[2023-06-28 10:16:31,646] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:16:31,657] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:16:31,658] [INFO] DQC Reference Directory: /var/lib/cwl/stgae5e1459-bab8-40db-920e-ddfc5bfa312e/dqc_reference
[2023-06-28 10:16:33,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:16:33,734] [INFO] Task started: Prodigal
[2023-06-28 10:16:33,734] [INFO] Running command: gunzip -c /var/lib/cwl/stgc31a1b30-a470-45d2-b901-e68d5a825922/GCA_002708445.1_ASM270844v1_genomic.fna.gz | prodigal -d GCA_002708445.1_ASM270844v1_genomic.fna/cds.fna -a GCA_002708445.1_ASM270844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:16:39,640] [INFO] Task succeeded: Prodigal
[2023-06-28 10:16:39,640] [INFO] Task started: HMMsearch
[2023-06-28 10:16:39,640] [INFO] Running command: hmmsearch --tblout GCA_002708445.1_ASM270844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae5e1459-bab8-40db-920e-ddfc5bfa312e/dqc_reference/reference_markers.hmm GCA_002708445.1_ASM270844v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:16:39,909] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:16:39,911] [INFO] Found 6/6 markers.
[2023-06-28 10:16:39,936] [INFO] Query marker FASTA was written to GCA_002708445.1_ASM270844v1_genomic.fna/markers.fasta
[2023-06-28 10:16:39,937] [INFO] Task started: Blastn
[2023-06-28 10:16:39,937] [INFO] Running command: blastn -query GCA_002708445.1_ASM270844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae5e1459-bab8-40db-920e-ddfc5bfa312e/dqc_reference/reference_markers.fasta -out GCA_002708445.1_ASM270844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:40,552] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:40,559] [INFO] Selected 33 target genomes.
[2023-06-28 10:16:40,559] [INFO] Target genome list was writen to GCA_002708445.1_ASM270844v1_genomic.fna/target_genomes.txt
[2023-06-28 10:16:40,566] [INFO] Task started: fastANI
[2023-06-28 10:16:40,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgc31a1b30-a470-45d2-b901-e68d5a825922/GCA_002708445.1_ASM270844v1_genomic.fna.gz --refList GCA_002708445.1_ASM270844v1_genomic.fna/target_genomes.txt --output GCA_002708445.1_ASM270844v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:16:59,137] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:59,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae5e1459-bab8-40db-920e-ddfc5bfa312e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:16:59,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae5e1459-bab8-40db-920e-ddfc5bfa312e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:16:59,140] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:16:59,141] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:16:59,141] [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
--------------------------------------------------------------------------------
[2023-06-28 10:16:59,143] [INFO] DFAST Taxonomy check result was written to GCA_002708445.1_ASM270844v1_genomic.fna/tc_result.tsv
[2023-06-28 10:16:59,144] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:16:59,144] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:16:59,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae5e1459-bab8-40db-920e-ddfc5bfa312e/dqc_reference/checkm_data
[2023-06-28 10:16:59,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:16:59,168] [INFO] Task started: CheckM
[2023-06-28 10:16:59,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708445.1_ASM270844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708445.1_ASM270844v1_genomic.fna/checkm_input GCA_002708445.1_ASM270844v1_genomic.fna/checkm_result
[2023-06-28 10:17:23,019] [INFO] Task succeeded: CheckM
[2023-06-28 10:17:23,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:17:23,043] [INFO] ===== Completeness check finished =====
[2023-06-28 10:17:23,043] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:17:23,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708445.1_ASM270844v1_genomic.fna/markers.fasta)
[2023-06-28 10:17:23,044] [INFO] Task started: Blastn
[2023-06-28 10:17:23,044] [INFO] Running command: blastn -query GCA_002708445.1_ASM270844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae5e1459-bab8-40db-920e-ddfc5bfa312e/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708445.1_ASM270844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:17:23,894] [INFO] Task succeeded: Blastn
[2023-06-28 10:17:23,899] [INFO] Selected 22 target genomes.
[2023-06-28 10:17:23,900] [INFO] Target genome list was writen to GCA_002708445.1_ASM270844v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:17:23,951] [INFO] Task started: fastANI
[2023-06-28 10:17:23,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgc31a1b30-a470-45d2-b901-e68d5a825922/GCA_002708445.1_ASM270844v1_genomic.fna.gz --refList GCA_002708445.1_ASM270844v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708445.1_ASM270844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:17:31,888] [INFO] Task succeeded: fastANI
[2023-06-28 10:17:31,898] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:17:31,898] [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_002708445.1	s__UBA7428 sp002708445	100.0	486	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003023645.1	s__UBA7428 sp003023645	77.9095	174	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_002477625.1	s__UBA7428 sp002477625	77.7973	143	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
GCA_018608425.1	s__UBA7428 sp018608425	77.7326	132	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181615.1	s__UBA7428 sp905181615	77.6606	186	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_905478905.1	s__UBA7428 sp905478905	76.3223	65	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-28 10:17:31,900] [INFO] GTDB search result was written to GCA_002708445.1_ASM270844v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:17:31,901] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:17:31,904] [INFO] DFAST_QC result json was written to GCA_002708445.1_ASM270844v1_genomic.fna/dqc_result.json
[2023-06-28 10:17:31,904] [INFO] DFAST_QC completed!
[2023-06-28 10:17:31,904] [INFO] Total running time: 0h1m0s