[2024-01-25 17:54:05,508] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:54:05,511] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:54:05,511] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2c2a792-4c61-4560-a792-42d198cbf822/dqc_reference
[2024-01-25 17:54:06,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:54:06,601] [INFO] Task started: Prodigal
[2024-01-25 17:54:06,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg28ef1604-c0f1-4a46-8bdd-4d407ca37072/GCF_003663945.1_ASM366394v1_genomic.fna.gz | prodigal -d GCF_003663945.1_ASM366394v1_genomic.fna/cds.fna -a GCF_003663945.1_ASM366394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:13,465] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:13,465] [INFO] Task started: HMMsearch
[2024-01-25 17:54:13,465] [INFO] Running command: hmmsearch --tblout GCF_003663945.1_ASM366394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2c2a792-4c61-4560-a792-42d198cbf822/dqc_reference/reference_markers.hmm GCF_003663945.1_ASM366394v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:13,656] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:13,657] [INFO] Found 6/6 markers.
[2024-01-25 17:54:13,681] [INFO] Query marker FASTA was written to GCF_003663945.1_ASM366394v1_genomic.fna/markers.fasta
[2024-01-25 17:54:13,682] [INFO] Task started: Blastn
[2024-01-25 17:54:13,682] [INFO] Running command: blastn -query GCF_003663945.1_ASM366394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2c2a792-4c61-4560-a792-42d198cbf822/dqc_reference/reference_markers.fasta -out GCF_003663945.1_ASM366394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:14,349] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:14,352] [INFO] Selected 20 target genomes.
[2024-01-25 17:54:14,353] [INFO] Target genome list was writen to GCF_003663945.1_ASM366394v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:14,382] [INFO] Task started: fastANI
[2024-01-25 17:54:14,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg28ef1604-c0f1-4a46-8bdd-4d407ca37072/GCF_003663945.1_ASM366394v1_genomic.fna.gz --refList GCF_003663945.1_ASM366394v1_genomic.fna/target_genomes.txt --output GCF_003663945.1_ASM366394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:28,481] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:28,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2c2a792-4c61-4560-a792-42d198cbf822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:28,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2c2a792-4c61-4560-a792-42d198cbf822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:28,493] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:54:28,493] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:54:28,493] [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 algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	81.7663	708	1032	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	81.5537	720	1032	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	80.9589	621	1032	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	79.6414	474	1032	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	79.246	455	1032	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	79.1071	440	1032	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	79.1047	432	1032	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	79.0111	466	1032	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	78.9585	431	1032	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	78.9192	461	1032	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.4056	343	1032	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.3628	348	1032	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	78.2059	336	1032	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	78.1574	319	1032	95	below_threshold
Bizionia paragorgiae	strain=DSM 23842	GCA_900107625.1	283786	283786	type	True	78.071	332	1032	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.554	243	1032	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.46	214	1032	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.4545	243	1032	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.4004	245	1032	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.9782	216	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:28,494] [INFO] DFAST Taxonomy check result was written to GCF_003663945.1_ASM366394v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:28,495] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:28,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:28,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2c2a792-4c61-4560-a792-42d198cbf822/dqc_reference/checkm_data
[2024-01-25 17:54:28,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:28,528] [INFO] Task started: CheckM
[2024-01-25 17:54:28,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003663945.1_ASM366394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003663945.1_ASM366394v1_genomic.fna/checkm_input GCF_003663945.1_ASM366394v1_genomic.fna/checkm_result
[2024-01-25 17:54:52,886] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:52,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:52,901] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:52,901] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:52,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003663945.1_ASM366394v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:52,902] [INFO] Task started: Blastn
[2024-01-25 17:54:52,902] [INFO] Running command: blastn -query GCF_003663945.1_ASM366394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2c2a792-4c61-4560-a792-42d198cbf822/dqc_reference/reference_markers_gtdb.fasta -out GCF_003663945.1_ASM366394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:53,844] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:53,846] [INFO] Selected 10 target genomes.
[2024-01-25 17:54:53,847] [INFO] Target genome list was writen to GCF_003663945.1_ASM366394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:53,857] [INFO] Task started: fastANI
[2024-01-25 17:54:53,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg28ef1604-c0f1-4a46-8bdd-4d407ca37072/GCF_003663945.1_ASM366394v1_genomic.fna.gz --refList GCF_003663945.1_ASM366394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003663945.1_ASM366394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:55:01,591] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:01,598] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:55:01,598] [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_003663945.1	s__Lacinutrix venerupis	100.0	1031	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	conclusive
GCF_000211855.2	s__Lacinutrix sp000211855	83.1718	709	1032	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	83.1057	683	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831665.1	s__Lacinutrix sp002831665	81.8788	733	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418085.1	s__Lacinutrix algicola	81.7656	708	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418015.1	s__Lacinutrix mariniflava	81.5569	720	1032	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	80.9679	620	1032	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	79.2402	456	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934685.1	s__Lacinutrix sp000934685	78.7187	435	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067115.1	s__Bizionia sp018067115	78.2844	265	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bizionia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:55:01,599] [INFO] GTDB search result was written to GCF_003663945.1_ASM366394v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:55:01,599] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:55:01,602] [INFO] DFAST_QC result json was written to GCF_003663945.1_ASM366394v1_genomic.fna/dqc_result.json
[2024-01-25 17:55:01,602] [INFO] DFAST_QC completed!
[2024-01-25 17:55:01,602] [INFO] Total running time: 0h0m56s