[2024-01-24 13:37:25,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a3c8f96-8521-4b8a-ba4b-1fdd1b9c8e6d/dqc_reference
[2024-01-24 13:37:27,218] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,219] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,219] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a89cf7c-cc92-4e6a-8b04-7b16ec599d16/GCF_000166775.1_ASM16677v1_genomic.fna.gz | prodigal -d GCF_000166775.1_ASM16677v1_genomic.fna/cds.fna -a GCF_000166775.1_ASM16677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:32,947] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:32,947] [INFO] Task started: HMMsearch
[2024-01-24 13:37:32,947] [INFO] Running command: hmmsearch --tblout GCF_000166775.1_ASM16677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a3c8f96-8521-4b8a-ba4b-1fdd1b9c8e6d/dqc_reference/reference_markers.hmm GCF_000166775.1_ASM16677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:33,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:33,222] [INFO] Found 6/6 markers.
[2024-01-24 13:37:33,245] [INFO] Query marker FASTA was written to GCF_000166775.1_ASM16677v1_genomic.fna/markers.fasta
[2024-01-24 13:37:33,246] [INFO] Task started: Blastn
[2024-01-24 13:37:33,246] [INFO] Running command: blastn -query GCF_000166775.1_ASM16677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a3c8f96-8521-4b8a-ba4b-1fdd1b9c8e6d/dqc_reference/reference_markers.fasta -out GCF_000166775.1_ASM16677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:33,797] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:33,800] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:33,800] [INFO] Target genome list was writen to GCF_000166775.1_ASM16677v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:33,807] [INFO] Task started: fastANI
[2024-01-24 13:37:33,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a89cf7c-cc92-4e6a-8b04-7b16ec599d16/GCF_000166775.1_ASM16677v1_genomic.fna.gz --refList GCF_000166775.1_ASM16677v1_genomic.fna/target_genomes.txt --output GCF_000166775.1_ASM16677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:38,937] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:38,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a3c8f96-8521-4b8a-ba4b-1fdd1b9c8e6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:38,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a3c8f96-8521-4b8a-ba4b-1fdd1b9c8e6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:38,943] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:38,943] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:37:38,943] [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 kronotskyensis	strain=2002	GCA_000166775.1	413889	413889	type	True	100.0	947	947	95	inconclusive
Caldicellulosiruptor bescii	strain=DSM 6725	GCA_000022325.1	31899	31899	type	True	96.1507	770	947	95	inconclusive
Caldicellulosiruptor hydrothermalis	strain=108	GCA_000166355.1	413888	413888	type	True	92.5178	721	947	95	below_threshold
Caldicellulosiruptor diazotrophicus	strain=YA01	GCA_017347585.1	2806205	2806205	type	True	91.1291	725	947	95	below_threshold
Caldicellulosiruptor acetigenus	strain=DSM 7040	GCA_000421725.1	301953	301953	type	True	90.6479	682	947	95	below_threshold
Caldicellulosiruptor obsidiansis	strain=OB47	GCA_000145215.1	717609	717609	type	True	89.1211	687	947	95	below_threshold
Caldicellulosiruptor owensensis	strain=OL	GCA_000166335.1	55205	55205	type	True	88.337	659	947	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:38,945] [INFO] DFAST Taxonomy check result was written to GCF_000166775.1_ASM16677v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:38,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:38,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:38,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a3c8f96-8521-4b8a-ba4b-1fdd1b9c8e6d/dqc_reference/checkm_data
[2024-01-24 13:37:38,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:38,974] [INFO] Task started: CheckM
[2024-01-24 13:37:38,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000166775.1_ASM16677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000166775.1_ASM16677v1_genomic.fna/checkm_input GCF_000166775.1_ASM16677v1_genomic.fna/checkm_result
[2024-01-24 13:38:00,695] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:00,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:00,713] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:00,713] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:00,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000166775.1_ASM16677v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:00,714] [INFO] Task started: Blastn
[2024-01-24 13:38:00,714] [INFO] Running command: blastn -query GCF_000166775.1_ASM16677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a3c8f96-8521-4b8a-ba4b-1fdd1b9c8e6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000166775.1_ASM16677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:01,501] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:01,504] [INFO] Selected 7 target genomes.
[2024-01-24 13:38:01,504] [INFO] Target genome list was writen to GCF_000166775.1_ASM16677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:01,516] [INFO] Task started: fastANI
[2024-01-24 13:38:01,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a89cf7c-cc92-4e6a-8b04-7b16ec599d16/GCF_000166775.1_ASM16677v1_genomic.fna.gz --refList GCF_000166775.1_ASM16677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000166775.1_ASM16677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:06,618] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:06,623] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:38:06,624] [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_000166775.1	s__Caldicellulosiruptor kronotskyensis	100.0	947	947	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	96.1491	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000022325.1	s__Caldicellulosiruptor bescii	96.1609	772	947	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	96.1491	99.98	99.96	0.99	0.98	23	inconclusive
GCF_000166355.1	s__Caldicellulosiruptor hydrothermalis	92.5307	719	947	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_017347585.1	s__Caldicellulosiruptor sp017347585	91.1256	724	947	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	90.6821	680	947	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	89.0933	691	947	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	88.3576	658	947	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 13:38:06,625] [INFO] GTDB search result was written to GCF_000166775.1_ASM16677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:06,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:06,627] [INFO] DFAST_QC result json was written to GCF_000166775.1_ASM16677v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:06,628] [INFO] DFAST_QC completed!
[2024-01-24 13:38:06,628] [INFO] Total running time: 0h0m41s