[2024-01-24 12:30:48,909] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:48,911] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:48,911] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f7aba5c-3733-42f3-ad65-5121c6c70f82/dqc_reference
[2024-01-24 12:30:50,259] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:50,260] [INFO] Task started: Prodigal
[2024-01-24 12:30:50,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b8647da-cffb-4bcc-ac0d-456929d90eab/GCF_000016545.1_ASM1654v1_genomic.fna.gz | prodigal -d GCF_000016545.1_ASM1654v1_genomic.fna/cds.fna -a GCF_000016545.1_ASM1654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:56,843] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:56,843] [INFO] Task started: HMMsearch
[2024-01-24 12:30:56,843] [INFO] Running command: hmmsearch --tblout GCF_000016545.1_ASM1654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f7aba5c-3733-42f3-ad65-5121c6c70f82/dqc_reference/reference_markers.hmm GCF_000016545.1_ASM1654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:57,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:57,124] [INFO] Found 6/6 markers.
[2024-01-24 12:30:57,156] [INFO] Query marker FASTA was written to GCF_000016545.1_ASM1654v1_genomic.fna/markers.fasta
[2024-01-24 12:30:57,157] [INFO] Task started: Blastn
[2024-01-24 12:30:57,157] [INFO] Running command: blastn -query GCF_000016545.1_ASM1654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f7aba5c-3733-42f3-ad65-5121c6c70f82/dqc_reference/reference_markers.fasta -out GCF_000016545.1_ASM1654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:57,719] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:57,722] [INFO] Selected 9 target genomes.
[2024-01-24 12:30:57,722] [INFO] Target genome list was writen to GCF_000016545.1_ASM1654v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:57,726] [INFO] Task started: fastANI
[2024-01-24 12:30:57,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b8647da-cffb-4bcc-ac0d-456929d90eab/GCF_000016545.1_ASM1654v1_genomic.fna.gz --refList GCF_000016545.1_ASM1654v1_genomic.fna/target_genomes.txt --output GCF_000016545.1_ASM1654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:05,243] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:05,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f7aba5c-3733-42f3-ad65-5121c6c70f82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:05,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f7aba5c-3733-42f3-ad65-5121c6c70f82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:05,253] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:05,253] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:31:05,253] [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
Caldicellulosiruptor saccharolyticus	strain=DSM 8903	GCA_000016545.1	44001	44001	type	True	100.0	990	990	95	inconclusive
Caldicellulosiruptor changbaiensis	strain=CBS-Z	GCA_003999255.1	1222016	1222016	type	True	95.2159	766	990	95	inconclusive
Caldicellulosiruptor naganoensis	strain=NA10	GCA_000955735.1	29324	29324	type	True	89.8163	638	990	95	below_threshold
Caldicellulosiruptor bescii	strain=DSM 6725	GCA_000022325.1	31899	31899	type	True	84.6176	553	990	95	below_threshold
Caldicellulosiruptor hydrothermalis	strain=108	GCA_000166355.1	413888	413888	type	True	84.1096	524	990	95	below_threshold
Caldicellulosiruptor kronotskyensis	strain=2002	GCA_000166775.1	413889	413889	type	True	83.9384	538	990	95	below_threshold
Caldicellulosiruptor acetigenus	strain=DSM 7040	GCA_000421725.1	301953	301953	type	True	82.4948	490	990	95	below_threshold
Caldicellulosiruptor obsidiansis	strain=OB47	GCA_000145215.1	717609	717609	type	True	82.2628	496	990	95	below_threshold
Caldicellulosiruptor owensensis	strain=OL	GCA_000166335.1	55205	55205	type	True	81.7843	440	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:05,255] [INFO] DFAST Taxonomy check result was written to GCF_000016545.1_ASM1654v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:05,256] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:05,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:05,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f7aba5c-3733-42f3-ad65-5121c6c70f82/dqc_reference/checkm_data
[2024-01-24 12:31:05,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:05,294] [INFO] Task started: CheckM
[2024-01-24 12:31:05,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000016545.1_ASM1654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000016545.1_ASM1654v1_genomic.fna/checkm_input GCF_000016545.1_ASM1654v1_genomic.fna/checkm_result
[2024-01-24 12:31:32,575] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:32,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:32,602] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:32,603] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:32,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000016545.1_ASM1654v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:32,603] [INFO] Task started: Blastn
[2024-01-24 12:31:32,603] [INFO] Running command: blastn -query GCF_000016545.1_ASM1654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f7aba5c-3733-42f3-ad65-5121c6c70f82/dqc_reference/reference_markers_gtdb.fasta -out GCF_000016545.1_ASM1654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:33,488] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:33,493] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:33,493] [INFO] Target genome list was writen to GCF_000016545.1_ASM1654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:33,502] [INFO] Task started: fastANI
[2024-01-24 12:31:33,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b8647da-cffb-4bcc-ac0d-456929d90eab/GCF_000016545.1_ASM1654v1_genomic.fna.gz --refList GCF_000016545.1_ASM1654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000016545.1_ASM1654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:42,251] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:42,269] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:42,269] [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_000016545.1	s__Caldicellulosiruptor saccharolyticus	100.0	990	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	96.00	95.22	0.88	0.80	3	conclusive
GCF_000955735.1	s__Caldicellulosiruptor naganoensis	89.8187	637	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000955725.1	s__Caldicellulosiruptor danielii	84.7795	575	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022325.1	s__Caldicellulosiruptor bescii	84.5916	552	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	96.1491	99.98	99.96	0.99	0.98	23	-
GCF_017347585.1	s__Caldicellulosiruptor sp017347585	84.1543	514	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166355.1	s__Caldicellulosiruptor hydrothermalis	84.0923	525	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166775.1	s__Caldicellulosiruptor kronotskyensis	83.9584	538	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	96.1491	N/A	N/A	N/A	N/A	1	-
GCF_000955745.1	s__Caldicellulosiruptor morganii	83.3448	554	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421725.1	s__Caldicellulosiruptor acetigenus	82.5224	489	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	97.40	97.22	0.81	0.79	3	-
GCF_000145215.1	s__Caldicellulosiruptor obsidiansis	82.2404	492	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166335.1	s__Caldicellulosiruptor owensensis	81.744	439	990	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	95.74	95.71	0.88	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:42,271] [INFO] GTDB search result was written to GCF_000016545.1_ASM1654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:42,272] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:42,276] [INFO] DFAST_QC result json was written to GCF_000016545.1_ASM1654v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:42,276] [INFO] DFAST_QC completed!
[2024-01-24 12:31:42,277] [INFO] Total running time: 0h0m53s