[2024-01-25 20:19:35,468] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:35,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:35,471] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd109715-ef0d-4273-a7f2-24744d1d210c/dqc_reference
[2024-01-25 20:19:36,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:36,622] [INFO] Task started: Prodigal
[2024-01-25 20:19:36,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg89600d02-fa1f-4b5a-ad4e-df8aa1bb96fc/GCF_014640155.1_ASM1464015v1_genomic.fna.gz | prodigal -d GCF_014640155.1_ASM1464015v1_genomic.fna/cds.fna -a GCF_014640155.1_ASM1464015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:47,266] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:47,267] [INFO] Task started: HMMsearch
[2024-01-25 20:19:47,267] [INFO] Running command: hmmsearch --tblout GCF_014640155.1_ASM1464015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd109715-ef0d-4273-a7f2-24744d1d210c/dqc_reference/reference_markers.hmm GCF_014640155.1_ASM1464015v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:47,509] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:47,510] [INFO] Found 6/6 markers.
[2024-01-25 20:19:47,537] [INFO] Query marker FASTA was written to GCF_014640155.1_ASM1464015v1_genomic.fna/markers.fasta
[2024-01-25 20:19:47,538] [INFO] Task started: Blastn
[2024-01-25 20:19:47,538] [INFO] Running command: blastn -query GCF_014640155.1_ASM1464015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd109715-ef0d-4273-a7f2-24744d1d210c/dqc_reference/reference_markers.fasta -out GCF_014640155.1_ASM1464015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:48,138] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:48,143] [INFO] Selected 26 target genomes.
[2024-01-25 20:19:48,143] [INFO] Target genome list was writen to GCF_014640155.1_ASM1464015v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:48,151] [INFO] Task started: fastANI
[2024-01-25 20:19:48,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg89600d02-fa1f-4b5a-ad4e-df8aa1bb96fc/GCF_014640155.1_ASM1464015v1_genomic.fna.gz --refList GCF_014640155.1_ASM1464015v1_genomic.fna/target_genomes.txt --output GCF_014640155.1_ASM1464015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:03,254] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:03,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd109715-ef0d-4273-a7f2-24744d1d210c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:03,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd109715-ef0d-4273-a7f2-24744d1d210c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:03,266] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:03,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:03,267] [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
Planktosalinus lacus	strain=CGMCC 1.12924	GCA_014640155.1	1526573	1526573	type	True	100.0	969	969	95	conclusive
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.8605	75	969	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6375	67	969	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.5945	77	969	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.5844	57	969	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.4223	58	969	95	below_threshold
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	76.4059	69	969	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.3668	57	969	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.3552	61	969	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.3457	59	969	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	76.3423	54	969	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.3333	82	969	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.3186	54	969	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.2525	59	969	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	76.2337	78	969	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	76.0931	54	969	95	below_threshold
Gelidibacter japonicus	strain=Bio7-1	GCA_010725055.1	1962232	1962232	type	True	75.9694	61	969	95	below_threshold
Salegentibacter salinarum	strain=KCTC 12975	GCA_002833365.1	447422	447422	type	True	75.9673	75	969	95	below_threshold
Salegentibacter salinarum	strain=DSM 23400	GCA_900168115.1	447422	447422	type	True	75.9673	75	969	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:03,268] [INFO] DFAST Taxonomy check result was written to GCF_014640155.1_ASM1464015v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:03,268] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:03,268] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:03,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd109715-ef0d-4273-a7f2-24744d1d210c/dqc_reference/checkm_data
[2024-01-25 20:20:03,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:03,299] [INFO] Task started: CheckM
[2024-01-25 20:20:03,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640155.1_ASM1464015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640155.1_ASM1464015v1_genomic.fna/checkm_input GCF_014640155.1_ASM1464015v1_genomic.fna/checkm_result
[2024-01-25 20:20:38,022] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:38,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:38,040] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:38,040] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:38,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640155.1_ASM1464015v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:38,041] [INFO] Task started: Blastn
[2024-01-25 20:20:38,041] [INFO] Running command: blastn -query GCF_014640155.1_ASM1464015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd109715-ef0d-4273-a7f2-24744d1d210c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640155.1_ASM1464015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:38,899] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:38,902] [INFO] Selected 23 target genomes.
[2024-01-25 20:20:38,902] [INFO] Target genome list was writen to GCF_014640155.1_ASM1464015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:38,917] [INFO] Task started: fastANI
[2024-01-25 20:20:38,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg89600d02-fa1f-4b5a-ad4e-df8aa1bb96fc/GCF_014640155.1_ASM1464015v1_genomic.fna.gz --refList GCF_014640155.1_ASM1464015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640155.1_ASM1464015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:55,273] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:55,286] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:55,287] [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_014640155.1	s__Planktosalinus lacus	100.0	969	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018402385.1	s__Planktosalinus sp018402385	79.8827	424	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842575.1	s__Planktosalinus sp002842575	77.7195	194	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997135.1	s__Aequorivita lipolytica	76.7226	83	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001641085.1	s__Aequorivita soesokkakensis	76.6989	77	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_016649715.1	s__Aequorivita sp016649715	76.6635	66	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014526325.1	s__Psychroserpens algicola	76.5991	61	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295415.1	s__Altibacter sp014295415	76.5945	77	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	76.5322	64	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCF_013249065.1	s__Winogradskyella litoriviva	76.4558	57	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	76.4281	72	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993795.1	s__Gillisia arcticum	76.4059	69	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	76.3668	57	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375495.1	s__Marinirhabdus sp002375495	76.3341	72	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_013403985.1	s__Winogradskyella ludwigii	76.3186	54	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222875.1	s__Psychroserpens sp018222875	76.2824	57	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375695.1	s__Aequorivita sp002375695	76.2757	67	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003650305.1	s__PRS1 sp003650305	76.2622	61	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	76.0079	56	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299535.1	s__Aquimarina sp900299535	76.0064	54	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_900168115.1	s__Salegentibacter salinarum	75.9673	75	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002482975.1	s__Flavobacterium sp002482975	75.4624	60	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:55,288] [INFO] GTDB search result was written to GCF_014640155.1_ASM1464015v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:55,289] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:55,292] [INFO] DFAST_QC result json was written to GCF_014640155.1_ASM1464015v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:55,292] [INFO] DFAST_QC completed!
[2024-01-25 20:20:55,293] [INFO] Total running time: 0h1m20s