[2024-01-24 14:06:44,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:44,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:44,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg170393f7-510d-450f-93ea-8fd74098f9ff/dqc_reference
[2024-01-24 14:06:45,609] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:45,610] [INFO] Task started: Prodigal
[2024-01-24 14:06:45,610] [INFO] Running command: gunzip -c /var/lib/cwl/stgafe621ec-afe9-4f98-9129-bb7b8208c9d9/GCF_003253565.1_ASM325356v1_genomic.fna.gz | prodigal -d GCF_003253565.1_ASM325356v1_genomic.fna/cds.fna -a GCF_003253565.1_ASM325356v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:06,939] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:06,940] [INFO] Task started: HMMsearch
[2024-01-24 14:07:06,940] [INFO] Running command: hmmsearch --tblout GCF_003253565.1_ASM325356v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg170393f7-510d-450f-93ea-8fd74098f9ff/dqc_reference/reference_markers.hmm GCF_003253565.1_ASM325356v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:07,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:07,408] [INFO] Found 6/6 markers.
[2024-01-24 14:07:07,477] [INFO] Query marker FASTA was written to GCF_003253565.1_ASM325356v1_genomic.fna/markers.fasta
[2024-01-24 14:07:07,478] [INFO] Task started: Blastn
[2024-01-24 14:07:07,478] [INFO] Running command: blastn -query GCF_003253565.1_ASM325356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg170393f7-510d-450f-93ea-8fd74098f9ff/dqc_reference/reference_markers.fasta -out GCF_003253565.1_ASM325356v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:08,071] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:08,075] [INFO] Selected 16 target genomes.
[2024-01-24 14:07:08,075] [INFO] Target genome list was writen to GCF_003253565.1_ASM325356v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:08,093] [INFO] Task started: fastANI
[2024-01-24 14:07:08,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe621ec-afe9-4f98-9129-bb7b8208c9d9/GCF_003253565.1_ASM325356v1_genomic.fna.gz --refList GCF_003253565.1_ASM325356v1_genomic.fna/target_genomes.txt --output GCF_003253565.1_ASM325356v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:24,050] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:24,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg170393f7-510d-450f-93ea-8fd74098f9ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:24,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg170393f7-510d-450f-93ea-8fd74098f9ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:24,064] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:24,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:24,064] [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
Thermosporothrix hazakensis	strain=ATCC BAA-1881	GCA_003253565.1	644383	644383	type	True	100.0	2377	2380	95	conclusive
Thermosporothrix hazakensis	strain=SK20-1	GCA_005402645.1	644383	644383	type	True	99.9966	2377	2380	95	conclusive
Ktedonospora formicarum	strain=SOSP1-1	GCA_016587355.1	2778364	2778364	type	True	76.6373	140	2380	95	below_threshold
Ktedonobacter racemifer	strain=SOSP1-21	GCA_000178855.1	363277	363277	type	True	76.4434	175	2380	95	below_threshold
Ktedonobacter robiniae	strain=SOSP1-30	GCA_016587375.1	2778365	2778365	type	True	76.3154	179	2380	95	below_threshold
Dictyobacter alpinus	strain=Uno16	GCA_003967575.1	2014873	2014873	type	True	76.1932	95	2380	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	76.143	109	2380	95	below_threshold
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	75.846	101	2380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:24,066] [INFO] DFAST Taxonomy check result was written to GCF_003253565.1_ASM325356v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:24,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:24,067] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:24,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg170393f7-510d-450f-93ea-8fd74098f9ff/dqc_reference/checkm_data
[2024-01-24 14:07:24,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:24,135] [INFO] Task started: CheckM
[2024-01-24 14:07:24,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003253565.1_ASM325356v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003253565.1_ASM325356v1_genomic.fna/checkm_input GCF_003253565.1_ASM325356v1_genomic.fna/checkm_result
[2024-01-24 14:08:28,530] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:28,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:28,556] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:28,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:28,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003253565.1_ASM325356v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:28,558] [INFO] Task started: Blastn
[2024-01-24 14:08:28,558] [INFO] Running command: blastn -query GCF_003253565.1_ASM325356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg170393f7-510d-450f-93ea-8fd74098f9ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_003253565.1_ASM325356v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:29,370] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:29,374] [INFO] Selected 26 target genomes.
[2024-01-24 14:08:29,374] [INFO] Target genome list was writen to GCF_003253565.1_ASM325356v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:29,397] [INFO] Task started: fastANI
[2024-01-24 14:08:29,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe621ec-afe9-4f98-9129-bb7b8208c9d9/GCF_003253565.1_ASM325356v1_genomic.fna.gz --refList GCF_003253565.1_ASM325356v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003253565.1_ASM325356v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:57,259] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:57,276] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:57,276] [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_003253565.1	s__Thermosporothrix hazakensis	100.0	2377	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermosporothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016587355.1	s__Ktedonobacter sp016587355	76.6387	141	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879655.1	s__CF-154 sp005879655	76.5144	80	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CF-154	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587415.1	s__Ktedonobacter sp016587415	76.5139	166	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178855.1	s__Ktedonobacter racemifer	76.4452	174	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015099395.1	s__Dictyobacter sp015099395	76.4143	91	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014896635.1	s__Bu33 sp014896635	76.3763	73	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Bu33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587375.1	s__Ktedonobacter sp016587375	76.306	179	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587435.1	s__Dictyobacter sp016587435	76.3021	103	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967515.1	s__Dictyobacter aurantiacus	76.143	109	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812455.1	s__CADDZH01 sp902812455	75.6242	62	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810755.1	s__CADDYT01 sp902810755	75.611	84	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDYT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001748285.1	s__Thermogemmatispora onikobensis	75.5044	63	2380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:57,278] [INFO] GTDB search result was written to GCF_003253565.1_ASM325356v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:57,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:57,282] [INFO] DFAST_QC result json was written to GCF_003253565.1_ASM325356v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:57,282] [INFO] DFAST_QC completed!
[2024-01-24 14:08:57,282] [INFO] Total running time: 0h2m13s