[2024-01-24 14:14:37,311] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,319] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg6346a204-06fd-4fea-aa42-294b167e56b3/dqc_reference
[2024-01-24 14:14:38,809] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,810] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg00e8ab74-2364-4fdd-9a45-5f0aeb11acd8/GCF_003664005.1_ASM366400v1_genomic.fna.gz | prodigal -d GCF_003664005.1_ASM366400v1_genomic.fna/cds.fna -a GCF_003664005.1_ASM366400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:46,104] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:46,105] [INFO] Task started: HMMsearch
[2024-01-24 14:14:46,105] [INFO] Running command: hmmsearch --tblout GCF_003664005.1_ASM366400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6346a204-06fd-4fea-aa42-294b167e56b3/dqc_reference/reference_markers.hmm GCF_003664005.1_ASM366400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:46,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:46,459] [INFO] Found 6/6 markers.
[2024-01-24 14:14:46,492] [INFO] Query marker FASTA was written to GCF_003664005.1_ASM366400v1_genomic.fna/markers.fasta
[2024-01-24 14:14:46,493] [INFO] Task started: Blastn
[2024-01-24 14:14:46,493] [INFO] Running command: blastn -query GCF_003664005.1_ASM366400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6346a204-06fd-4fea-aa42-294b167e56b3/dqc_reference/reference_markers.fasta -out GCF_003664005.1_ASM366400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:47,754] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:47,758] [INFO] Selected 3 target genomes.
[2024-01-24 14:14:47,758] [INFO] Target genome list was writen to GCF_003664005.1_ASM366400v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:47,785] [INFO] Task started: fastANI
[2024-01-24 14:14:47,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e8ab74-2364-4fdd-9a45-5f0aeb11acd8/GCF_003664005.1_ASM366400v1_genomic.fna.gz --refList GCF_003664005.1_ASM366400v1_genomic.fna/target_genomes.txt --output GCF_003664005.1_ASM366400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:49,622] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:49,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6346a204-06fd-4fea-aa42-294b167e56b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:49,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6346a204-06fd-4fea-aa42-294b167e56b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:49,668] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:49,668] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:49,669] [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
Hydrogenivirga caldilitoris	strain=DSM 16510	GCA_003664005.1	246264	246264	type	True	100.0	584	584	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:14:49,673] [INFO] DFAST Taxonomy check result was written to GCF_003664005.1_ASM366400v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:49,673] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:49,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:49,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6346a204-06fd-4fea-aa42-294b167e56b3/dqc_reference/checkm_data
[2024-01-24 14:14:49,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:49,713] [INFO] Task started: CheckM
[2024-01-24 14:14:49,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003664005.1_ASM366400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003664005.1_ASM366400v1_genomic.fna/checkm_input GCF_003664005.1_ASM366400v1_genomic.fna/checkm_result
[2024-01-24 14:15:19,930] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:19,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:19,961] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:19,962] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:19,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003664005.1_ASM366400v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:19,962] [INFO] Task started: Blastn
[2024-01-24 14:15:19,963] [INFO] Running command: blastn -query GCF_003664005.1_ASM366400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6346a204-06fd-4fea-aa42-294b167e56b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003664005.1_ASM366400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:20,744] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:20,749] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:20,749] [INFO] Target genome list was writen to GCF_003664005.1_ASM366400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:20,792] [INFO] Task started: fastANI
[2024-01-24 14:15:20,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e8ab74-2364-4fdd-9a45-5f0aeb11acd8/GCF_003664005.1_ASM366400v1_genomic.fna.gz --refList GCF_003664005.1_ASM366400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003664005.1_ASM366400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:26,201] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:26,210] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:26,210] [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_003664005.1	s__Hydrogenivirga caldilitoris	100.0	584	584	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__Hydrogenivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015492115.1	s__Hydrogenivirga sp015492115	77.8082	211	584	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__Hydrogenivirga	95.0	98.46	98.46	0.84	0.84	2	-
GCA_015487535.1	s__Hydrogenivirga sp015487535	77.4658	106	584	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__Hydrogenivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490115.1	s__Hydrogenivirga sp015490115	76.5741	58	584	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__Hydrogenivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487835.1	s__Hydrogenivirga sp015487835	76.4305	62	584	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__Hydrogenivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490155.1	s__WFYI01 sp015490155	76.3218	62	584	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__WFYI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:26,214] [INFO] GTDB search result was written to GCF_003664005.1_ASM366400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:26,215] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:26,218] [INFO] DFAST_QC result json was written to GCF_003664005.1_ASM366400v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:26,219] [INFO] DFAST_QC completed!
[2024-01-24 14:15:26,219] [INFO] Total running time: 0h0m49s