[2024-01-24 11:05:25,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,463] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ea9fe1e-c71a-4c3b-bfbf-e59f6fe245a8/dqc_reference
[2024-01-24 11:05:26,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,808] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,808] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a430cea-8dd8-4709-8248-e5afa87f9fcc/GCF_014836595.1_ASM1483659v1_genomic.fna.gz | prodigal -d GCF_014836595.1_ASM1483659v1_genomic.fna/cds.fna -a GCF_014836595.1_ASM1483659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:34,467] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:34,468] [INFO] Task started: HMMsearch
[2024-01-24 11:05:34,468] [INFO] Running command: hmmsearch --tblout GCF_014836595.1_ASM1483659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ea9fe1e-c71a-4c3b-bfbf-e59f6fe245a8/dqc_reference/reference_markers.hmm GCF_014836595.1_ASM1483659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:34,748] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:34,750] [INFO] Found 6/6 markers.
[2024-01-24 11:05:34,790] [INFO] Query marker FASTA was written to GCF_014836595.1_ASM1483659v1_genomic.fna/markers.fasta
[2024-01-24 11:05:34,790] [INFO] Task started: Blastn
[2024-01-24 11:05:34,791] [INFO] Running command: blastn -query GCF_014836595.1_ASM1483659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ea9fe1e-c71a-4c3b-bfbf-e59f6fe245a8/dqc_reference/reference_markers.fasta -out GCF_014836595.1_ASM1483659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:35,389] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:35,393] [INFO] Selected 18 target genomes.
[2024-01-24 11:05:35,393] [INFO] Target genome list was writen to GCF_014836595.1_ASM1483659v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:35,401] [INFO] Task started: fastANI
[2024-01-24 11:05:35,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a430cea-8dd8-4709-8248-e5afa87f9fcc/GCF_014836595.1_ASM1483659v1_genomic.fna.gz --refList GCF_014836595.1_ASM1483659v1_genomic.fna/target_genomes.txt --output GCF_014836595.1_ASM1483659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:47,607] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:47,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ea9fe1e-c71a-4c3b-bfbf-e59f6fe245a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:47,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ea9fe1e-c71a-4c3b-bfbf-e59f6fe245a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:47,627] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:47,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:47,628] [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 faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	100.0	1320	1321	95	conclusive
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	79.3567	373	1321	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	79.3095	368	1321	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	79.2661	392	1321	95	below_threshold
Psychrobacillus psychrotolerans	strain=DSM 11706	GCA_900115805.1	126156	126156	type	True	79.1641	359	1321	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	79.1441	400	1321	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	78.9665	358	1321	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	78.3908	289	1321	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	78.0168	129	1321	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	77.7156	100	1321	95	below_threshold
Lysinibacillus capsici	strain=PB300	GCA_003367505.1	2115968	2115968	type	True	77.5719	101	1321	95	below_threshold
Rossellomorea aquimaris	strain=TF12	GCA_001648555.1	189382	189382	suspected-type	True	77.0897	62	1321	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	77.056	58	1321	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.0507	51	1321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:47,629] [INFO] DFAST Taxonomy check result was written to GCF_014836595.1_ASM1483659v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:47,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:47,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:47,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ea9fe1e-c71a-4c3b-bfbf-e59f6fe245a8/dqc_reference/checkm_data
[2024-01-24 11:05:47,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:47,673] [INFO] Task started: CheckM
[2024-01-24 11:05:47,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836595.1_ASM1483659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836595.1_ASM1483659v1_genomic.fna/checkm_input GCF_014836595.1_ASM1483659v1_genomic.fna/checkm_result
[2024-01-24 11:06:16,471] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:16,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:16,501] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:16,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:16,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836595.1_ASM1483659v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:16,502] [INFO] Task started: Blastn
[2024-01-24 11:06:16,502] [INFO] Running command: blastn -query GCF_014836595.1_ASM1483659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ea9fe1e-c71a-4c3b-bfbf-e59f6fe245a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836595.1_ASM1483659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:17,290] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:17,296] [INFO] Selected 15 target genomes.
[2024-01-24 11:06:17,297] [INFO] Target genome list was writen to GCF_014836595.1_ASM1483659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:17,318] [INFO] Task started: fastANI
[2024-01-24 11:06:17,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a430cea-8dd8-4709-8248-e5afa87f9fcc/GCF_014836595.1_ASM1483659v1_genomic.fna.gz --refList GCF_014836595.1_ASM1483659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836595.1_ASM1483659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:29,010] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:29,030] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:29,031] [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_008807035.1	s__Psychrobacillus sp008807035	98.8785	1258	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	98.73	98.60	0.95	0.94	4	conclusive
GCF_012843435.1	s__Psychrobacillus sp012843435	82.8744	894	1321	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	79.3756	372	1321	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_006861795.1	s__Psychrobacillus lasiicapitis	79.307	388	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900103605.1	s__Psychrobacillus sp900103605	79.2464	348	1321	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_900111345.1	s__Psychrobacillus sp900111345	79.2307	380	1321	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	79.1699	358	1321	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	79.1627	390	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900114885.1	s__Psychrobacillus psychrodurans	79.1325	391	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	97.67	97.67	0.91	0.91	2	-
GCF_001278755.1	s__Psychrobacillus sp001278755	79.091	410	1321	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_018140925.1	s__Psychrobacillus sp018140925	79.0527	413	1321	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	78.9665	358	1321	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_003254155.1	s__Psychrobacillus insolitus	78.3947	288	1321	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_003711845.1	s__Ureibacillus halotolerans	77.4047	101	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049505.1	s__Metasolibacillus meyeri	77.0574	78	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:29,033] [INFO] GTDB search result was written to GCF_014836595.1_ASM1483659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:29,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:29,038] [INFO] DFAST_QC result json was written to GCF_014836595.1_ASM1483659v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:29,038] [INFO] DFAST_QC completed!
[2024-01-24 11:06:29,039] [INFO] Total running time: 0h1m4s