[2024-01-24 13:18:41,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,556] [INFO] DQC Reference Directory: /var/lib/cwl/stgc41f7abc-92f4-4b8a-8123-57f00ec369c6/dqc_reference
[2024-01-24 13:18:42,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,928] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dce393d-5e92-497c-843a-51d6bfe47cbc/GCF_008974285.1_ASM897428v1_genomic.fna.gz | prodigal -d GCF_008974285.1_ASM897428v1_genomic.fna/cds.fna -a GCF_008974285.1_ASM897428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:58,763] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:58,763] [INFO] Task started: HMMsearch
[2024-01-24 13:18:58,763] [INFO] Running command: hmmsearch --tblout GCF_008974285.1_ASM897428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc41f7abc-92f4-4b8a-8123-57f00ec369c6/dqc_reference/reference_markers.hmm GCF_008974285.1_ASM897428v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:59,093] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:59,094] [INFO] Found 6/6 markers.
[2024-01-24 13:18:59,141] [INFO] Query marker FASTA was written to GCF_008974285.1_ASM897428v1_genomic.fna/markers.fasta
[2024-01-24 13:18:59,141] [INFO] Task started: Blastn
[2024-01-24 13:18:59,141] [INFO] Running command: blastn -query GCF_008974285.1_ASM897428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc41f7abc-92f4-4b8a-8123-57f00ec369c6/dqc_reference/reference_markers.fasta -out GCF_008974285.1_ASM897428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:59,768] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:59,771] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:59,771] [INFO] Target genome list was writen to GCF_008974285.1_ASM897428v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:59,785] [INFO] Task started: fastANI
[2024-01-24 13:18:59,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dce393d-5e92-497c-843a-51d6bfe47cbc/GCF_008974285.1_ASM897428v1_genomic.fna.gz --refList GCF_008974285.1_ASM897428v1_genomic.fna/target_genomes.txt --output GCF_008974285.1_ASM897428v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:18,053] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:18,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc41f7abc-92f4-4b8a-8123-57f00ec369c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:18,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc41f7abc-92f4-4b8a-8123-57f00ec369c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:18,062] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:18,062] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:18,063] [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
Thermogemmatispora aurantia	strain=A1-2	GCA_008974285.1	2045279	2045279	type	True	100.0	1858	1858	95	conclusive
Thermogemmatispora tikiterensis	strain=T81	GCA_003268475.1	1825093	1825093	type	True	94.3841	1735	1858	95	below_threshold
Thermogemmatispora carboxidivorans	strain=PM5	GCA_000702505.1	1382306	1382306	type	True	88.602	1661	1858	95	below_threshold
Ktedonobacter racemifer	strain=SOSP1-21	GCA_000178855.1	363277	363277	type	True	75.8588	92	1858	95	below_threshold
Ktedonosporobacter rubrisoli	strain=SCAWS-G2	GCA_004208415.1	2509675	2509675	type	True	75.8115	81	1858	95	below_threshold
Ktedonobacter robiniae	strain=SOSP1-30	GCA_016587375.1	2778365	2778365	type	True	75.7564	100	1858	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	75.733	95	1858	95	below_threshold
Reticulibacter mediterranei	strain=150040	GCA_016587455.1	2778369	2778369	type	True	75.5003	82	1858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:18,065] [INFO] DFAST Taxonomy check result was written to GCF_008974285.1_ASM897428v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:18,065] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:18,065] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:18,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc41f7abc-92f4-4b8a-8123-57f00ec369c6/dqc_reference/checkm_data
[2024-01-24 13:19:18,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:18,123] [INFO] Task started: CheckM
[2024-01-24 13:19:18,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008974285.1_ASM897428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008974285.1_ASM897428v1_genomic.fna/checkm_input GCF_008974285.1_ASM897428v1_genomic.fna/checkm_result
[2024-01-24 13:20:03,038] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:03,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:03,067] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:03,067] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:03,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008974285.1_ASM897428v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:03,068] [INFO] Task started: Blastn
[2024-01-24 13:20:03,068] [INFO] Running command: blastn -query GCF_008974285.1_ASM897428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc41f7abc-92f4-4b8a-8123-57f00ec369c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_008974285.1_ASM897428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:03,883] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:03,886] [INFO] Selected 9 target genomes.
[2024-01-24 13:20:03,886] [INFO] Target genome list was writen to GCF_008974285.1_ASM897428v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:03,901] [INFO] Task started: fastANI
[2024-01-24 13:20:03,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dce393d-5e92-497c-843a-51d6bfe47cbc/GCF_008974285.1_ASM897428v1_genomic.fna.gz --refList GCF_008974285.1_ASM897428v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008974285.1_ASM897428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:15,827] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:15,840] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:15,840] [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_008974285.1	s__Thermogemmatispora aurantia	100.0	1858	1858	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	99.32	99.32	0.97	0.97	2	conclusive
GCF_003268475.1	s__Thermogemmatispora tikiterensis	94.3931	1734	1858	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001748285.1	s__Thermogemmatispora onikobensis	89.598	1614	1858	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702505.1	s__Thermogemmatispora carboxidivorans	88.6064	1660	1858	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014896635.1	s__Bu33 sp014896635	75.9246	79	1858	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Bu33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810755.1	s__CADDYT01 sp902810755	75.9016	133	1858	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDYT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389075.1	s__DTNP01 sp011389075	75.8797	74	1858	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__DTNP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587415.1	s__Ktedonobacter sp016587415	75.8279	103	1858	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967515.1	s__Dictyobacter aurantiacus	75.7206	96	1858	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:15,842] [INFO] GTDB search result was written to GCF_008974285.1_ASM897428v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:15,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:15,845] [INFO] DFAST_QC result json was written to GCF_008974285.1_ASM897428v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:15,845] [INFO] DFAST_QC completed!
[2024-01-24 13:20:15,845] [INFO] Total running time: 0h1m34s