[2023-06-13 21:20:32,842] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:20:32,844] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:20:32,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg51f93f4d-c400-494f-98d6-6e8597e362d9/dqc_reference
[2023-06-13 21:20:34,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:20:34,601] [INFO] Task started: Prodigal
[2023-06-13 21:20:34,601] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6dbedd7-8a20-4620-892b-550f649e6d3b/GCA_022508965.1_ASM2250896v1_genomic.fna.gz | prodigal -d GCA_022508965.1_ASM2250896v1_genomic.fna/cds.fna -a GCA_022508965.1_ASM2250896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:20:38,457] [INFO] Task succeeded: Prodigal
[2023-06-13 21:20:38,457] [INFO] Task started: HMMsearch
[2023-06-13 21:20:38,457] [INFO] Running command: hmmsearch --tblout GCA_022508965.1_ASM2250896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51f93f4d-c400-494f-98d6-6e8597e362d9/dqc_reference/reference_markers.hmm GCA_022508965.1_ASM2250896v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:20:38,664] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:20:38,667] [INFO] Found 6/6 markers.
[2023-06-13 21:20:38,690] [INFO] Query marker FASTA was written to GCA_022508965.1_ASM2250896v1_genomic.fna/markers.fasta
[2023-06-13 21:20:38,690] [INFO] Task started: Blastn
[2023-06-13 21:20:38,691] [INFO] Running command: blastn -query GCA_022508965.1_ASM2250896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51f93f4d-c400-494f-98d6-6e8597e362d9/dqc_reference/reference_markers.fasta -out GCA_022508965.1_ASM2250896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:39,225] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:39,228] [INFO] Selected 17 target genomes.
[2023-06-13 21:20:39,229] [INFO] Target genome list was writen to GCA_022508965.1_ASM2250896v1_genomic.fna/target_genomes.txt
[2023-06-13 21:20:39,232] [INFO] Task started: fastANI
[2023-06-13 21:20:39,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6dbedd7-8a20-4620-892b-550f649e6d3b/GCA_022508965.1_ASM2250896v1_genomic.fna.gz --refList GCA_022508965.1_ASM2250896v1_genomic.fna/target_genomes.txt --output GCA_022508965.1_ASM2250896v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:20:51,076] [INFO] Task succeeded: fastANI
[2023-06-13 21:20:51,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51f93f4d-c400-494f-98d6-6e8597e362d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:20:51,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51f93f4d-c400-494f-98d6-6e8597e362d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:20:51,078] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:20:51,078] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 21:20:51,079] [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 21:20:51,082] [INFO] DFAST Taxonomy check result was written to GCA_022508965.1_ASM2250896v1_genomic.fna/tc_result.tsv
[2023-06-13 21:20:51,082] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:20:51,083] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:20:51,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51f93f4d-c400-494f-98d6-6e8597e362d9/dqc_reference/checkm_data
[2023-06-13 21:20:51,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:20:51,110] [INFO] Task started: CheckM
[2023-06-13 21:20:51,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022508965.1_ASM2250896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022508965.1_ASM2250896v1_genomic.fna/checkm_input GCA_022508965.1_ASM2250896v1_genomic.fna/checkm_result
[2023-06-13 21:21:08,164] [INFO] Task succeeded: CheckM
[2023-06-13 21:21:08,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:21:08,190] [INFO] ===== Completeness check finished =====
[2023-06-13 21:21:08,191] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:21:08,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022508965.1_ASM2250896v1_genomic.fna/markers.fasta)
[2023-06-13 21:21:08,191] [INFO] Task started: Blastn
[2023-06-13 21:21:08,191] [INFO] Running command: blastn -query GCA_022508965.1_ASM2250896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51f93f4d-c400-494f-98d6-6e8597e362d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_022508965.1_ASM2250896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:08,938] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:08,942] [INFO] Selected 20 target genomes.
[2023-06-13 21:21:08,942] [INFO] Target genome list was writen to GCA_022508965.1_ASM2250896v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:21:08,978] [INFO] Task started: fastANI
[2023-06-13 21:21:08,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6dbedd7-8a20-4620-892b-550f649e6d3b/GCA_022508965.1_ASM2250896v1_genomic.fna.gz --refList GCA_022508965.1_ASM2250896v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022508965.1_ASM2250896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:21:17,013] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:17,023] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 21:21:17,023] [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_014799395.1	s__CAG-115 sp014799395	78.5509	249	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579125.1	s__CAG-115 sp910579125	77.9042	256	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587465.1	s__CAG-115 sp910587465	77.8474	228	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425305.1	s__CAG-115 sp002425305	77.5353	168	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492075.1	s__CAG-115 sp002492075	77.4581	135	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	97.62	97.62	0.68	0.67	3	-
GCA_004554555.1	s__CAG-115 sp004554555	77.2001	167	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799385.1	s__CAG-115 sp014799385	77.0733	145	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555855.1	s__CAG-115 sp004555855	77.0225	144	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003531585.1	s__CAG-115 sp003531585	76.7766	119	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.38	98.23	0.90	0.86	9	-
GCA_004555635.1	s__CAG-115 sp004555635	76.7319	93	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.06	98.06	0.73	0.73	2	-
GCA_017847835.1	s__CAG-115 sp017847835	76.7149	158	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432175.1	s__CAG-115 sp000432175	76.526	89	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.02	98.02	0.85	0.84	3	-
GCA_900768705.1	s__CAG-115 sp900768705	76.1372	74	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465665.1	s__CAG-115 sp017465665	76.0658	68	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:21:17,033] [INFO] GTDB search result was written to GCA_022508965.1_ASM2250896v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:21:17,034] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:21:17,037] [INFO] DFAST_QC result json was written to GCA_022508965.1_ASM2250896v1_genomic.fna/dqc_result.json
[2023-06-13 21:21:17,037] [INFO] DFAST_QC completed!
[2023-06-13 21:21:17,037] [INFO] Total running time: 0h0m44s