[2023-06-13 03:52:33,400] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:52:33,403] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:52:33,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb3c91ed-8a2f-439a-a782-c2fd597b81fa/dqc_reference
[2023-06-13 03:52:34,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:52:34,778] [INFO] Task started: Prodigal
[2023-06-13 03:52:34,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fd629ca-4692-4659-b130-778b100d0aee/GCA_022508585.1_ASM2250858v1_genomic.fna.gz | prodigal -d GCA_022508585.1_ASM2250858v1_genomic.fna/cds.fna -a GCA_022508585.1_ASM2250858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:52:45,023] [INFO] Task succeeded: Prodigal
[2023-06-13 03:52:45,024] [INFO] Task started: HMMsearch
[2023-06-13 03:52:45,024] [INFO] Running command: hmmsearch --tblout GCA_022508585.1_ASM2250858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb3c91ed-8a2f-439a-a782-c2fd597b81fa/dqc_reference/reference_markers.hmm GCA_022508585.1_ASM2250858v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:52:45,254] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:52:45,255] [INFO] Found 6/6 markers.
[2023-06-13 03:52:45,279] [INFO] Query marker FASTA was written to GCA_022508585.1_ASM2250858v1_genomic.fna/markers.fasta
[2023-06-13 03:52:45,280] [INFO] Task started: Blastn
[2023-06-13 03:52:45,280] [INFO] Running command: blastn -query GCA_022508585.1_ASM2250858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb3c91ed-8a2f-439a-a782-c2fd597b81fa/dqc_reference/reference_markers.fasta -out GCA_022508585.1_ASM2250858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:52:45,862] [INFO] Task succeeded: Blastn
[2023-06-13 03:52:45,868] [INFO] Selected 28 target genomes.
[2023-06-13 03:52:45,868] [INFO] Target genome list was writen to GCA_022508585.1_ASM2250858v1_genomic.fna/target_genomes.txt
[2023-06-13 03:52:45,874] [INFO] Task started: fastANI
[2023-06-13 03:52:45,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fd629ca-4692-4659-b130-778b100d0aee/GCA_022508585.1_ASM2250858v1_genomic.fna.gz --refList GCA_022508585.1_ASM2250858v1_genomic.fna/target_genomes.txt --output GCA_022508585.1_ASM2250858v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:53:00,474] [INFO] Task succeeded: fastANI
[2023-06-13 03:53:00,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb3c91ed-8a2f-439a-a782-c2fd597b81fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:53:00,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb3c91ed-8a2f-439a-a782-c2fd597b81fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:53:00,478] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:53:00,478] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 03:53:00,478] [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
--------------------------------------------------------------------------------
[2023-06-13 03:53:00,481] [INFO] DFAST Taxonomy check result was written to GCA_022508585.1_ASM2250858v1_genomic.fna/tc_result.tsv
[2023-06-13 03:53:00,482] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:53:00,482] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:53:00,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb3c91ed-8a2f-439a-a782-c2fd597b81fa/dqc_reference/checkm_data
[2023-06-13 03:53:00,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:53:00,518] [INFO] Task started: CheckM
[2023-06-13 03:53:00,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022508585.1_ASM2250858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022508585.1_ASM2250858v1_genomic.fna/checkm_input GCA_022508585.1_ASM2250858v1_genomic.fna/checkm_result
[2023-06-13 03:53:34,150] [INFO] Task succeeded: CheckM
[2023-06-13 03:53:34,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:53:34,172] [INFO] ===== Completeness check finished =====
[2023-06-13 03:53:34,172] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:53:34,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022508585.1_ASM2250858v1_genomic.fna/markers.fasta)
[2023-06-13 03:53:34,173] [INFO] Task started: Blastn
[2023-06-13 03:53:34,173] [INFO] Running command: blastn -query GCA_022508585.1_ASM2250858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb3c91ed-8a2f-439a-a782-c2fd597b81fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_022508585.1_ASM2250858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:53:34,983] [INFO] Task succeeded: Blastn
[2023-06-13 03:53:34,989] [INFO] Selected 25 target genomes.
[2023-06-13 03:53:34,989] [INFO] Target genome list was writen to GCA_022508585.1_ASM2250858v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:53:35,004] [INFO] Task started: fastANI
[2023-06-13 03:53:35,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fd629ca-4692-4659-b130-778b100d0aee/GCA_022508585.1_ASM2250858v1_genomic.fna.gz --refList GCA_022508585.1_ASM2250858v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022508585.1_ASM2250858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:53:45,603] [INFO] Task succeeded: fastANI
[2023-06-13 03:53:45,617] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 03:53:45,618] [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_017458585.1	s__UBA6382 sp017458585	77.6286	158	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792555.1	s__UBA6382 sp902792555	77.5255	165	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382	95.0	96.62	96.42	0.86	0.84	6	-
GCA_017616915.1	s__UBA6382 sp017616915	77.3443	97	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382	95.0	98.04	98.04	0.80	0.80	2	-
GCA_017963785.1	s__UBA6382 sp017963785	77.1269	134	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017618515.1	s__UBA6382 sp017618515	76.9903	93	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 03:53:45,621] [INFO] GTDB search result was written to GCA_022508585.1_ASM2250858v1_genomic.fna/result_gtdb.tsv
[2023-06-13 03:53:45,622] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:53:45,625] [INFO] DFAST_QC result json was written to GCA_022508585.1_ASM2250858v1_genomic.fna/dqc_result.json
[2023-06-13 03:53:45,625] [INFO] DFAST_QC completed!
[2023-06-13 03:53:45,626] [INFO] Total running time: 0h1m12s