[2024-01-24 11:12:28,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,072] [INFO] DQC Reference Directory: /var/lib/cwl/stgb14b169d-df12-4c3b-92ec-b272a513c212/dqc_reference
[2024-01-24 11:12:29,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,524] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,524] [INFO] Running command: gunzip -c /var/lib/cwl/stgcad34f13-e3f8-48e6-b1bb-8266e768234d/GCF_017347585.1_ASM1734758v1_genomic.fna.gz | prodigal -d GCF_017347585.1_ASM1734758v1_genomic.fna/cds.fna -a GCF_017347585.1_ASM1734758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:35,654] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:35,654] [INFO] Task started: HMMsearch
[2024-01-24 11:12:35,654] [INFO] Running command: hmmsearch --tblout GCF_017347585.1_ASM1734758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb14b169d-df12-4c3b-92ec-b272a513c212/dqc_reference/reference_markers.hmm GCF_017347585.1_ASM1734758v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:35,934] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:35,936] [INFO] Found 6/6 markers.
[2024-01-24 11:12:35,995] [INFO] Query marker FASTA was written to GCF_017347585.1_ASM1734758v1_genomic.fna/markers.fasta
[2024-01-24 11:12:35,995] [INFO] Task started: Blastn
[2024-01-24 11:12:35,995] [INFO] Running command: blastn -query GCF_017347585.1_ASM1734758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb14b169d-df12-4c3b-92ec-b272a513c212/dqc_reference/reference_markers.fasta -out GCF_017347585.1_ASM1734758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:36,619] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:36,622] [INFO] Selected 7 target genomes.
[2024-01-24 11:12:36,623] [INFO] Target genome list was writen to GCF_017347585.1_ASM1734758v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:36,626] [INFO] Task started: fastANI
[2024-01-24 11:12:36,626] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad34f13-e3f8-48e6-b1bb-8266e768234d/GCF_017347585.1_ASM1734758v1_genomic.fna.gz --refList GCF_017347585.1_ASM1734758v1_genomic.fna/target_genomes.txt --output GCF_017347585.1_ASM1734758v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:41,619] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:41,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb14b169d-df12-4c3b-92ec-b272a513c212/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:41,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb14b169d-df12-4c3b-92ec-b272a513c212/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:41,627] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:41,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:41,628] [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 diazotrophicus	strain=YA01	GCA_017347585.1	2806205	2806205	type	True	100.0	865	865	95	conclusive
Caldicellulosiruptor hydrothermalis	strain=108	GCA_000166355.1	413888	413888	type	True	92.0537	705	865	95	below_threshold
Caldicellulosiruptor bescii	strain=DSM 6725	GCA_000022325.1	31899	31899	type	True	91.1839	698	865	95	below_threshold
Caldicellulosiruptor kronotskyensis	strain=2002	GCA_000166775.1	413889	413889	type	True	91.1641	716	865	95	below_threshold
Caldicellulosiruptor acetigenus	strain=DSM 7040	GCA_000421725.1	301953	301953	type	True	89.5528	659	865	95	below_threshold
Caldicellulosiruptor obsidiansis	strain=OB47	GCA_000145215.1	717609	717609	type	True	88.5569	669	865	95	below_threshold
Caldicellulosiruptor owensensis	strain=OL	GCA_000166335.1	55205	55205	type	True	88.1896	666	865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:41,629] [INFO] DFAST Taxonomy check result was written to GCF_017347585.1_ASM1734758v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:41,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:41,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:41,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb14b169d-df12-4c3b-92ec-b272a513c212/dqc_reference/checkm_data
[2024-01-24 11:12:41,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:41,663] [INFO] Task started: CheckM
[2024-01-24 11:12:41,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017347585.1_ASM1734758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017347585.1_ASM1734758v1_genomic.fna/checkm_input GCF_017347585.1_ASM1734758v1_genomic.fna/checkm_result
[2024-01-24 11:13:06,697] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:06,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:06,718] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:06,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:06,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017347585.1_ASM1734758v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:06,719] [INFO] Task started: Blastn
[2024-01-24 11:13:06,719] [INFO] Running command: blastn -query GCF_017347585.1_ASM1734758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb14b169d-df12-4c3b-92ec-b272a513c212/dqc_reference/reference_markers_gtdb.fasta -out GCF_017347585.1_ASM1734758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:07,528] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:07,532] [INFO] Selected 7 target genomes.
[2024-01-24 11:13:07,532] [INFO] Target genome list was writen to GCF_017347585.1_ASM1734758v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:07,538] [INFO] Task started: fastANI
[2024-01-24 11:13:07,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad34f13-e3f8-48e6-b1bb-8266e768234d/GCF_017347585.1_ASM1734758v1_genomic.fna.gz --refList GCF_017347585.1_ASM1734758v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017347585.1_ASM1734758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:12,830] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:12,837] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:12,837] [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_017347585.1	s__Caldicellulosiruptor sp017347585	100.0	864	865	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Caldicellulosiruptorales;f__Caldicellulosiruptoraceae;g__Caldicellulosiruptor	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000166355.1	s__Caldicellulosiruptor hydrothermalis	92.0365	704	865	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	91.1828	716	865	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_000022325.1	s__Caldicellulosiruptor bescii	91.158	700	865	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_000421725.1	s__Caldicellulosiruptor acetigenus	89.5612	659	865	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	88.533	671	865	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	88.2017	665	865	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 11:13:12,839] [INFO] GTDB search result was written to GCF_017347585.1_ASM1734758v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:12,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:12,843] [INFO] DFAST_QC result json was written to GCF_017347585.1_ASM1734758v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:12,843] [INFO] DFAST_QC completed!
[2024-01-24 11:13:12,843] [INFO] Total running time: 0h0m45s