[2024-01-24 11:51:06,667] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,670] [INFO] DQC Reference Directory: /var/lib/cwl/stga53a0244-83ca-4e21-9e20-5cca65b987b1/dqc_reference
[2024-01-24 11:51:07,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:07,943] [INFO] Task started: Prodigal
[2024-01-24 11:51:07,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bad17e1-a8c6-4890-afcf-6ea46357e2f4/GCF_014642405.1_ASM1464240v1_genomic.fna.gz | prodigal -d GCF_014642405.1_ASM1464240v1_genomic.fna/cds.fna -a GCF_014642405.1_ASM1464240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:16,521] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:16,522] [INFO] Task started: HMMsearch
[2024-01-24 11:51:16,522] [INFO] Running command: hmmsearch --tblout GCF_014642405.1_ASM1464240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga53a0244-83ca-4e21-9e20-5cca65b987b1/dqc_reference/reference_markers.hmm GCF_014642405.1_ASM1464240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:16,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:16,859] [INFO] Found 6/6 markers.
[2024-01-24 11:51:16,896] [INFO] Query marker FASTA was written to GCF_014642405.1_ASM1464240v1_genomic.fna/markers.fasta
[2024-01-24 11:51:16,897] [INFO] Task started: Blastn
[2024-01-24 11:51:16,897] [INFO] Running command: blastn -query GCF_014642405.1_ASM1464240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga53a0244-83ca-4e21-9e20-5cca65b987b1/dqc_reference/reference_markers.fasta -out GCF_014642405.1_ASM1464240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:17,486] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:17,508] [INFO] Selected 20 target genomes.
[2024-01-24 11:51:17,508] [INFO] Target genome list was writen to GCF_014642405.1_ASM1464240v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:17,569] [INFO] Task started: fastANI
[2024-01-24 11:51:17,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bad17e1-a8c6-4890-afcf-6ea46357e2f4/GCF_014642405.1_ASM1464240v1_genomic.fna.gz --refList GCF_014642405.1_ASM1464240v1_genomic.fna/target_genomes.txt --output GCF_014642405.1_ASM1464240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:32,259] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:32,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga53a0244-83ca-4e21-9e20-5cca65b987b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:32,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga53a0244-83ca-4e21-9e20-5cca65b987b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:32,274] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:32,274] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:32,275] [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
Pontibacillus salipaludis	strain=CGMCC 1.15353	GCA_014642405.1	1697394	1697394	type	True	100.0	1361	1363	95	conclusive
Pontibacillus chungwhensis	strain=BH030062	GCA_000770675.1	265426	265426	type	True	90.6958	1158	1363	95	below_threshold
Pontibacillus marinus	strain=DSM 16465	GCA_000425225.1	273164	273164	type	True	77.6809	246	1363	95	below_threshold
Pontibacillus litoralis	strain=JSM 072002	GCA_000775615.1	516703	516703	type	True	77.6696	105	1363	95	below_threshold
Pontibacillus marinus	strain=BH030004	GCA_000775605.1	273164	273164	type	True	77.5827	234	1363	95	below_threshold
Halobacillus andaensis	strain=CGMCC 1.12153	GCA_014636475.1	1176239	1176239	type	True	77.511	74	1363	95	below_threshold
Halobacillus kuroshimensis	strain=DSM 18393	GCA_000425705.1	302481	302481	type	True	77.445	65	1363	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	77.4296	53	1363	95	below_threshold
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	77.3139	71	1363	95	below_threshold
Salinibacillus xinjiangensis	strain=J4	GCA_009649735.1	1229268	1229268	type	True	77.2407	52	1363	95	below_threshold
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	77.0066	57	1363	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:32,276] [INFO] DFAST Taxonomy check result was written to GCF_014642405.1_ASM1464240v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:32,277] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:32,277] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:32,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga53a0244-83ca-4e21-9e20-5cca65b987b1/dqc_reference/checkm_data
[2024-01-24 11:51:32,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:32,317] [INFO] Task started: CheckM
[2024-01-24 11:51:32,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642405.1_ASM1464240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642405.1_ASM1464240v1_genomic.fna/checkm_input GCF_014642405.1_ASM1464240v1_genomic.fna/checkm_result
[2024-01-24 11:52:04,210] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:04,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:04,234] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:04,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:04,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642405.1_ASM1464240v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:04,235] [INFO] Task started: Blastn
[2024-01-24 11:52:04,235] [INFO] Running command: blastn -query GCF_014642405.1_ASM1464240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga53a0244-83ca-4e21-9e20-5cca65b987b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642405.1_ASM1464240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:05,010] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:05,014] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:05,015] [INFO] Target genome list was writen to GCF_014642405.1_ASM1464240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:05,030] [INFO] Task started: fastANI
[2024-01-24 11:52:05,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bad17e1-a8c6-4890-afcf-6ea46357e2f4/GCF_014642405.1_ASM1464240v1_genomic.fna.gz --refList GCF_014642405.1_ASM1464240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642405.1_ASM1464240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:17,776] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:17,787] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:17,788] [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_014642405.1	s__Pontibacillus salipaludis	100.0	1361	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000770675.1	s__Pontibacillus chungwhensis	90.6958	1158	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000770635.1	s__Pontibacillus yanchengensis	77.8173	212	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858175.1	s__Pontibacillus sp009858175	77.7941	232	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856295.1	s__Pontibacillus yanchengensis_A	77.7911	222	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	99.50	99.50	0.96	0.96	2	-
GCA_004078665.1	s__Halobacillus sp004078665	77.7694	69	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775615.1	s__Pontibacillus litoralis	77.6802	106	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425225.1	s__Pontibacillus marinus	77.6438	246	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014636475.1	s__Halobacillus_A andaensis	77.511	74	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425705.1	s__Halobacillus kuroshimensis	77.445	65	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.79	98.79	0.92	0.92	2	-
GCF_009649735.1	s__Salinibacillus xinjiangensis	77.2407	52	1363	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:17,789] [INFO] GTDB search result was written to GCF_014642405.1_ASM1464240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:17,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:17,793] [INFO] DFAST_QC result json was written to GCF_014642405.1_ASM1464240v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:17,793] [INFO] DFAST_QC completed!
[2024-01-24 11:52:17,793] [INFO] Total running time: 0h1m11s