[2023-06-30 01:32:38,267] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:32:38,269] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:32:38,270] [INFO] DQC Reference Directory: /var/lib/cwl/stg612ec944-04e2-40f0-954c-a65c16b79a51/dqc_reference
[2023-06-30 01:32:39,708] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:32:39,709] [INFO] Task started: Prodigal
[2023-06-30 01:32:39,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bf68d02-b8a6-4deb-b342-ddd49d584da6/GCA_016708545.1_ASM1670854v1_genomic.fna.gz | prodigal -d GCA_016708545.1_ASM1670854v1_genomic.fna/cds.fna -a GCA_016708545.1_ASM1670854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:32:57,982] [INFO] Task succeeded: Prodigal
[2023-06-30 01:32:57,983] [INFO] Task started: HMMsearch
[2023-06-30 01:32:57,983] [INFO] Running command: hmmsearch --tblout GCA_016708545.1_ASM1670854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg612ec944-04e2-40f0-954c-a65c16b79a51/dqc_reference/reference_markers.hmm GCA_016708545.1_ASM1670854v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:32:58,286] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:32:58,287] [INFO] Found 6/6 markers.
[2023-06-30 01:32:58,331] [INFO] Query marker FASTA was written to GCA_016708545.1_ASM1670854v1_genomic.fna/markers.fasta
[2023-06-30 01:32:58,332] [INFO] Task started: Blastn
[2023-06-30 01:32:58,332] [INFO] Running command: blastn -query GCA_016708545.1_ASM1670854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg612ec944-04e2-40f0-954c-a65c16b79a51/dqc_reference/reference_markers.fasta -out GCA_016708545.1_ASM1670854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:32:59,053] [INFO] Task succeeded: Blastn
[2023-06-30 01:32:59,058] [INFO] Selected 35 target genomes.
[2023-06-30 01:32:59,059] [INFO] Target genome list was writen to GCA_016708545.1_ASM1670854v1_genomic.fna/target_genomes.txt
[2023-06-30 01:32:59,065] [INFO] Task started: fastANI
[2023-06-30 01:32:59,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf68d02-b8a6-4deb-b342-ddd49d584da6/GCA_016708545.1_ASM1670854v1_genomic.fna.gz --refList GCA_016708545.1_ASM1670854v1_genomic.fna/target_genomes.txt --output GCA_016708545.1_ASM1670854v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:33:22,692] [INFO] Task succeeded: fastANI
[2023-06-30 01:33:22,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg612ec944-04e2-40f0-954c-a65c16b79a51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:33:22,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg612ec944-04e2-40f0-954c-a65c16b79a51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:33:22,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:33:22,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 01:33:22,696] [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 01:33:22,699] [INFO] DFAST Taxonomy check result was written to GCA_016708545.1_ASM1670854v1_genomic.fna/tc_result.tsv
[2023-06-30 01:33:22,699] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:33:22,700] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:33:22,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg612ec944-04e2-40f0-954c-a65c16b79a51/dqc_reference/checkm_data
[2023-06-30 01:33:22,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:33:22,749] [INFO] Task started: CheckM
[2023-06-30 01:33:22,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708545.1_ASM1670854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708545.1_ASM1670854v1_genomic.fna/checkm_input GCA_016708545.1_ASM1670854v1_genomic.fna/checkm_result
[2023-06-30 01:34:15,846] [INFO] Task succeeded: CheckM
[2023-06-30 01:34:15,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 01:34:15,870] [INFO] ===== Completeness check finished =====
[2023-06-30 01:34:15,870] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:34:15,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708545.1_ASM1670854v1_genomic.fna/markers.fasta)
[2023-06-30 01:34:15,871] [INFO] Task started: Blastn
[2023-06-30 01:34:15,871] [INFO] Running command: blastn -query GCA_016708545.1_ASM1670854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg612ec944-04e2-40f0-954c-a65c16b79a51/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708545.1_ASM1670854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:34:16,854] [INFO] Task succeeded: Blastn
[2023-06-30 01:34:16,860] [INFO] Selected 23 target genomes.
[2023-06-30 01:34:16,860] [INFO] Target genome list was writen to GCA_016708545.1_ASM1670854v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:34:16,868] [INFO] Task started: fastANI
[2023-06-30 01:34:16,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf68d02-b8a6-4deb-b342-ddd49d584da6/GCA_016708545.1_ASM1670854v1_genomic.fna.gz --refList GCA_016708545.1_ASM1670854v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708545.1_ASM1670854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:34:28,839] [INFO] Task succeeded: fastANI
[2023-06-30 01:34:28,853] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 01:34:28,853] [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_016711825.1	s__OLB11 sp016711825	98.8545	1150	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__OLB11	95.0	98.95	98.85	0.91	0.88	7	conclusive
GCA_016712665.1	s__OLB11 sp016712665	77.8196	324	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__OLB11	95.0	99.25	99.12	0.95	0.93	3	-
GCA_013414745.1	s__OLB11 sp013414745	76.8409	75	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__OLB11	95.0	97.57	97.57	0.94	0.94	2	-
GCA_016715505.1	s__OLB11 sp016715505	76.5091	87	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__OLB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786845.1	s__OLB11 sp016786845	76.4578	92	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__OLB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706595.1	s__OLB11 sp016706595	76.3302	137	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__OLB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001567165.1	s__OLB11 sp001567165	76.1501	111	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__OLB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881265.1	s__OLB11 sp903881265	75.986	76	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__OLB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875055.1	s__OLB11 sp903875055	75.7615	87	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__OLB11	95.0	99.64	99.53	0.93	0.92	3	-
GCA_017988595.1	s__JAGNRR01 sp017988595	75.3392	57	1381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAGNRR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 01:34:28,855] [INFO] GTDB search result was written to GCA_016708545.1_ASM1670854v1_genomic.fna/result_gtdb.tsv
[2023-06-30 01:34:28,855] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:34:28,858] [INFO] DFAST_QC result json was written to GCA_016708545.1_ASM1670854v1_genomic.fna/dqc_result.json
[2023-06-30 01:34:28,858] [INFO] DFAST_QC completed!
[2023-06-30 01:34:28,858] [INFO] Total running time: 0h1m51s