[2024-01-24 13:58:10,914] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,916] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,916] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ac8cbe5-1d15-4b25-abba-f040d299451b/dqc_reference
[2024-01-24 13:58:12,147] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,148] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,148] [INFO] Running command: gunzip -c /var/lib/cwl/stg90666af1-5ead-473c-841f-22e91998dbfb/GCF_022410535.1_ASM2241053v1_genomic.fna.gz | prodigal -d GCF_022410535.1_ASM2241053v1_genomic.fna/cds.fna -a GCF_022410535.1_ASM2241053v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:21,439] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:21,439] [INFO] Task started: HMMsearch
[2024-01-24 13:58:21,439] [INFO] Running command: hmmsearch --tblout GCF_022410535.1_ASM2241053v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ac8cbe5-1d15-4b25-abba-f040d299451b/dqc_reference/reference_markers.hmm GCF_022410535.1_ASM2241053v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:21,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:21,738] [INFO] Found 6/6 markers.
[2024-01-24 13:58:21,772] [INFO] Query marker FASTA was written to GCF_022410535.1_ASM2241053v1_genomic.fna/markers.fasta
[2024-01-24 13:58:21,772] [INFO] Task started: Blastn
[2024-01-24 13:58:21,772] [INFO] Running command: blastn -query GCF_022410535.1_ASM2241053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ac8cbe5-1d15-4b25-abba-f040d299451b/dqc_reference/reference_markers.fasta -out GCF_022410535.1_ASM2241053v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:22,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:22,397] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:22,398] [INFO] Target genome list was writen to GCF_022410535.1_ASM2241053v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:22,410] [INFO] Task started: fastANI
[2024-01-24 13:58:22,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg90666af1-5ead-473c-841f-22e91998dbfb/GCF_022410535.1_ASM2241053v1_genomic.fna.gz --refList GCF_022410535.1_ASM2241053v1_genomic.fna/target_genomes.txt --output GCF_022410535.1_ASM2241053v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:35,003] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:35,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ac8cbe5-1d15-4b25-abba-f040d299451b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:35,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ac8cbe5-1d15-4b25-abba-f040d299451b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:35,010] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:35,011] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:35,011] [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
Pelotomaculum terephthalicicum	strain=JT	GCA_022410535.1	206393	206393	type	True	100.0	1204	1208	95	conclusive
Pelotomaculum propionicicum	strain=MGP	GCA_004369225.1	258475	258475	type	True	77.7892	117	1208	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:35,013] [INFO] DFAST Taxonomy check result was written to GCF_022410535.1_ASM2241053v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:35,013] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:35,013] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:35,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ac8cbe5-1d15-4b25-abba-f040d299451b/dqc_reference/checkm_data
[2024-01-24 13:58:35,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:35,059] [INFO] Task started: CheckM
[2024-01-24 13:58:35,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022410535.1_ASM2241053v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022410535.1_ASM2241053v1_genomic.fna/checkm_input GCF_022410535.1_ASM2241053v1_genomic.fna/checkm_result
[2024-01-24 13:59:09,663] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:09,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:09,683] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:09,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:09,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022410535.1_ASM2241053v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:09,684] [INFO] Task started: Blastn
[2024-01-24 13:59:09,685] [INFO] Running command: blastn -query GCF_022410535.1_ASM2241053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ac8cbe5-1d15-4b25-abba-f040d299451b/dqc_reference/reference_markers_gtdb.fasta -out GCF_022410535.1_ASM2241053v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:10,685] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:10,689] [INFO] Selected 15 target genomes.
[2024-01-24 13:59:10,690] [INFO] Target genome list was writen to GCF_022410535.1_ASM2241053v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:10,698] [INFO] Task started: fastANI
[2024-01-24 13:59:10,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg90666af1-5ead-473c-841f-22e91998dbfb/GCF_022410535.1_ASM2241053v1_genomic.fna.gz --refList GCF_022410535.1_ASM2241053v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022410535.1_ASM2241053v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:17,755] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:17,764] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:17,764] [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
GCA_002067395.1	s__MVQK01 sp002067395	99.2314	847	1208	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__MVQK01	95.0	99.51	99.51	0.78	0.78	2	conclusive
GCA_002067515.1	s__MVQK01 sp002067515	84.1709	406	1208	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__MVQK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002067205.1	s__MVQL01 sp002067205	81.0991	278	1208	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__MVQL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002067965.1	s__MVRN01 sp002067965	80.5217	284	1208	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__MVRN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004369225.1	s__Pelotomaculum_B propionicicum	77.7439	118	1208	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__Pelotomaculum_B	95.0	99.42	99.42	0.93	0.93	2	-
GCA_002365855.1	s__UBA3103 sp002365855	77.0304	70	1208	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Pelotomaculaceae;g__UBA3103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:17,766] [INFO] GTDB search result was written to GCF_022410535.1_ASM2241053v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:17,767] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:17,770] [INFO] DFAST_QC result json was written to GCF_022410535.1_ASM2241053v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:17,770] [INFO] DFAST_QC completed!
[2024-01-24 13:59:17,771] [INFO] Total running time: 0h1m7s