[2024-01-24 12:40:08,042] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:08,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:08,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b6319bc-5802-40fb-8f07-bb287fbe05f7/dqc_reference
[2024-01-24 12:40:09,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,356] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg809f1d18-bf02-4f90-a7f6-9b4968517c26/GCF_000430885.1_ASM43088v1_genomic.fna.gz | prodigal -d GCF_000430885.1_ASM43088v1_genomic.fna/cds.fna -a GCF_000430885.1_ASM43088v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:18,366] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:18,366] [INFO] Task started: HMMsearch
[2024-01-24 12:40:18,367] [INFO] Running command: hmmsearch --tblout GCF_000430885.1_ASM43088v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b6319bc-5802-40fb-8f07-bb287fbe05f7/dqc_reference/reference_markers.hmm GCF_000430885.1_ASM43088v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:18,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:18,651] [INFO] Found 6/6 markers.
[2024-01-24 12:40:18,691] [INFO] Query marker FASTA was written to GCF_000430885.1_ASM43088v1_genomic.fna/markers.fasta
[2024-01-24 12:40:18,691] [INFO] Task started: Blastn
[2024-01-24 12:40:18,691] [INFO] Running command: blastn -query GCF_000430885.1_ASM43088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b6319bc-5802-40fb-8f07-bb287fbe05f7/dqc_reference/reference_markers.fasta -out GCF_000430885.1_ASM43088v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:19,276] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:19,281] [INFO] Selected 18 target genomes.
[2024-01-24 12:40:19,282] [INFO] Target genome list was writen to GCF_000430885.1_ASM43088v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:19,291] [INFO] Task started: fastANI
[2024-01-24 12:40:19,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg809f1d18-bf02-4f90-a7f6-9b4968517c26/GCF_000430885.1_ASM43088v1_genomic.fna.gz --refList GCF_000430885.1_ASM43088v1_genomic.fna/target_genomes.txt --output GCF_000430885.1_ASM43088v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:32,009] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:32,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b6319bc-5802-40fb-8f07-bb287fbe05f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:32,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b6319bc-5802-40fb-8f07-bb287fbe05f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:32,015] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:32,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:32,015] [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
Desulfotruncus alcoholivorax	strain=DSM 16058	GCA_000430885.1	265477	265477	type	True	100.0	1115	1122	95	conclusive
Desulfotruncus arcticus	strain=DSM 17038	GCA_900113335.1	341036	341036	type	True	85.5523	796	1122	95	below_threshold
Desulfoscipio geothermicus	strain=DSM 3669	GCA_900115975.1	39060	39060	type	True	78.5134	211	1122	95	below_threshold
Sporotomaculum syntrophicum	strain=FB	GCA_009932395.1	182264	182264	type	True	77.2285	66	1122	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:32,017] [INFO] DFAST Taxonomy check result was written to GCF_000430885.1_ASM43088v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:32,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:32,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:32,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b6319bc-5802-40fb-8f07-bb287fbe05f7/dqc_reference/checkm_data
[2024-01-24 12:40:32,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:32,060] [INFO] Task started: CheckM
[2024-01-24 12:40:32,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430885.1_ASM43088v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430885.1_ASM43088v1_genomic.fna/checkm_input GCF_000430885.1_ASM43088v1_genomic.fna/checkm_result
[2024-01-24 12:41:02,324] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:02,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:02,346] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:02,347] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:02,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430885.1_ASM43088v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:02,347] [INFO] Task started: Blastn
[2024-01-24 12:41:02,348] [INFO] Running command: blastn -query GCF_000430885.1_ASM43088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b6319bc-5802-40fb-8f07-bb287fbe05f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430885.1_ASM43088v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:03,187] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:03,191] [INFO] Selected 17 target genomes.
[2024-01-24 12:41:03,191] [INFO] Target genome list was writen to GCF_000430885.1_ASM43088v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:03,225] [INFO] Task started: fastANI
[2024-01-24 12:41:03,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg809f1d18-bf02-4f90-a7f6-9b4968517c26/GCF_000430885.1_ASM43088v1_genomic.fna.gz --refList GCF_000430885.1_ASM43088v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430885.1_ASM43088v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:12,171] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:12,178] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:12,178] [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_000430885.1	s__Desulfotruncus alcoholivorax	100.0	1115	1122	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Desulfotruncus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900113335.1	s__Desulfotruncus arcticus	85.5593	794	1122	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Desulfotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015594625.1	s__Desulfotruncus sp015594625	79.2943	254	1122	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Desulfotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115975.1	s__Desulfoscipio geothermicus	78.4737	211	1122	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Desulfoscipio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932395.1	s__Sporotomaculum syntrophicum	77.2706	65	1122	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124625.1	s__Sporotomaculum thermosapovorans	77.2637	152	1122	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000214705.1	s__Desulfofundulus kuznetsovii	76.1775	56	1122	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	97.21	97.21	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:12,180] [INFO] GTDB search result was written to GCF_000430885.1_ASM43088v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:12,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:12,184] [INFO] DFAST_QC result json was written to GCF_000430885.1_ASM43088v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:12,184] [INFO] DFAST_QC completed!
[2024-01-24 12:41:12,184] [INFO] Total running time: 0h1m4s