[2024-01-24 11:05:28,077] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,079] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b255874-2e4f-49d6-8abf-ce950d8d32c0/dqc_reference
[2024-01-24 11:05:29,472] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,473] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,473] [INFO] Running command: gunzip -c /var/lib/cwl/stg6496a260-f86b-4c43-b9f9-920007082b12/GCF_021568805.1_ASM2156880v1_genomic.fna.gz | prodigal -d GCF_021568805.1_ASM2156880v1_genomic.fna/cds.fna -a GCF_021568805.1_ASM2156880v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:36,093] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:36,094] [INFO] Task started: HMMsearch
[2024-01-24 11:05:36,094] [INFO] Running command: hmmsearch --tblout GCF_021568805.1_ASM2156880v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b255874-2e4f-49d6-8abf-ce950d8d32c0/dqc_reference/reference_markers.hmm GCF_021568805.1_ASM2156880v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:36,381] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:36,382] [INFO] Found 6/6 markers.
[2024-01-24 11:05:36,410] [INFO] Query marker FASTA was written to GCF_021568805.1_ASM2156880v1_genomic.fna/markers.fasta
[2024-01-24 11:05:36,411] [INFO] Task started: Blastn
[2024-01-24 11:05:36,411] [INFO] Running command: blastn -query GCF_021568805.1_ASM2156880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b255874-2e4f-49d6-8abf-ce950d8d32c0/dqc_reference/reference_markers.fasta -out GCF_021568805.1_ASM2156880v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:37,039] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:37,042] [INFO] Selected 11 target genomes.
[2024-01-24 11:05:37,042] [INFO] Target genome list was writen to GCF_021568805.1_ASM2156880v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:37,046] [INFO] Task started: fastANI
[2024-01-24 11:05:37,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg6496a260-f86b-4c43-b9f9-920007082b12/GCF_021568805.1_ASM2156880v1_genomic.fna.gz --refList GCF_021568805.1_ASM2156880v1_genomic.fna/target_genomes.txt --output GCF_021568805.1_ASM2156880v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:43,342] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:43,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b255874-2e4f-49d6-8abf-ce950d8d32c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:43,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b255874-2e4f-49d6-8abf-ce950d8d32c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:43,349] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:43,349] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:43,349] [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
Dethiosulfovibrio peptidovorans	strain=DSM 11002	GCA_000172975.1	47055	47055	type	True	94.0733	764	859	95	below_threshold
Dethiosulfovibrio faecalis	strain=F2B	GCA_021568795.1	2720018	2720018	type	True	92.8441	753	859	95	below_threshold
Dethiosulfovibrio salsuginis	strain=USBA 82	GCA_900177735.1	561720	561720	type	True	78.0119	242	859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:43,351] [INFO] DFAST Taxonomy check result was written to GCF_021568805.1_ASM2156880v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:43,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:43,352] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:43,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b255874-2e4f-49d6-8abf-ce950d8d32c0/dqc_reference/checkm_data
[2024-01-24 11:05:43,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:43,386] [INFO] Task started: CheckM
[2024-01-24 11:05:43,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021568805.1_ASM2156880v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021568805.1_ASM2156880v1_genomic.fna/checkm_input GCF_021568805.1_ASM2156880v1_genomic.fna/checkm_result
[2024-01-24 11:06:09,790] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:09,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:09,814] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:09,815] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:09,815] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021568805.1_ASM2156880v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:09,816] [INFO] Task started: Blastn
[2024-01-24 11:06:09,816] [INFO] Running command: blastn -query GCF_021568805.1_ASM2156880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b255874-2e4f-49d6-8abf-ce950d8d32c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_021568805.1_ASM2156880v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:10,730] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:10,738] [INFO] Selected 20 target genomes.
[2024-01-24 11:06:10,739] [INFO] Target genome list was writen to GCF_021568805.1_ASM2156880v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:10,758] [INFO] Task started: fastANI
[2024-01-24 11:06:10,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg6496a260-f86b-4c43-b9f9-920007082b12/GCF_021568805.1_ASM2156880v1_genomic.fna.gz --refList GCF_021568805.1_ASM2156880v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021568805.1_ASM2156880v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:21,942] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:21,946] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:21,946] [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_000172975.1	s__Dethiosulfovibrio peptidovorans	94.0573	765	859	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Dethiosulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177735.1	s__Dethiosulfovibrio salsuginis	78.0082	243	859	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Dethiosulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748665.1	s__Dethiosulfovibrio peptidovorans_A	76.4151	82	859	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Dethiosulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:21,948] [INFO] GTDB search result was written to GCF_021568805.1_ASM2156880v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:21,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:21,951] [INFO] DFAST_QC result json was written to GCF_021568805.1_ASM2156880v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:21,951] [INFO] DFAST_QC completed!
[2024-01-24 11:06:21,951] [INFO] Total running time: 0h0m54s