[2024-01-24 14:12:47,085] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg8886dd1e-8bf7-45b8-86ba-9415ced0def5/dqc_reference
[2024-01-24 14:12:48,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,294] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,294] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8b7c19e-b6c6-4823-949a-7ad32d1f3ff5/GCF_003751385.1_ASM375138v1_genomic.fna.gz | prodigal -d GCF_003751385.1_ASM375138v1_genomic.fna/cds.fna -a GCF_003751385.1_ASM375138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:59,944] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:59,944] [INFO] Task started: HMMsearch
[2024-01-24 14:12:59,944] [INFO] Running command: hmmsearch --tblout GCF_003751385.1_ASM375138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8886dd1e-8bf7-45b8-86ba-9415ced0def5/dqc_reference/reference_markers.hmm GCF_003751385.1_ASM375138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:00,183] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:00,185] [INFO] Found 6/6 markers.
[2024-01-24 14:13:00,215] [INFO] Query marker FASTA was written to GCF_003751385.1_ASM375138v1_genomic.fna/markers.fasta
[2024-01-24 14:13:00,216] [INFO] Task started: Blastn
[2024-01-24 14:13:00,216] [INFO] Running command: blastn -query GCF_003751385.1_ASM375138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8886dd1e-8bf7-45b8-86ba-9415ced0def5/dqc_reference/reference_markers.fasta -out GCF_003751385.1_ASM375138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:00,822] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:00,826] [INFO] Selected 19 target genomes.
[2024-01-24 14:13:00,826] [INFO] Target genome list was writen to GCF_003751385.1_ASM375138v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:00,835] [INFO] Task started: fastANI
[2024-01-24 14:13:00,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b7c19e-b6c6-4823-949a-7ad32d1f3ff5/GCF_003751385.1_ASM375138v1_genomic.fna.gz --refList GCF_003751385.1_ASM375138v1_genomic.fna/target_genomes.txt --output GCF_003751385.1_ASM375138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:12,801] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:12,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8886dd1e-8bf7-45b8-86ba-9415ced0def5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:12,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8886dd1e-8bf7-45b8-86ba-9415ced0def5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:12,811] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:12,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:12,811] [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
Desulfosoma caldarium	strain=DSM 22027	GCA_003751385.1	610254	610254	type	True	100.0	1129	1131	95	conclusive
Desulfacinum hydrothermale	strain=DSM 13146	GCA_900176285.1	109258	109258	type	True	77.0212	213	1131	95	below_threshold
Desulfacinum infernum	strain=DSM 9756	GCA_900129305.1	35837	35837	type	True	76.9815	255	1131	95	below_threshold
Desulfoglaeba alkanexedens	strain=ALDC	GCA_005377625.1	361111	361111	type	True	76.6582	102	1131	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:12,814] [INFO] DFAST Taxonomy check result was written to GCF_003751385.1_ASM375138v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:12,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:12,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:12,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8886dd1e-8bf7-45b8-86ba-9415ced0def5/dqc_reference/checkm_data
[2024-01-24 14:13:12,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:12,855] [INFO] Task started: CheckM
[2024-01-24 14:13:12,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003751385.1_ASM375138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003751385.1_ASM375138v1_genomic.fna/checkm_input GCF_003751385.1_ASM375138v1_genomic.fna/checkm_result
[2024-01-24 14:13:50,409] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:50,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:50,428] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:50,429] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:50,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003751385.1_ASM375138v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:50,430] [INFO] Task started: Blastn
[2024-01-24 14:13:50,430] [INFO] Running command: blastn -query GCF_003751385.1_ASM375138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8886dd1e-8bf7-45b8-86ba-9415ced0def5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003751385.1_ASM375138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:51,268] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:51,275] [INFO] Selected 13 target genomes.
[2024-01-24 14:13:51,275] [INFO] Target genome list was writen to GCF_003751385.1_ASM375138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:51,310] [INFO] Task started: fastANI
[2024-01-24 14:13:51,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b7c19e-b6c6-4823-949a-7ad32d1f3ff5/GCF_003751385.1_ASM375138v1_genomic.fna.gz --refList GCF_003751385.1_ASM375138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003751385.1_ASM375138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:59,312] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:59,320] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:59,320] [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_003751385.1	s__Desulfosoma caldarium	100.0	1129	1131	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfosoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011329395.1	s__Desulfosoma infernum_A	78.8673	539	1131	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359885.1	s__Desulfacinum sp014359885	77.1486	262	1131	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176285.1	s__Desulfacinum hydrothermale	77.0226	212	1131	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129305.1	s__Desulfacinum infernum	76.9914	254	1131	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005377625.1	s__Desulfoglaeba alkanexedens	76.6791	101	1131	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfoglaeba	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873705.1	s__CG2-30-61-12 sp001873705	76.2236	90	1131	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__CG2-30-61-12	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:59,321] [INFO] GTDB search result was written to GCF_003751385.1_ASM375138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:59,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:59,324] [INFO] DFAST_QC result json was written to GCF_003751385.1_ASM375138v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:59,325] [INFO] DFAST_QC completed!
[2024-01-24 14:13:59,325] [INFO] Total running time: 0h1m12s