[2024-01-24 13:27:59,970] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:59,972] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:59,973] [INFO] DQC Reference Directory: /var/lib/cwl/stgd45964e3-621c-40b1-866a-4634af8ca500/dqc_reference
[2024-01-24 13:28:01,210] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:01,213] [INFO] Task started: Prodigal
[2024-01-24 13:28:01,214] [INFO] Running command: gunzip -c /var/lib/cwl/stga9424422-87ba-4001-94e6-c41b5b08c052/GCF_006861795.1_ASM686179v1_genomic.fna.gz | prodigal -d GCF_006861795.1_ASM686179v1_genomic.fna/cds.fna -a GCF_006861795.1_ASM686179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:10,852] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:10,853] [INFO] Task started: HMMsearch
[2024-01-24 13:28:10,853] [INFO] Running command: hmmsearch --tblout GCF_006861795.1_ASM686179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd45964e3-621c-40b1-866a-4634af8ca500/dqc_reference/reference_markers.hmm GCF_006861795.1_ASM686179v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:11,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:11,137] [INFO] Found 6/6 markers.
[2024-01-24 13:28:11,182] [INFO] Query marker FASTA was written to GCF_006861795.1_ASM686179v1_genomic.fna/markers.fasta
[2024-01-24 13:28:11,182] [INFO] Task started: Blastn
[2024-01-24 13:28:11,182] [INFO] Running command: blastn -query GCF_006861795.1_ASM686179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd45964e3-621c-40b1-866a-4634af8ca500/dqc_reference/reference_markers.fasta -out GCF_006861795.1_ASM686179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:11,806] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:11,810] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:11,810] [INFO] Target genome list was writen to GCF_006861795.1_ASM686179v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:11,819] [INFO] Task started: fastANI
[2024-01-24 13:28:11,820] [INFO] Running command: fastANI --query /var/lib/cwl/stga9424422-87ba-4001-94e6-c41b5b08c052/GCF_006861795.1_ASM686179v1_genomic.fna.gz --refList GCF_006861795.1_ASM686179v1_genomic.fna/target_genomes.txt --output GCF_006861795.1_ASM686179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:22,545] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:22,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd45964e3-621c-40b1-866a-4634af8ca500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:22,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd45964e3-621c-40b1-866a-4634af8ca500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:22,555] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:22,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:22,555] [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
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	100.0	1482	1482	95	conclusive
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	99.9885	1474	1482	95	conclusive
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	85.7526	972	1482	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	80.648	641	1482	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	79.7464	573	1482	95	below_threshold
Psychrobacillus psychrotolerans	strain=DSM 11706	GCA_900115805.1	126156	126156	type	True	79.4636	483	1482	95	below_threshold
Paenisporosarcina antarctica	strain=CGMCC 1.6503	GCA_004367585.1	417367	417367	type	True	77.6526	158	1482	95	below_threshold
Rossellomorea arthrocnemi	strain=EAR8	GCA_904424705.1	2769542	2769542	type	True	77.1298	51	1482	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.6423	78	1482	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.4604	81	1482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:22,557] [INFO] DFAST Taxonomy check result was written to GCF_006861795.1_ASM686179v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:22,557] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:22,557] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:22,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd45964e3-621c-40b1-866a-4634af8ca500/dqc_reference/checkm_data
[2024-01-24 13:28:22,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:22,601] [INFO] Task started: CheckM
[2024-01-24 13:28:22,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006861795.1_ASM686179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006861795.1_ASM686179v1_genomic.fna/checkm_input GCF_006861795.1_ASM686179v1_genomic.fna/checkm_result
[2024-01-24 13:28:55,007] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:55,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:55,029] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:55,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:55,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006861795.1_ASM686179v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:55,030] [INFO] Task started: Blastn
[2024-01-24 13:28:55,030] [INFO] Running command: blastn -query GCF_006861795.1_ASM686179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd45964e3-621c-40b1-866a-4634af8ca500/dqc_reference/reference_markers_gtdb.fasta -out GCF_006861795.1_ASM686179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:55,863] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:55,871] [INFO] Selected 7 target genomes.
[2024-01-24 13:28:55,871] [INFO] Target genome list was writen to GCF_006861795.1_ASM686179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:55,900] [INFO] Task started: fastANI
[2024-01-24 13:28:55,900] [INFO] Running command: fastANI --query /var/lib/cwl/stga9424422-87ba-4001-94e6-c41b5b08c052/GCF_006861795.1_ASM686179v1_genomic.fna.gz --refList GCF_006861795.1_ASM686179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006861795.1_ASM686179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:04,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:04,062] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:04,063] [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_006861795.1	s__Psychrobacillus lasiicapitis	100.0	1482	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_900111345.1	s__Psychrobacillus sp900111345	86.2529	1045	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861775.1	s__Psychrobacillus soli	85.7872	969	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007676755.1	s__Psychrobacillus sp007676755	81.9041	804	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861825.1	s__Psychrobacillus vulpis	80.6499	639	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973485.1	s__Psychrobacillus glaciei	79.7444	572	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103605.1	s__Psychrobacillus sp900103605	79.6709	493	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:04,064] [INFO] GTDB search result was written to GCF_006861795.1_ASM686179v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:04,065] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:04,068] [INFO] DFAST_QC result json was written to GCF_006861795.1_ASM686179v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:04,068] [INFO] DFAST_QC completed!
[2024-01-24 13:29:04,068] [INFO] Total running time: 0h1m4s