58/dqc_reference/reference_markers.hmm GCF_016827595.1_ASM1682759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:08,257] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:08,259] [INFO] Found 6/6 markers.
[2024-01-24 11:59:08,305] [INFO] Query marker FASTA was written to GCF_016827595.1_ASM1682759v1_genomic.fna/markers.fasta
[2024-01-24 11:59:08,305] [INFO] Task started: Blastn
[2024-01-24 11:59:08,305] [INFO] Running command: blastn -query GCF_016827595.1_ASM1682759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf296e5ac-d97f-443c-87c5-db5900b57a58/dqc_reference/reference_markers.fasta -out GCF_016827595.1_ASM1682759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:08,914] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:08,917] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:08,918] [INFO] Target genome list was writen to GCF_016827595.1_ASM1682759v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:08,925] [INFO] Task started: fastANI
[2024-01-24 11:59:08,925] [INFO] Running command: fastANI --query /var/lib/cwl/stgef584e38-113b-4595-8e32-8848b8d8d819/GCF_016827595.1_ASM1682759v1_genomic.fna.gz --refList GCF_016827595.1_ASM1682759v1_genomic.fna/target_genomes.txt --output GCF_016827595.1_ASM1682759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:19,539] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:19,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf296e5ac-d97f-443c-87c5-db5900b57a58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:19,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf296e5ac-d97f-443c-87c5-db5900b57a58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:19,553] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:19,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:19,554] [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
Luteirhabdus pelagi	strain=A3-108	GCA_016827595.1	2792783	2792783	type	True	100.0	1112	1113	95	conclusive
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	78.8101	113	1113	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	77.952	163	1113	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	77.534	144	1113	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	77.2182	105	1113	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	76.9358	112	1113	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.8526	123	1113	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.81	75	1113	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.8033	93	1113	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.7742	97	1113	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.5444	99	1113	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.4553	101	1113	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.4519	100	1113	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	76.429	74	1113	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	76.3411	109	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:19,555] [INFO] DFAST Taxonomy check result was written to GCF_016827595.1_ASM1682759v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:19,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:19,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:19,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf296e5ac-d97f-443c-87c5-db5900b57a58/dqc_reference/checkm_data
[2024-01-24 11:59:19,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:19,593] [INFO] Task started: CheckM
[2024-01-24 11:59:19,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016827595.1_ASM1682759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016827595.1_ASM1682759v1_genomic.fna/checkm_input GCF_016827595.1_ASM1682759v1_genomic.fna/checkm_result
[2024-01-24 12:00:05,276] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:05,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:05,297] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:05,298] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:05,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016827595.1_ASM1682759v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:05,298] [INFO] Task started: Blastn
[2024-01-24 12:00:05,298] [INFO] Running command: blastn -query GCF_016827595.1_ASM1682759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf296e5ac-d97f-443c-87c5-db5900b57a58/dqc_reference/reference_markers_gtdb.fasta -out GCF_016827595.1_ASM1682759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:06,178] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:06,182] [INFO] Selected 24 target genomes.
[2024-01-24 12:00:06,182] [INFO] Target genome list was writen to GCF_016827595.1_ASM1682759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:06,228] [INFO] Task started: fastANI
[2024-01-24 12:00:06,229] [INFO] Running command: fastANI --query /var/lib/cwl/stgef584e38-113b-4595-8e32-8848b8d8d819/GCF_016827595.1_ASM1682759v1_genomic.fna.gz --refList GCF_016827595.1_ASM1682759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016827595.1_ASM1682759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:18,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:18,443] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:18,444] [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_016827595.1	s__Marixanthomonas sp016827595	100.0	1112	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003333325.1	s__Ulvibacter_A alkanivorans	80.3339	112	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter_A	95.0	98.51	98.51	0.88	0.88	2	-
GCA_002360635.1	s__Marixanthomonas sp002360635	80.0056	168	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_002631855.1	s__Marixanthomonas sp002631855	78.9729	194	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375495.1	s__Marinirhabdus sp002375495	78.9037	132	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_003353425.1	s__Marinirhabdus gelatinilytica	78.8425	112	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364215.1	s__Aequorivita sp002364215	78.6868	123	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_003413745.1	s__Marixanthomonas ophiurae	77.9704	162	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095375.1	s__Marixanthomonas sp003095375	77.5392	143	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501705.1	s__Pukyongia sp008501705	77.1343	78	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	76.9758	110	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_002715485.1	s__Aequorivita sp002715485	76.8972	85	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCA_002693605.1	s__Marixanthomonas sp002693605	76.8856	83	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	76.8694	121	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641085.1	s__Aequorivita soesokkakensis	76.7928	96	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_002707745.1	s__Marinirhabdus sp002707745	76.7389	69	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	99.79	99.79	0.83	0.83	2	-
GCA_002379985.1	s__Marixanthomonas sp002379985	76.5979	100	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	99.95	99.94	0.93	0.86	4	-
GCF_900102055.1	s__Ulvibacter litoralis	76.4553	101	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_018476645.1	s__Aequorivita echinoideorum	76.429	74	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900489465.1	s__Aequorivita sp900489465	76.3981	110	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001573155.1	s__Aequorivita aquimaris	76.3411	109	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:18,446] [INFO] GTDB search result was written to GCF_016827595.1_ASM1682759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:18,446] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:18,451] [INFO] DFAST_QC result json was written to GCF_016827595.1_ASM1682759v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:18,451] [INFO] DFAST_QC completed!
[2024-01-24 12:00:18,451] [INFO] Total running time: 0h1m27s