[2024-01-25 17:34:07,127] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,135] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,135] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcecc038-9677-4735-83d1-18731a761b11/dqc_reference
[2024-01-25 17:34:08,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,950] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,950] [INFO] Running command: gunzip -c /var/lib/cwl/stga28df3a3-a9c4-4d56-96fd-a572c1a0985e/GCF_026109735.1_ASM2610973v1_genomic.fna.gz | prodigal -d GCF_026109735.1_ASM2610973v1_genomic.fna/cds.fna -a GCF_026109735.1_ASM2610973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:22,056] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:22,056] [INFO] Task started: HMMsearch
[2024-01-25 17:34:22,057] [INFO] Running command: hmmsearch --tblout GCF_026109735.1_ASM2610973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcecc038-9677-4735-83d1-18731a761b11/dqc_reference/reference_markers.hmm GCF_026109735.1_ASM2610973v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:22,344] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:22,346] [INFO] Found 6/6 markers.
[2024-01-25 17:34:22,373] [INFO] Query marker FASTA was written to GCF_026109735.1_ASM2610973v1_genomic.fna/markers.fasta
[2024-01-25 17:34:22,374] [INFO] Task started: Blastn
[2024-01-25 17:34:22,374] [INFO] Running command: blastn -query GCF_026109735.1_ASM2610973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcecc038-9677-4735-83d1-18731a761b11/dqc_reference/reference_markers.fasta -out GCF_026109735.1_ASM2610973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:23,049] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:23,052] [INFO] Selected 13 target genomes.
[2024-01-25 17:34:23,052] [INFO] Target genome list was writen to GCF_026109735.1_ASM2610973v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:23,057] [INFO] Task started: fastANI
[2024-01-25 17:34:23,057] [INFO] Running command: fastANI --query /var/lib/cwl/stga28df3a3-a9c4-4d56-96fd-a572c1a0985e/GCF_026109735.1_ASM2610973v1_genomic.fna.gz --refList GCF_026109735.1_ASM2610973v1_genomic.fna/target_genomes.txt --output GCF_026109735.1_ASM2610973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:32,250] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:32,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcecc038-9677-4735-83d1-18731a761b11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:32,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcecc038-9677-4735-83d1-18731a761b11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:32,258] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:34:32,258] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:34:32,258] [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
Salinimicrobium oceani	strain=J15B91	GCA_012037645.1	2722702	2722702	type	True	79.9445	474	1169	95	below_threshold
Salinimicrobium terrae	strain=DSM 17865	GCA_000424665.1	470866	470866	type	True	79.6542	582	1169	95	below_threshold
Salinimicrobium sediminis	strain=CGMCC 1.12641	GCA_900215295.1	1343891	1343891	type	True	79.5621	489	1169	95	below_threshold
Salinimicrobium xinjiangense	strain=DSM 19287	GCA_000423585.1	438596	438596	type	True	79.3303	467	1169	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	78.7238	327	1169	95	below_threshold
Salinimicrobium catena	strain=CGMCC 1.6101	GCA_900102915.1	390640	390640	type	True	78.6233	354	1169	95	below_threshold
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	77.6456	124	1169	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	77.5478	121	1169	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_001752425.1	435906	435906	type	True	77.5441	123	1169	95	below_threshold
Sinomicrobium kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	77.1065	63	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:32,259] [INFO] DFAST Taxonomy check result was written to GCF_026109735.1_ASM2610973v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:32,260] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:32,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:32,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcecc038-9677-4735-83d1-18731a761b11/dqc_reference/checkm_data
[2024-01-25 17:34:32,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:32,296] [INFO] Task started: CheckM
[2024-01-25 17:34:32,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026109735.1_ASM2610973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026109735.1_ASM2610973v1_genomic.fna/checkm_input GCF_026109735.1_ASM2610973v1_genomic.fna/checkm_result
[2024-01-25 17:35:12,393] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:12,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:12,411] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:12,411] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:12,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026109735.1_ASM2610973v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:12,412] [INFO] Task started: Blastn
[2024-01-25 17:35:12,412] [INFO] Running command: blastn -query GCF_026109735.1_ASM2610973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcecc038-9677-4735-83d1-18731a761b11/dqc_reference/reference_markers_gtdb.fasta -out GCF_026109735.1_ASM2610973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:13,379] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:13,383] [INFO] Selected 10 target genomes.
[2024-01-25 17:35:13,383] [INFO] Target genome list was writen to GCF_026109735.1_ASM2610973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:13,389] [INFO] Task started: fastANI
[2024-01-25 17:35:13,389] [INFO] Running command: fastANI --query /var/lib/cwl/stga28df3a3-a9c4-4d56-96fd-a572c1a0985e/GCF_026109735.1_ASM2610973v1_genomic.fna.gz --refList GCF_026109735.1_ASM2610973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026109735.1_ASM2610973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:21,060] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:21,069] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:35:21,069] [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_000424665.1	s__Salinimicrobium terrae	79.6517	584	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215295.1	s__Salinimicrobium sediminis	79.562	489	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012038135.1	s__Salinimicrobium sp012038135	79.5488	491	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423585.1	s__Salinimicrobium xinjiangense	79.325	468	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651535.1	s__Salinimicrobium marinum	78.7238	327	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102915.1	s__Salinimicrobium catena	78.619	355	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002900095.1	s__Salegentibacter mishustinae	77.7478	136	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_900168265.1	s__Salegentibacter salarius	77.6392	125	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_004362395.1	s__Salegentibacter sp004362395	76.9233	131	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649715.1	s__Aequorivita sp016649715	76.6045	51	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:21,071] [INFO] GTDB search result was written to GCF_026109735.1_ASM2610973v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:21,071] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:21,074] [INFO] DFAST_QC result json was written to GCF_026109735.1_ASM2610973v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:21,074] [INFO] DFAST_QC completed!
[2024-01-25 17:35:21,074] [INFO] Total running time: 0h1m14s