[2024-01-24 13:13:12,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg1da40983-b5f7-4df0-9e01-4b4f93c83170/dqc_reference
[2024-01-24 13:13:14,003] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:14,004] [INFO] Task started: Prodigal
[2024-01-24 13:13:14,004] [INFO] Running command: gunzip -c /var/lib/cwl/stg01b4abb5-92e2-4832-b622-a6f363ace49c/GCF_003121925.1_ASM312192v1_genomic.fna.gz | prodigal -d GCF_003121925.1_ASM312192v1_genomic.fna/cds.fna -a GCF_003121925.1_ASM312192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:19,315] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:19,315] [INFO] Task started: HMMsearch
[2024-01-24 13:13:19,315] [INFO] Running command: hmmsearch --tblout GCF_003121925.1_ASM312192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1da40983-b5f7-4df0-9e01-4b4f93c83170/dqc_reference/reference_markers.hmm GCF_003121925.1_ASM312192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:19,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:19,579] [INFO] Found 6/6 markers.
[2024-01-24 13:13:19,601] [INFO] Query marker FASTA was written to GCF_003121925.1_ASM312192v1_genomic.fna/markers.fasta
[2024-01-24 13:13:19,601] [INFO] Task started: Blastn
[2024-01-24 13:13:19,601] [INFO] Running command: blastn -query GCF_003121925.1_ASM312192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1da40983-b5f7-4df0-9e01-4b4f93c83170/dqc_reference/reference_markers.fasta -out GCF_003121925.1_ASM312192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:20,274] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:20,277] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:20,278] [INFO] Target genome list was writen to GCF_003121925.1_ASM312192v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:21,059] [INFO] Task started: fastANI
[2024-01-24 13:13:21,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg01b4abb5-92e2-4832-b622-a6f363ace49c/GCF_003121925.1_ASM312192v1_genomic.fna.gz --refList GCF_003121925.1_ASM312192v1_genomic.fna/target_genomes.txt --output GCF_003121925.1_ASM312192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:32,398] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:32,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1da40983-b5f7-4df0-9e01-4b4f93c83170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:32,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1da40983-b5f7-4df0-9e01-4b4f93c83170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:32,406] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:32,406] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:32,406] [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
Ignatzschineria indica	strain=KCTC 22643	GCA_003121925.1	472583	472583	type	True	100.0	824	825	95	conclusive
Ignatzschineria indica	strain=KCTC 22643	GCA_014652015.1	472583	472583	type	True	99.9832	817	825	95	conclusive
Ignatzschineria cameli	strain=UAE-HKU57	GCA_003121895.1	2182793	2182793	type	True	85.6845	678	825	95	below_threshold
Ignatzschineria ureiclastica	strain=KCTC 22644	GCA_003121845.1	472582	472582	type	True	78.6304	243	825	95	below_threshold
Ignatzschineria ureiclastica	strain=KCTC 22644	GCA_014652035.1	472582	472582	type	True	78.504	242	825	95	below_threshold
Ignatzschineria larvae	strain=DSM 13226	GCA_000510805.1	112009	112009	type	True	78.498	226	825	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:32,408] [INFO] DFAST Taxonomy check result was written to GCF_003121925.1_ASM312192v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:32,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:32,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:32,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1da40983-b5f7-4df0-9e01-4b4f93c83170/dqc_reference/checkm_data
[2024-01-24 13:13:32,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:32,438] [INFO] Task started: CheckM
[2024-01-24 13:13:32,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003121925.1_ASM312192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003121925.1_ASM312192v1_genomic.fna/checkm_input GCF_003121925.1_ASM312192v1_genomic.fna/checkm_result
[2024-01-24 13:13:56,087] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:56,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:56,105] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:56,105] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:56,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003121925.1_ASM312192v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:56,106] [INFO] Task started: Blastn
[2024-01-24 13:13:56,106] [INFO] Running command: blastn -query GCF_003121925.1_ASM312192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1da40983-b5f7-4df0-9e01-4b4f93c83170/dqc_reference/reference_markers_gtdb.fasta -out GCF_003121925.1_ASM312192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:57,221] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:57,225] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:57,225] [INFO] Target genome list was writen to GCF_003121925.1_ASM312192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:57,473] [INFO] Task started: fastANI
[2024-01-24 13:13:57,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg01b4abb5-92e2-4832-b622-a6f363ace49c/GCF_003121925.1_ASM312192v1_genomic.fna.gz --refList GCF_003121925.1_ASM312192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003121925.1_ASM312192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:05,086] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:05,100] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:05,101] [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_003121925.1	s__Ignatzschineria indica	100.0	824	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002252045.1	s__Ignatzschineria sp002252045	94.5058	722	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121895.1	s__Ignatzschineria cameli	85.681	678	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	99.12	98.86	0.95	0.93	5	-
GCF_003121845.1	s__Ignatzschineria ureiclastica	78.5988	243	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000510805.1	s__Ignatzschineria larvae	78.4986	226	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113305.1	s__Ignatzschineria merdigallinarum	78.2786	195	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513365.1	s__JAAZCI01 sp012513365	76.736	66	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__JAAZCI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:05,102] [INFO] GTDB search result was written to GCF_003121925.1_ASM312192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:05,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:05,106] [INFO] DFAST_QC result json was written to GCF_003121925.1_ASM312192v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:05,106] [INFO] DFAST_QC completed!
[2024-01-24 13:14:05,106] [INFO] Total running time: 0h0m52s