[2024-01-24 13:41:20,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg8753ab50-75aa-40b0-be13-1c11ff1a202d/dqc_reference
[2024-01-24 13:41:22,047] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:22,053] [INFO] Task started: Prodigal
[2024-01-24 13:41:22,054] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8720aec-643d-4fb8-8244-06ad99430bf5/GCF_022662175.1_ASM2266217v1_genomic.fna.gz | prodigal -d GCF_022662175.1_ASM2266217v1_genomic.fna/cds.fna -a GCF_022662175.1_ASM2266217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:34,036] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:34,037] [INFO] Task started: HMMsearch
[2024-01-24 13:41:34,037] [INFO] Running command: hmmsearch --tblout GCF_022662175.1_ASM2266217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8753ab50-75aa-40b0-be13-1c11ff1a202d/dqc_reference/reference_markers.hmm GCF_022662175.1_ASM2266217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:34,334] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:34,335] [INFO] Found 6/6 markers.
[2024-01-24 13:41:34,376] [INFO] Query marker FASTA was written to GCF_022662175.1_ASM2266217v1_genomic.fna/markers.fasta
[2024-01-24 13:41:34,377] [INFO] Task started: Blastn
[2024-01-24 13:41:34,377] [INFO] Running command: blastn -query GCF_022662175.1_ASM2266217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8753ab50-75aa-40b0-be13-1c11ff1a202d/dqc_reference/reference_markers.fasta -out GCF_022662175.1_ASM2266217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:35,043] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:35,046] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:35,046] [INFO] Target genome list was writen to GCF_022662175.1_ASM2266217v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:35,056] [INFO] Task started: fastANI
[2024-01-24 13:41:35,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8720aec-643d-4fb8-8244-06ad99430bf5/GCF_022662175.1_ASM2266217v1_genomic.fna.gz --refList GCF_022662175.1_ASM2266217v1_genomic.fna/target_genomes.txt --output GCF_022662175.1_ASM2266217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:47,897] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:47,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8753ab50-75aa-40b0-be13-1c11ff1a202d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:47,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8753ab50-75aa-40b0-be13-1c11ff1a202d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:47,914] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:47,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:47,915] [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
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	100.0	1065	1065	95	conclusive
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	79.8061	582	1065	95	below_threshold
Aestuariivivens sediminis	strain=S-DT1-15	GCA_022662105.1	2913557	2913557	type	True	78.3628	408	1065	95	below_threshold
Aestuariivivens sediminicola	strain=MTV5-3	GCA_022662015.1	2913560	2913560	type	True	78.2356	297	1065	95	below_threshold
Algibacter onchidii	strain=XY-114	GCA_004804355.1	2562860	2562860	type	True	77.8263	213	1065	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.7999	267	1065	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	77.6594	249	1065	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	77.5777	273	1065	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.4779	214	1065	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	77.4739	246	1065	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.4545	243	1065	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.4355	246	1065	95	below_threshold
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	77.4167	229	1065	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	77.3264	224	1065	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.1567	117	1065	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.1105	161	1065	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.9699	158	1065	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.8421	124	1065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,917] [INFO] DFAST Taxonomy check result was written to GCF_022662175.1_ASM2266217v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:47,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:47,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:47,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8753ab50-75aa-40b0-be13-1c11ff1a202d/dqc_reference/checkm_data
[2024-01-24 13:41:47,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:47,955] [INFO] Task started: CheckM
[2024-01-24 13:41:47,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022662175.1_ASM2266217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022662175.1_ASM2266217v1_genomic.fna/checkm_input GCF_022662175.1_ASM2266217v1_genomic.fna/checkm_result
[2024-01-24 13:42:25,560] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:25,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:25,581] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:25,581] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:25,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022662175.1_ASM2266217v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:25,582] [INFO] Task started: Blastn
[2024-01-24 13:42:25,582] [INFO] Running command: blastn -query GCF_022662175.1_ASM2266217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8753ab50-75aa-40b0-be13-1c11ff1a202d/dqc_reference/reference_markers_gtdb.fasta -out GCF_022662175.1_ASM2266217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:26,494] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:26,498] [INFO] Selected 34 target genomes.
[2024-01-24 13:42:26,499] [INFO] Target genome list was writen to GCF_022662175.1_ASM2266217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:26,527] [INFO] Task started: fastANI
[2024-01-24 13:42:26,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8720aec-643d-4fb8-8244-06ad99430bf5/GCF_022662175.1_ASM2266217v1_genomic.fna.gz --refList GCF_022662175.1_ASM2266217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022662175.1_ASM2266217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:46,744] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:46,776] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:42:46,776] [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_000789235.1	s__Wocania ichthyoenteri	77.8518	322	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	77.8379	237	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	77.8372	278	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.8125	266	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804355.1	s__Tamlana_C sp004804355	77.8044	212	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	77.7591	278	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265225.1	s__Tamlana_C fucoidanivorans	77.7463	251	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	77.7177	317	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	77.6619	248	1065	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_900114265.1	s__Flaviramulus basaltis	77.6431	324	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943565.1	s__Tamlana_B sedimentorum	77.5996	229	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	77.584	269	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	77.4861	222	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428965.1	s__Jejuia sp002428965	77.4711	197	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943555.1	s__Tamlana_B nanhaiensis	77.4684	245	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	77.4562	242	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	77.4355	246	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001642835.1	s__Tamlana_A agarivorans	77.4092	220	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	77.4081	214	1065	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_001310225.1	s__Algibacter_A alginicilyticus	77.3792	258	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900112395.1	s__Algibacter lectus	77.3608	229	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_006974145.1	s__Changchengzhania lutea	77.3276	223	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Changchengzhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	77.3174	205	1065	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_003148645.1	s__Xanthomarina spongicola	77.2941	179	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.2909	182	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	77.1272	160	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	77.1244	116	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCA_001874145.1	s__Lacinutrix sp001874145	77.0589	153	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.0421	177	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067265.1	s__Oceanihabitans sp018067265	77.0011	120	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.9829	187	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042715.1	s__Site-B15 sp013042715	76.9517	99	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Site-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	76.8559	122	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222915.1	s__Psychroserpens sp018222915	76.3754	113	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:46,778] [INFO] GTDB search result was written to GCF_022662175.1_ASM2266217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:46,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:46,786] [INFO] DFAST_QC result json was written to GCF_022662175.1_ASM2266217v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:46,786] [INFO] DFAST_QC completed!
[2024-01-24 13:42:46,786] [INFO] Total running time: 0h1m26s