[2024-01-24 11:58:57,352] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg167e6ca0-8e92-4f77-a97a-8c0e95a414c7/dqc_reference
[2024-01-24 11:58:58,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,605] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg39f0fab8-2a34-4a5d-b78e-10fc2e55cace/GCF_003688405.1_ASM368840v1_genomic.fna.gz | prodigal -d GCF_003688405.1_ASM368840v1_genomic.fna/cds.fna -a GCF_003688405.1_ASM368840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:12,589] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:12,590] [INFO] Task started: HMMsearch
[2024-01-24 11:59:12,590] [INFO] Running command: hmmsearch --tblout GCF_003688405.1_ASM368840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg167e6ca0-8e92-4f77-a97a-8c0e95a414c7/dqc_reference/reference_markers.hmm GCF_003688405.1_ASM368840v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:12,897] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:12,898] [INFO] Found 6/6 markers.
[2024-01-24 11:59:12,931] [INFO] Query marker FASTA was written to GCF_003688405.1_ASM368840v1_genomic.fna/markers.fasta
[2024-01-24 11:59:12,931] [INFO] Task started: Blastn
[2024-01-24 11:59:12,931] [INFO] Running command: blastn -query GCF_003688405.1_ASM368840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg167e6ca0-8e92-4f77-a97a-8c0e95a414c7/dqc_reference/reference_markers.fasta -out GCF_003688405.1_ASM368840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:13,613] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:13,618] [INFO] Selected 24 target genomes.
[2024-01-24 11:59:13,618] [INFO] Target genome list was writen to GCF_003688405.1_ASM368840v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:13,627] [INFO] Task started: fastANI
[2024-01-24 11:59:13,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f0fab8-2a34-4a5d-b78e-10fc2e55cace/GCF_003688405.1_ASM368840v1_genomic.fna.gz --refList GCF_003688405.1_ASM368840v1_genomic.fna/target_genomes.txt --output GCF_003688405.1_ASM368840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:29,537] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:29,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg167e6ca0-8e92-4f77-a97a-8c0e95a414c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:29,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg167e6ca0-8e92-4f77-a97a-8c0e95a414c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:29,553] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:29,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:29,554] [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
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	100.0	1270	1271	95	conclusive
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	78.1247	361	1271	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	78.105	361	1271	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	77.3312	146	1271	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	77.2261	152	1271	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.2194	211	1271	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	77.1942	160	1271	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	77.0912	133	1271	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	77.01	96	1271	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	76.9892	143	1271	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	76.8247	106	1271	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.7727	145	1271	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	76.6078	113	1271	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	76.5694	115	1271	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.5244	74	1271	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.4624	85	1271	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	76.4584	70	1271	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	76.4427	78	1271	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	76.4337	80	1271	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:29,555] [INFO] DFAST Taxonomy check result was written to GCF_003688405.1_ASM368840v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:29,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:29,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:29,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg167e6ca0-8e92-4f77-a97a-8c0e95a414c7/dqc_reference/checkm_data
[2024-01-24 11:59:29,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:29,597] [INFO] Task started: CheckM
[2024-01-24 11:59:29,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003688405.1_ASM368840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003688405.1_ASM368840v1_genomic.fna/checkm_input GCF_003688405.1_ASM368840v1_genomic.fna/checkm_result
[2024-01-24 12:00:13,715] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:13,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:13,736] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:13,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:13,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003688405.1_ASM368840v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:13,736] [INFO] Task started: Blastn
[2024-01-24 12:00:13,737] [INFO] Running command: blastn -query GCF_003688405.1_ASM368840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg167e6ca0-8e92-4f77-a97a-8c0e95a414c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003688405.1_ASM368840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:14,622] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:14,626] [INFO] Selected 24 target genomes.
[2024-01-24 12:00:14,626] [INFO] Target genome list was writen to GCF_003688405.1_ASM368840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:14,638] [INFO] Task started: fastANI
[2024-01-24 12:00:14,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f0fab8-2a34-4a5d-b78e-10fc2e55cace/GCF_003688405.1_ASM368840v1_genomic.fna.gz --refList GCF_003688405.1_ASM368840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003688405.1_ASM368840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:27,732] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:27,750] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:27,750] [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_003688405.1	s__Ulvibacter antarcticus	100.0	1270	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900102055.1	s__Ulvibacter litoralis	78.1541	365	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009014635.1	s__Patiriisocius marinistellae	77.3312	146	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	77.2778	206	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997135.1	s__Aequorivita lipolytica	77.2241	153	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	77.2194	211	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974325.1	s__Patiriisocius marinus	77.1942	160	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375495.1	s__Marinirhabdus sp002375495	77.1577	131	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_900489465.1	s__Aequorivita sp900489465	77.1427	178	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	77.071	134	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCF_003333325.1	s__Ulvibacter_A alkanivorans	77.0359	146	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter_A	95.0	98.51	98.51	0.88	0.88	2	-
GCF_013403915.1	s__Winogradskyella pacifica	77.0082	94	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_009901525.1	s__Kordia antarctica	76.987	97	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746845.1	s__Altibacter lentus	76.9713	144	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011044175.1	s__Marinirhabdus sp011044175	76.86	156	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694465.1	s__IN17 sp002694465	76.8357	144	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCF_018476645.1	s__Aequorivita echinoideorum	76.8247	106	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364245.1	s__Marixanthomonas sp002364245	76.7776	99	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	76.7247	144	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106795.1	s__Aequorivita viscosa	76.6078	113	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010671565.1	s__Spongiivirga citrea	76.5408	55	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Spongiivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002065.1	s__SMXJ01 sp013002065	76.4682	122	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033385.1	s__Algibacter pacificus	76.4624	85	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224335.1	s__Algorimicrobium argentinense	76.4337	80	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:27,751] [INFO] GTDB search result was written to GCF_003688405.1_ASM368840v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:27,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:27,756] [INFO] DFAST_QC result json was written to GCF_003688405.1_ASM368840v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:27,756] [INFO] DFAST_QC completed!
[2024-01-24 12:00:27,756] [INFO] Total running time: 0h1m30s