[2023-06-13 17:12:17,417] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:12:17,422] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:12:17,422] [INFO] DQC Reference Directory: /var/lib/cwl/stgffa33d4f-0d70-40ca-b40c-e2ceb6d033d1/dqc_reference
[2023-06-13 17:12:18,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:12:18,699] [INFO] Task started: Prodigal
[2023-06-13 17:12:18,699] [INFO] Running command: gunzip -c /var/lib/cwl/stg99e8c831-773c-4d40-9812-5a01aa23c5e3/GCA_022793775.1_ASM2279377v1_genomic.fna.gz | prodigal -d GCA_022793775.1_ASM2279377v1_genomic.fna/cds.fna -a GCA_022793775.1_ASM2279377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:12:26,412] [INFO] Task succeeded: Prodigal
[2023-06-13 17:12:26,412] [INFO] Task started: HMMsearch
[2023-06-13 17:12:26,412] [INFO] Running command: hmmsearch --tblout GCA_022793775.1_ASM2279377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffa33d4f-0d70-40ca-b40c-e2ceb6d033d1/dqc_reference/reference_markers.hmm GCA_022793775.1_ASM2279377v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:12:26,668] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:12:26,670] [INFO] Found 6/6 markers.
[2023-06-13 17:12:26,704] [INFO] Query marker FASTA was written to GCA_022793775.1_ASM2279377v1_genomic.fna/markers.fasta
[2023-06-13 17:12:26,705] [INFO] Task started: Blastn
[2023-06-13 17:12:26,705] [INFO] Running command: blastn -query GCA_022793775.1_ASM2279377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa33d4f-0d70-40ca-b40c-e2ceb6d033d1/dqc_reference/reference_markers.fasta -out GCA_022793775.1_ASM2279377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:27,294] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:27,297] [INFO] Selected 25 target genomes.
[2023-06-13 17:12:27,298] [INFO] Target genome list was writen to GCA_022793775.1_ASM2279377v1_genomic.fna/target_genomes.txt
[2023-06-13 17:12:27,299] [INFO] Task started: fastANI
[2023-06-13 17:12:27,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e8c831-773c-4d40-9812-5a01aa23c5e3/GCA_022793775.1_ASM2279377v1_genomic.fna.gz --refList GCA_022793775.1_ASM2279377v1_genomic.fna/target_genomes.txt --output GCA_022793775.1_ASM2279377v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:12:42,202] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:42,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffa33d4f-0d70-40ca-b40c-e2ceb6d033d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:12:42,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffa33d4f-0d70-40ca-b40c-e2ceb6d033d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:12:42,209] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:12:42,209] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:12:42,209] [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
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.6982	80	1195	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	76.6426	57	1195	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.5486	79	1195	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.529	55	1195	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.5183	100	1195	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.5171	84	1195	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:12:42,211] [INFO] DFAST Taxonomy check result was written to GCA_022793775.1_ASM2279377v1_genomic.fna/tc_result.tsv
[2023-06-13 17:12:42,212] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:12:42,212] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:12:42,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffa33d4f-0d70-40ca-b40c-e2ceb6d033d1/dqc_reference/checkm_data
[2023-06-13 17:12:42,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:12:42,250] [INFO] Task started: CheckM
[2023-06-13 17:12:42,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022793775.1_ASM2279377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022793775.1_ASM2279377v1_genomic.fna/checkm_input GCA_022793775.1_ASM2279377v1_genomic.fna/checkm_result
[2023-06-13 17:13:08,380] [INFO] Task succeeded: CheckM
[2023-06-13 17:13:08,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:13:08,404] [INFO] ===== Completeness check finished =====
[2023-06-13 17:13:08,404] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:13:08,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022793775.1_ASM2279377v1_genomic.fna/markers.fasta)
[2023-06-13 17:13:08,405] [INFO] Task started: Blastn
[2023-06-13 17:13:08,405] [INFO] Running command: blastn -query GCA_022793775.1_ASM2279377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa33d4f-0d70-40ca-b40c-e2ceb6d033d1/dqc_reference/reference_markers_gtdb.fasta -out GCA_022793775.1_ASM2279377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:13:09,403] [INFO] Task succeeded: Blastn
[2023-06-13 17:13:09,407] [INFO] Selected 14 target genomes.
[2023-06-13 17:13:09,407] [INFO] Target genome list was writen to GCA_022793775.1_ASM2279377v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:13:09,408] [INFO] Task started: fastANI
[2023-06-13 17:13:09,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e8c831-773c-4d40-9812-5a01aa23c5e3/GCA_022793775.1_ASM2279377v1_genomic.fna.gz --refList GCA_022793775.1_ASM2279377v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022793775.1_ASM2279377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:13:19,505] [INFO] Task succeeded: fastANI
[2023-06-13 17:13:19,513] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:13:19,513] [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_003612395.1	s__CAG-95 sp003612395	99.1536	1148	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910587305.1	s__CAG-95 sp910587305	82.2697	806	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917485.1	s__CAG-95 sp009917485	82.2448	817	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585075.1	s__CAG-95 sp910585075	80.0336	652	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804785.1	s__CAG-95 sp014804785	78.1661	281	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911035.1	s__CAG-95 sp009911035	78.1214	324	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	96.92	95.99	0.83	0.79	4	-
GCA_002492465.1	s__CAG-95 sp002492465	77.6084	267	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002490775.1	s__CAG-95 sp002490775	77.5434	227	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577445.1	s__CAG-95 sp910577445	77.401	215	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579425.1	s__CAG-95 sp910579425	77.2952	259	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436115.1	s__CAG-95 sp000436115	77.048	175	1195	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.37	99.32	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-13 17:13:19,514] [INFO] GTDB search result was written to GCA_022793775.1_ASM2279377v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:13:19,515] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:13:19,517] [INFO] DFAST_QC result json was written to GCA_022793775.1_ASM2279377v1_genomic.fna/dqc_result.json
[2023-06-13 17:13:19,517] [INFO] DFAST_QC completed!
[2023-06-13 17:13:19,518] [INFO] Total running time: 0h1m2s