[2024-01-24 12:54:05,373] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg61a17b4d-0f49-43fa-8a32-13a010b10813/dqc_reference
[2024-01-24 12:54:07,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,723] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,724] [INFO] Running command: gunzip -c /var/lib/cwl/stgba03eaf4-3728-4d96-9e3a-6fa5808feb26/GCF_031845265.1_ASM3184526v1_genomic.fna.gz | prodigal -d GCF_031845265.1_ASM3184526v1_genomic.fna/cds.fna -a GCF_031845265.1_ASM3184526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:19,133] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:19,133] [INFO] Task started: HMMsearch
[2024-01-24 12:54:19,133] [INFO] Running command: hmmsearch --tblout GCF_031845265.1_ASM3184526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61a17b4d-0f49-43fa-8a32-13a010b10813/dqc_reference/reference_markers.hmm GCF_031845265.1_ASM3184526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:19,520] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:19,521] [INFO] Found 6/6 markers.
[2024-01-24 12:54:19,557] [INFO] Query marker FASTA was written to GCF_031845265.1_ASM3184526v1_genomic.fna/markers.fasta
[2024-01-24 12:54:19,557] [INFO] Task started: Blastn
[2024-01-24 12:54:19,558] [INFO] Running command: blastn -query GCF_031845265.1_ASM3184526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61a17b4d-0f49-43fa-8a32-13a010b10813/dqc_reference/reference_markers.fasta -out GCF_031845265.1_ASM3184526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:20,250] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:20,253] [INFO] Selected 21 target genomes.
[2024-01-24 12:54:20,253] [INFO] Target genome list was writen to GCF_031845265.1_ASM3184526v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:20,291] [INFO] Task started: fastANI
[2024-01-24 12:54:20,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgba03eaf4-3728-4d96-9e3a-6fa5808feb26/GCF_031845265.1_ASM3184526v1_genomic.fna.gz --refList GCF_031845265.1_ASM3184526v1_genomic.fna/target_genomes.txt --output GCF_031845265.1_ASM3184526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:34,052] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:34,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61a17b4d-0f49-43fa-8a32-13a010b10813/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:34,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61a17b4d-0f49-43fa-8a32-13a010b10813/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:34,069] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:54:34,070] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:54:34,070] [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
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	80.877	603	1091	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	77.5657	269	1091	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	77.4964	266	1091	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	77.4604	271	1091	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	77.1689	257	1091	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	77.1637	142	1091	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.9101	123	1091	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	76.8807	127	1091	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.8214	83	1091	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	76.8191	132	1091	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.785	92	1091	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.7617	132	1091	95	below_threshold
Salegentibacter salinarum	strain=KCTC 12975	GCA_002833365.1	447422	447422	type	True	76.7111	128	1091	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	76.6462	131	1091	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.6413	67	1091	95	below_threshold
Mangrovimonas yunxiaonensis	strain=CGMCC 1.12280	GCA_014636995.1	1197477	1197477	type	True	76.5979	59	1091	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.5978	142	1091	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.5805	85	1091	95	below_threshold
Salegentibacter salinarum	strain=DSM 23400	GCA_900168115.1	447422	447422	type	True	76.5502	127	1091	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.4516	79	1091	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.3167	97	1091	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:34,072] [INFO] DFAST Taxonomy check result was written to GCF_031845265.1_ASM3184526v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:34,073] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:34,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:34,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61a17b4d-0f49-43fa-8a32-13a010b10813/dqc_reference/checkm_data
[2024-01-24 12:54:34,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:34,113] [INFO] Task started: CheckM
[2024-01-24 12:54:34,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031845265.1_ASM3184526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031845265.1_ASM3184526v1_genomic.fna/checkm_input GCF_031845265.1_ASM3184526v1_genomic.fna/checkm_result
[2024-01-24 12:55:11,699] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:11,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:11,724] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:11,724] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:11,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031845265.1_ASM3184526v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:11,725] [INFO] Task started: Blastn
[2024-01-24 12:55:11,725] [INFO] Running command: blastn -query GCF_031845265.1_ASM3184526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61a17b4d-0f49-43fa-8a32-13a010b10813/dqc_reference/reference_markers_gtdb.fasta -out GCF_031845265.1_ASM3184526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:12,614] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:12,619] [INFO] Selected 15 target genomes.
[2024-01-24 12:55:12,619] [INFO] Target genome list was writen to GCF_031845265.1_ASM3184526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:12,631] [INFO] Task started: fastANI
[2024-01-24 12:55:12,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgba03eaf4-3728-4d96-9e3a-6fa5808feb26/GCF_031845265.1_ASM3184526v1_genomic.fna.gz --refList GCF_031845265.1_ASM3184526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031845265.1_ASM3184526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:21,729] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:21,747] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:55:21,748] [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_003253545.1	s__Mesonia algae	80.8701	604	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	-
GCF_003667275.1	s__Mesonia aquimarina	77.6224	265	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008692195.1	s__Mesonia sp008692195	77.5957	271	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141885.1	s__Mesonia phycicola	77.5523	271	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423405.1	s__Mesonia mobilis	77.4717	270	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_902499555.1	s__Mesonia oceanica	77.1692	257	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCA_012964435.1	s__Mesonia sp012964435	77.1062	251	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900142975.1	s__Salegentibacter salegens	77.0505	140	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000745315.1	s__Salegentibacter sp000745315	77.0015	136	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168265.1	s__Salegentibacter salarius	76.8947	132	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_900168045.1	s__Salegentibacter holothuriorum	76.6462	131	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094855.1	s__Zunongwangia atlantica	76.5978	142	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.5195	104	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.415	131	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862805.1	s__Flavobacterium sp002862805	76.1494	77	1091	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:21,749] [INFO] GTDB search result was written to GCF_031845265.1_ASM3184526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:21,750] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:21,754] [INFO] DFAST_QC result json was written to GCF_031845265.1_ASM3184526v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:21,755] [INFO] DFAST_QC completed!
[2024-01-24 12:55:21,755] [INFO] Total running time: 0h1m16s