[2024-01-25 18:20:05,845] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:05,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:05,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e21a399-30c0-4a68-bdff-924ecb332da0/dqc_reference
[2024-01-25 18:20:07,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:07,013] [INFO] Task started: Prodigal
[2024-01-25 18:20:07,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg111bbfa6-a320-4a0b-8e48-f1a2ea422a88/GCF_026625145.1_ASM2662514v1_genomic.fna.gz | prodigal -d GCF_026625145.1_ASM2662514v1_genomic.fna/cds.fna -a GCF_026625145.1_ASM2662514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:20:18,246] [INFO] Task succeeded: Prodigal
[2024-01-25 18:20:18,246] [INFO] Task started: HMMsearch
[2024-01-25 18:20:18,246] [INFO] Running command: hmmsearch --tblout GCF_026625145.1_ASM2662514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e21a399-30c0-4a68-bdff-924ecb332da0/dqc_reference/reference_markers.hmm GCF_026625145.1_ASM2662514v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:20:18,477] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:20:18,480] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg111bbfa6-a320-4a0b-8e48-f1a2ea422a88/GCF_026625145.1_ASM2662514v1_genomic.fna.gz]
[2024-01-25 18:20:18,518] [INFO] Query marker FASTA was written to GCF_026625145.1_ASM2662514v1_genomic.fna/markers.fasta
[2024-01-25 18:20:18,518] [INFO] Task started: Blastn
[2024-01-25 18:20:18,518] [INFO] Running command: blastn -query GCF_026625145.1_ASM2662514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e21a399-30c0-4a68-bdff-924ecb332da0/dqc_reference/reference_markers.fasta -out GCF_026625145.1_ASM2662514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:19,142] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:19,145] [INFO] Selected 24 target genomes.
[2024-01-25 18:20:19,146] [INFO] Target genome list was writen to GCF_026625145.1_ASM2662514v1_genomic.fna/target_genomes.txt
[2024-01-25 18:20:19,167] [INFO] Task started: fastANI
[2024-01-25 18:20:19,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg111bbfa6-a320-4a0b-8e48-f1a2ea422a88/GCF_026625145.1_ASM2662514v1_genomic.fna.gz --refList GCF_026625145.1_ASM2662514v1_genomic.fna/target_genomes.txt --output GCF_026625145.1_ASM2662514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:20:34,246] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:34,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e21a399-30c0-4a68-bdff-924ecb332da0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:20:34,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e21a399-30c0-4a68-bdff-924ecb332da0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:20:34,260] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:20:34,260] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:20:34,261] [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
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	78.588	406	1301	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	78.5151	430	1301	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	78.4302	426	1301	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	78.0957	319	1301	95	below_threshold
Bizionia paragorgiae	strain=DSM 23842	GCA_900107625.1	283786	283786	type	True	78.044	276	1301	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.8725	303	1301	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	77.6396	272	1301	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	77.5862	283	1301	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	77.5709	221	1301	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.5516	189	1301	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.5396	235	1301	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	77.5067	302	1301	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.4957	193	1301	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.4692	185	1301	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.4191	237	1301	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	77.4048	273	1301	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.3718	232	1301	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	77.3434	229	1301	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.1791	227	1301	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.1757	213	1301	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.1607	162	1301	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.1249	121	1301	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.472	51	1301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:20:34,262] [INFO] DFAST Taxonomy check result was written to GCF_026625145.1_ASM2662514v1_genomic.fna/tc_result.tsv
[2024-01-25 18:20:34,262] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:20:34,262] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:20:34,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e21a399-30c0-4a68-bdff-924ecb332da0/dqc_reference/checkm_data
[2024-01-25 18:20:34,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:20:34,302] [INFO] Task started: CheckM
[2024-01-25 18:20:34,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026625145.1_ASM2662514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026625145.1_ASM2662514v1_genomic.fna/checkm_input GCF_026625145.1_ASM2662514v1_genomic.fna/checkm_result
[2024-01-25 18:21:09,452] [INFO] Task succeeded: CheckM
[2024-01-25 18:21:09,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:21:09,479] [INFO] ===== Completeness check finished =====
[2024-01-25 18:21:09,479] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:21:09,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026625145.1_ASM2662514v1_genomic.fna/markers.fasta)
[2024-01-25 18:21:09,480] [INFO] Task started: Blastn
[2024-01-25 18:21:09,480] [INFO] Running command: blastn -query GCF_026625145.1_ASM2662514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e21a399-30c0-4a68-bdff-924ecb332da0/dqc_reference/reference_markers_gtdb.fasta -out GCF_026625145.1_ASM2662514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:21:10,305] [INFO] Task succeeded: Blastn
[2024-01-25 18:21:10,307] [INFO] Selected 18 target genomes.
[2024-01-25 18:21:10,307] [INFO] Target genome list was writen to GCF_026625145.1_ASM2662514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:21:10,325] [INFO] Task started: fastANI
[2024-01-25 18:21:10,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg111bbfa6-a320-4a0b-8e48-f1a2ea422a88/GCF_026625145.1_ASM2662514v1_genomic.fna.gz --refList GCF_026625145.1_ASM2662514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026625145.1_ASM2662514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:21:22,314] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:22,325] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:21:22,326] [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_000934685.1	s__Lacinutrix sp000934685	84.6531	950	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827365.1	s__Olleya sp002323495	78.9528	338	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_002831665.1	s__Lacinutrix sp002831665	78.8797	421	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000211855.2	s__Lacinutrix sp000211855	78.6386	427	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797445.1	s__Lacinutrix jangbogonensis	78.5821	405	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	78.3439	419	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	78.1501	320	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	78.1488	405	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_000518485.1	s__Olleya marilimosa	78.089	321	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_016864015.1	s__Oceanihabitans sp016864015	77.9657	303	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	77.8593	304	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	77.6306	252	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	77.5723	282	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_002886045.1	s__Flavivirga eckloniae	77.5676	189	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893765.1	s__Tamlana_A carrageenivorans	77.5423	190	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	77.3936	225	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	77.3744	231	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	77.2025	228	1301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:21:22,327] [INFO] GTDB search result was written to GCF_026625145.1_ASM2662514v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:21:22,328] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:21:22,333] [INFO] DFAST_QC result json was written to GCF_026625145.1_ASM2662514v1_genomic.fna/dqc_result.json
[2024-01-25 18:21:22,334] [INFO] DFAST_QC completed!
[2024-01-25 18:21:22,334] [INFO] Total running time: 0h1m16s