[2024-01-24 12:40:19,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:19,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:19,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg196b1e20-c6a6-4b69-bd2e-132e806832a6/dqc_reference
[2024-01-24 12:40:20,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:20,643] [INFO] Task started: Prodigal
[2024-01-24 12:40:20,644] [INFO] Running command: gunzip -c /var/lib/cwl/stg647bedba-a624-4f52-9230-62a8e31295cb/GCF_000425645.1_ASM42564v1_genomic.fna.gz | prodigal -d GCF_000425645.1_ASM42564v1_genomic.fna/cds.fna -a GCF_000425645.1_ASM42564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:30,184] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:30,185] [INFO] Task started: HMMsearch
[2024-01-24 12:40:30,185] [INFO] Running command: hmmsearch --tblout GCF_000425645.1_ASM42564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg196b1e20-c6a6-4b69-bd2e-132e806832a6/dqc_reference/reference_markers.hmm GCF_000425645.1_ASM42564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:30,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:30,445] [INFO] Found 6/6 markers.
[2024-01-24 12:40:30,476] [INFO] Query marker FASTA was written to GCF_000425645.1_ASM42564v1_genomic.fna/markers.fasta
[2024-01-24 12:40:30,476] [INFO] Task started: Blastn
[2024-01-24 12:40:30,477] [INFO] Running command: blastn -query GCF_000425645.1_ASM42564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg196b1e20-c6a6-4b69-bd2e-132e806832a6/dqc_reference/reference_markers.fasta -out GCF_000425645.1_ASM42564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:31,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:31,191] [INFO] Selected 23 target genomes.
[2024-01-24 12:40:31,191] [INFO] Target genome list was writen to GCF_000425645.1_ASM42564v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:31,200] [INFO] Task started: fastANI
[2024-01-24 12:40:31,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg647bedba-a624-4f52-9230-62a8e31295cb/GCF_000425645.1_ASM42564v1_genomic.fna.gz --refList GCF_000425645.1_ASM42564v1_genomic.fna/target_genomes.txt --output GCF_000425645.1_ASM42564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:45,595] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:45,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg196b1e20-c6a6-4b69-bd2e-132e806832a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:45,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg196b1e20-c6a6-4b69-bd2e-132e806832a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:45,620] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:45,621] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:45,621] [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
Aestuariibaculum suncheonense	strain=SC17	GCA_014596935.1	1028745	1028745	type	True	79.1036	411	1024	95	below_threshold
Aestuariibaculum marinum	strain=IP7	GCA_014596975.1	2683592	2683592	type	True	78.9246	413	1024	95	below_threshold
Aestuariibaculum sediminum	strain=TT11	GCA_014596945.1	2770637	2770637	type	True	78.7957	369	1024	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.2916	336	1024	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.1945	345	1024	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	78.1888	286	1024	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.0868	296	1024	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.0703	268	1024	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.0691	308	1024	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.0519	301	1024	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.0174	281	1024	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	77.9803	226	1024	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.9511	314	1024	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.9079	289	1024	95	below_threshold
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	77.7785	292	1024	95	below_threshold
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	77.7655	244	1024	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7313	309	1024	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.6694	173	1024	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.6166	222	1024	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.4735	176	1024	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	77.466	208	1024	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.2823	96	1024	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	76.2319	96	1024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:45,622] [INFO] DFAST Taxonomy check result was written to GCF_000425645.1_ASM42564v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:45,624] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:45,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:45,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg196b1e20-c6a6-4b69-bd2e-132e806832a6/dqc_reference/checkm_data
[2024-01-24 12:40:45,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:45,657] [INFO] Task started: CheckM
[2024-01-24 12:40:45,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425645.1_ASM42564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425645.1_ASM42564v1_genomic.fna/checkm_input GCF_000425645.1_ASM42564v1_genomic.fna/checkm_result
[2024-01-24 12:41:17,875] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:17,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:17,925] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:17,925] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:17,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425645.1_ASM42564v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:17,927] [INFO] Task started: Blastn
[2024-01-24 12:41:17,927] [INFO] Running command: blastn -query GCF_000425645.1_ASM42564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg196b1e20-c6a6-4b69-bd2e-132e806832a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425645.1_ASM42564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:18,883] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:18,886] [INFO] Selected 19 target genomes.
[2024-01-24 12:41:18,886] [INFO] Target genome list was writen to GCF_000425645.1_ASM42564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:18,900] [INFO] Task started: fastANI
[2024-01-24 12:41:18,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg647bedba-a624-4f52-9230-62a8e31295cb/GCF_000425645.1_ASM42564v1_genomic.fna.gz --refList GCF_000425645.1_ASM42564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425645.1_ASM42564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:31,761] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:31,783] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:31,783] [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_000425645.1	s__Gaetbulibacter saemankumensis	100.0	1024	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014596935.1	s__Aestuariibaculum suncheonense	79.1036	411	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596975.1	s__Aestuariibaculum marinum	78.9246	413	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596945.1	s__Aestuariibaculum sediminum	78.7957	369	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	78.5897	372	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	78.2916	336	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425985.1	s__Mariniflexile sp002848895	78.2473	357	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.1946	345	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.1526	321	1024	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_006265225.1	s__Tamlana_C fucoidanivorans	78.095	300	1024	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_900141715.1	s__Arenitalea lutea	78.0691	308	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008806375.1	s__Tamlana_A haliotis	78.0669	269	1024	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_000789235.1	s__Wocania ichthyoenteri	77.9573	310	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	77.916	289	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	77.869	332	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	77.7681	303	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807055.1	s__Confluentibacter citreus	77.7518	245	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033385.1	s__Algibacter pacificus	77.7207	310	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197735.1	s__Formosa sediminum	77.4377	211	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:31,785] [INFO] GTDB search result was written to GCF_000425645.1_ASM42564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:31,785] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:31,789] [INFO] DFAST_QC result json was written to GCF_000425645.1_ASM42564v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:31,790] [INFO] DFAST_QC completed!
[2024-01-24 12:41:31,790] [INFO] Total running time: 0h1m12s