[2023-06-30 15:20:37,725] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:20:37,729] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:20:37,729] [INFO] DQC Reference Directory: /var/lib/cwl/stga91166c0-9dc4-491c-b713-1760696312ef/dqc_reference
[2023-06-30 15:20:40,035] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:20:40,037] [INFO] Task started: Prodigal
[2023-06-30 15:20:40,037] [INFO] Running command: gunzip -c /var/lib/cwl/stg75876a5f-1fae-4a0b-863e-39c12f430055/GCA_016708125.1_ASM1670812v1_genomic.fna.gz | prodigal -d GCA_016708125.1_ASM1670812v1_genomic.fna/cds.fna -a GCA_016708125.1_ASM1670812v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:20:48,305] [INFO] Task succeeded: Prodigal
[2023-06-30 15:20:48,305] [INFO] Task started: HMMsearch
[2023-06-30 15:20:48,305] [INFO] Running command: hmmsearch --tblout GCA_016708125.1_ASM1670812v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga91166c0-9dc4-491c-b713-1760696312ef/dqc_reference/reference_markers.hmm GCA_016708125.1_ASM1670812v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:20:48,588] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:20:48,589] [INFO] Found 6/6 markers.
[2023-06-30 15:20:48,629] [INFO] Query marker FASTA was written to GCA_016708125.1_ASM1670812v1_genomic.fna/markers.fasta
[2023-06-30 15:20:48,630] [INFO] Task started: Blastn
[2023-06-30 15:20:48,630] [INFO] Running command: blastn -query GCA_016708125.1_ASM1670812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga91166c0-9dc4-491c-b713-1760696312ef/dqc_reference/reference_markers.fasta -out GCA_016708125.1_ASM1670812v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:20:49,207] [INFO] Task succeeded: Blastn
[2023-06-30 15:20:49,211] [INFO] Selected 21 target genomes.
[2023-06-30 15:20:49,211] [INFO] Target genome list was writen to GCA_016708125.1_ASM1670812v1_genomic.fna/target_genomes.txt
[2023-06-30 15:20:49,217] [INFO] Task started: fastANI
[2023-06-30 15:20:49,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg75876a5f-1fae-4a0b-863e-39c12f430055/GCA_016708125.1_ASM1670812v1_genomic.fna.gz --refList GCA_016708125.1_ASM1670812v1_genomic.fna/target_genomes.txt --output GCA_016708125.1_ASM1670812v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:21:00,359] [INFO] Task succeeded: fastANI
[2023-06-30 15:21:00,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga91166c0-9dc4-491c-b713-1760696312ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:21:00,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga91166c0-9dc4-491c-b713-1760696312ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:21:00,371] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:21:00,372] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:21:00,372] [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
Ignavibacterium album	strain=JCM 16511	GCA_000258405.1	591197	591197	type	True	75.4769	94	1534	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	74.8643	67	1534	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	74.7704	63	1534	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	74.6172	59	1534	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	74.5974	55	1534	95	below_threshold
Cetobacterium ceti	strain=ATCC 700028	GCA_900167275.1	180163	180163	type	True	74.5914	58	1534	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:21:00,374] [INFO] DFAST Taxonomy check result was written to GCA_016708125.1_ASM1670812v1_genomic.fna/tc_result.tsv
[2023-06-30 15:21:00,375] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:21:00,375] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:21:00,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga91166c0-9dc4-491c-b713-1760696312ef/dqc_reference/checkm_data
[2023-06-30 15:21:00,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:21:00,423] [INFO] Task started: CheckM
[2023-06-30 15:21:00,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708125.1_ASM1670812v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708125.1_ASM1670812v1_genomic.fna/checkm_input GCA_016708125.1_ASM1670812v1_genomic.fna/checkm_result
[2023-06-30 15:21:30,833] [INFO] Task succeeded: CheckM
[2023-06-30 15:21:30,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:21:30,856] [INFO] ===== Completeness check finished =====
[2023-06-30 15:21:30,857] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:21:30,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708125.1_ASM1670812v1_genomic.fna/markers.fasta)
[2023-06-30 15:21:30,858] [INFO] Task started: Blastn
[2023-06-30 15:21:30,858] [INFO] Running command: blastn -query GCA_016708125.1_ASM1670812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga91166c0-9dc4-491c-b713-1760696312ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708125.1_ASM1670812v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:21:31,667] [INFO] Task succeeded: Blastn
[2023-06-30 15:21:31,684] [INFO] Selected 10 target genomes.
[2023-06-30 15:21:31,684] [INFO] Target genome list was writen to GCA_016708125.1_ASM1670812v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:21:31,692] [INFO] Task started: fastANI
[2023-06-30 15:21:31,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg75876a5f-1fae-4a0b-863e-39c12f430055/GCA_016708125.1_ASM1670812v1_genomic.fna.gz --refList GCA_016708125.1_ASM1670812v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708125.1_ASM1670812v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:21:39,763] [INFO] Task succeeded: fastANI
[2023-06-30 15:21:39,775] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:21:39,776] [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_016708125.1	s__GCA-2746605 sp016708125	100.0	1533	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016716225.1	s__GCA-2746605 sp016716225	87.4956	1139	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713565.1	s__GCA-2746605 sp016713565	79.482	829	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	99.17	99.17	0.95	0.95	2	-
GCA_002746605.1	s__GCA-2746605 sp002746605	76.573	224	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698995.1	s__GCA-2698995 sp002698995	76.1792	211	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2698995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013112585.1	s__IGN16 sp013112585	75.9254	141	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__IGN16	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018829205.1	s__JAHJUE01 sp018829205	75.6401	163	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__JAHJUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002898175.1	s__BMS3ABIN04 sp002898175	75.6177	114	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__BMS3ABIN04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002790395.1	s__UM-FILTER-34-10 sp002790395	75.589	96	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__UM-FILTER-34-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829545.1	s__JAHJTX01 sp018829545	75.4939	101	1534	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__JAHJTX01	95.0	99.23	99.17	0.85	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-30 15:21:39,778] [INFO] GTDB search result was written to GCA_016708125.1_ASM1670812v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:21:39,778] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:21:39,781] [INFO] DFAST_QC result json was written to GCA_016708125.1_ASM1670812v1_genomic.fna/dqc_result.json
[2023-06-30 15:21:39,782] [INFO] DFAST_QC completed!
[2023-06-30 15:21:39,782] [INFO] Total running time: 0h1m2s