[2023-06-30 06:39:00,107] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:39:00,110] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:39:00,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d9797a0-ae62-4e3f-90c7-21145c412ce9/dqc_reference
[2023-06-30 06:39:02,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:39:02,518] [INFO] Task started: Prodigal
[2023-06-30 06:39:02,518] [INFO] Running command: gunzip -c /var/lib/cwl/stg1118e810-99f3-48d1-8969-16d4f3fd5825/GCA_016708675.1_ASM1670867v1_genomic.fna.gz | prodigal -d GCA_016708675.1_ASM1670867v1_genomic.fna/cds.fna -a GCA_016708675.1_ASM1670867v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:39:26,804] [INFO] Task succeeded: Prodigal
[2023-06-30 06:39:26,805] [INFO] Task started: HMMsearch
[2023-06-30 06:39:26,805] [INFO] Running command: hmmsearch --tblout GCA_016708675.1_ASM1670867v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d9797a0-ae62-4e3f-90c7-21145c412ce9/dqc_reference/reference_markers.hmm GCA_016708675.1_ASM1670867v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:39:27,111] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:39:27,112] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1118e810-99f3-48d1-8969-16d4f3fd5825/GCA_016708675.1_ASM1670867v1_genomic.fna.gz]
[2023-06-30 06:39:27,154] [INFO] Query marker FASTA was written to GCA_016708675.1_ASM1670867v1_genomic.fna/markers.fasta
[2023-06-30 06:39:27,155] [INFO] Task started: Blastn
[2023-06-30 06:39:27,155] [INFO] Running command: blastn -query GCA_016708675.1_ASM1670867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d9797a0-ae62-4e3f-90c7-21145c412ce9/dqc_reference/reference_markers.fasta -out GCA_016708675.1_ASM1670867v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:39:27,747] [INFO] Task succeeded: Blastn
[2023-06-30 06:39:27,751] [INFO] Selected 20 target genomes.
[2023-06-30 06:39:27,751] [INFO] Target genome list was writen to GCA_016708675.1_ASM1670867v1_genomic.fna/target_genomes.txt
[2023-06-30 06:39:27,753] [INFO] Task started: fastANI
[2023-06-30 06:39:27,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg1118e810-99f3-48d1-8969-16d4f3fd5825/GCA_016708675.1_ASM1670867v1_genomic.fna.gz --refList GCA_016708675.1_ASM1670867v1_genomic.fna/target_genomes.txt --output GCA_016708675.1_ASM1670867v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:39:41,510] [INFO] Task succeeded: fastANI
[2023-06-30 06:39:41,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d9797a0-ae62-4e3f-90c7-21145c412ce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:39:41,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d9797a0-ae62-4e3f-90c7-21145c412ce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:39:41,513] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:39:41,513] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 06:39:41,514] [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
--------------------------------------------------------------------------------
[2023-06-30 06:39:41,516] [INFO] DFAST Taxonomy check result was written to GCA_016708675.1_ASM1670867v1_genomic.fna/tc_result.tsv
[2023-06-30 06:39:41,517] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:39:41,517] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:39:41,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d9797a0-ae62-4e3f-90c7-21145c412ce9/dqc_reference/checkm_data
[2023-06-30 06:39:41,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:39:41,572] [INFO] Task started: CheckM
[2023-06-30 06:39:41,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708675.1_ASM1670867v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708675.1_ASM1670867v1_genomic.fna/checkm_input GCA_016708675.1_ASM1670867v1_genomic.fna/checkm_result
[2023-06-30 06:40:49,544] [INFO] Task succeeded: CheckM
[2023-06-30 06:40:49,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:40:49,565] [INFO] ===== Completeness check finished =====
[2023-06-30 06:40:49,565] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:40:49,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708675.1_ASM1670867v1_genomic.fna/markers.fasta)
[2023-06-30 06:40:49,566] [INFO] Task started: Blastn
[2023-06-30 06:40:49,566] [INFO] Running command: blastn -query GCA_016708675.1_ASM1670867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d9797a0-ae62-4e3f-90c7-21145c412ce9/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708675.1_ASM1670867v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:40:50,321] [INFO] Task succeeded: Blastn
[2023-06-30 06:40:50,326] [INFO] Selected 21 target genomes.
[2023-06-30 06:40:50,326] [INFO] Target genome list was writen to GCA_016708675.1_ASM1670867v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:40:50,332] [INFO] Task started: fastANI
[2023-06-30 06:40:50,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg1118e810-99f3-48d1-8969-16d4f3fd5825/GCA_016708675.1_ASM1670867v1_genomic.fna.gz --refList GCA_016708675.1_ASM1670867v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708675.1_ASM1670867v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:41:07,979] [INFO] Task succeeded: fastANI
[2023-06-30 06:41:07,988] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 06:41:07,988] [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_016717655.1	s__JADKBO01 sp016717655	98.5571	1417	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADKBO01	95.0	98.50	98.17	0.93	0.91	7	conclusive
GCA_017987975.1	s__JADKBO01 sp017987975	86.8053	943	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADKBO01	95.0	98.99	98.99	0.82	0.82	2	-
GCA_016715465.1	s__JADKBO01 sp016715465	78.2583	270	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADKBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714895.1	s__OLB9 sp016714895	76.134	57	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:41:07,990] [INFO] GTDB search result was written to GCA_016708675.1_ASM1670867v1_genomic.fna/result_gtdb.tsv
[2023-06-30 06:41:07,991] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:41:07,993] [INFO] DFAST_QC result json was written to GCA_016708675.1_ASM1670867v1_genomic.fna/dqc_result.json
[2023-06-30 06:41:07,993] [INFO] DFAST_QC completed!
[2023-06-30 06:41:07,993] [INFO] Total running time: 0h2m8s