[2024-01-24 13:09:28,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:28,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:28,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7f1bdeb-8701-4deb-9bd9-48ebb1ad3ffc/dqc_reference
[2024-01-24 13:09:29,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:29,955] [INFO] Task started: Prodigal
[2024-01-24 13:09:29,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg58861f7c-f5ca-438c-a0ee-e2aa48f7d1ee/GCF_003254155.1_ASM325415v1_genomic.fna.gz | prodigal -d GCF_003254155.1_ASM325415v1_genomic.fna/cds.fna -a GCF_003254155.1_ASM325415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:36,426] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:36,427] [INFO] Task started: HMMsearch
[2024-01-24 13:09:36,427] [INFO] Running command: hmmsearch --tblout GCF_003254155.1_ASM325415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7f1bdeb-8701-4deb-9bd9-48ebb1ad3ffc/dqc_reference/reference_markers.hmm GCF_003254155.1_ASM325415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:36,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:36,763] [INFO] Found 6/6 markers.
[2024-01-24 13:09:36,791] [INFO] Query marker FASTA was written to GCF_003254155.1_ASM325415v1_genomic.fna/markers.fasta
[2024-01-24 13:09:36,792] [INFO] Task started: Blastn
[2024-01-24 13:09:36,792] [INFO] Running command: blastn -query GCF_003254155.1_ASM325415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7f1bdeb-8701-4deb-9bd9-48ebb1ad3ffc/dqc_reference/reference_markers.fasta -out GCF_003254155.1_ASM325415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:37,424] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:37,428] [INFO] Selected 17 target genomes.
[2024-01-24 13:09:37,428] [INFO] Target genome list was writen to GCF_003254155.1_ASM325415v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:37,458] [INFO] Task started: fastANI
[2024-01-24 13:09:37,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg58861f7c-f5ca-438c-a0ee-e2aa48f7d1ee/GCF_003254155.1_ASM325415v1_genomic.fna.gz --refList GCF_003254155.1_ASM325415v1_genomic.fna/target_genomes.txt --output GCF_003254155.1_ASM325415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:48,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:48,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7f1bdeb-8701-4deb-9bd9-48ebb1ad3ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:48,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7f1bdeb-8701-4deb-9bd9-48ebb1ad3ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:48,097] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:48,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:48,097] [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 insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	100.0	1077	1079	95	conclusive
Psychrobacillus psychrotolerans	strain=DSM 11706	GCA_900115805.1	126156	126156	type	True	79.6919	406	1079	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	79.6827	455	1079	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	79.5946	446	1079	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	79.563	439	1079	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	79.4109	427	1079	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	79.3193	438	1079	95	below_threshold
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	78.6355	283	1079	95	below_threshold
Paenisporosarcina cavernae	strain=K2R23-3	GCA_003595195.1	2320858	2320858	type	True	77.7151	94	1079	95	below_threshold
Rummeliibacillus pycnus	strain=DSM 15030	GCA_002884495.1	101070	101070	type	True	77.2593	125	1079	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.6021	53	1079	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.2006	57	1079	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.0494	58	1079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:48,099] [INFO] DFAST Taxonomy check result was written to GCF_003254155.1_ASM325415v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:48,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:48,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:48,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7f1bdeb-8701-4deb-9bd9-48ebb1ad3ffc/dqc_reference/checkm_data
[2024-01-24 13:09:48,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:48,142] [INFO] Task started: CheckM
[2024-01-24 13:09:48,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254155.1_ASM325415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254155.1_ASM325415v1_genomic.fna/checkm_input GCF_003254155.1_ASM325415v1_genomic.fna/checkm_result
[2024-01-24 13:10:14,472] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:14,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:14,499] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:14,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:14,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254155.1_ASM325415v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:14,501] [INFO] Task started: Blastn
[2024-01-24 13:10:14,501] [INFO] Running command: blastn -query GCF_003254155.1_ASM325415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7f1bdeb-8701-4deb-9bd9-48ebb1ad3ffc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254155.1_ASM325415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:15,321] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:15,325] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:15,325] [INFO] Target genome list was writen to GCF_003254155.1_ASM325415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:15,338] [INFO] Task started: fastANI
[2024-01-24 13:10:15,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg58861f7c-f5ca-438c-a0ee-e2aa48f7d1ee/GCF_003254155.1_ASM325415v1_genomic.fna.gz --refList GCF_003254155.1_ASM325415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254155.1_ASM325415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:24,838] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:24,849] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:24,849] [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_003254155.1	s__Psychrobacillus insolitus	100.0	1077	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111345.1	s__Psychrobacillus sp900111345	80.0438	460	1079	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_900115805.1	s__Psychrobacillus psychrotolerans	79.7042	405	1079	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	79.6944	456	1079	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_018140925.1	s__Psychrobacillus sp018140925	79.6869	432	1079	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	79.5981	437	1079	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	79.5946	446	1079	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_001278755.1	s__Psychrobacillus sp001278755	79.5239	433	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	97.52	97.52	0.91	0.91	2	-
GCF_007676755.1	s__Psychrobacillus sp007676755	79.2019	410	1079	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_012843435.1	s__Psychrobacillus sp012843435	78.5127	288	1079	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_002884495.1	s__Rummeliibacillus pycnus	77.2362	126	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018065935.1	s__Kurthia sp018065935	77.0239	83	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:24,851] [INFO] GTDB search result was written to GCF_003254155.1_ASM325415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:24,852] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:24,855] [INFO] DFAST_QC result json was written to GCF_003254155.1_ASM325415v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:24,856] [INFO] DFAST_QC completed!
[2024-01-24 13:10:24,856] [INFO] Total running time: 0h0m56s