[2023-06-13 15:14:34,145] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:14:34,147] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:14:34,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f91a738-e18f-46da-bfcd-f4c7e93ecba3/dqc_reference
[2023-06-13 15:14:35,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:14:35,387] [INFO] Task started: Prodigal
[2023-06-13 15:14:35,387] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa9f1c4d-9e41-48ac-8e91-fec201633832/GCA_022643535.1_ASM2264353v1_genomic.fna.gz | prodigal -d GCA_022643535.1_ASM2264353v1_genomic.fna/cds.fna -a GCA_022643535.1_ASM2264353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:14:41,923] [INFO] Task succeeded: Prodigal
[2023-06-13 15:14:41,924] [INFO] Task started: HMMsearch
[2023-06-13 15:14:41,924] [INFO] Running command: hmmsearch --tblout GCA_022643535.1_ASM2264353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f91a738-e18f-46da-bfcd-f4c7e93ecba3/dqc_reference/reference_markers.hmm GCA_022643535.1_ASM2264353v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:14:42,171] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:14:42,173] [INFO] Found 6/6 markers.
[2023-06-13 15:14:42,198] [INFO] Query marker FASTA was written to GCA_022643535.1_ASM2264353v1_genomic.fna/markers.fasta
[2023-06-13 15:14:42,198] [INFO] Task started: Blastn
[2023-06-13 15:14:42,198] [INFO] Running command: blastn -query GCA_022643535.1_ASM2264353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f91a738-e18f-46da-bfcd-f4c7e93ecba3/dqc_reference/reference_markers.fasta -out GCA_022643535.1_ASM2264353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:14:42,841] [INFO] Task succeeded: Blastn
[2023-06-13 15:14:42,846] [INFO] Selected 22 target genomes.
[2023-06-13 15:14:42,847] [INFO] Target genome list was writen to GCA_022643535.1_ASM2264353v1_genomic.fna/target_genomes.txt
[2023-06-13 15:14:42,849] [INFO] Task started: fastANI
[2023-06-13 15:14:42,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa9f1c4d-9e41-48ac-8e91-fec201633832/GCA_022643535.1_ASM2264353v1_genomic.fna.gz --refList GCA_022643535.1_ASM2264353v1_genomic.fna/target_genomes.txt --output GCA_022643535.1_ASM2264353v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:14:57,152] [INFO] Task succeeded: fastANI
[2023-06-13 15:14:57,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f91a738-e18f-46da-bfcd-f4c7e93ecba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:14:57,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f91a738-e18f-46da-bfcd-f4c7e93ecba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:14:57,159] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:14:57,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:14:57,159] [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
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	78.5721	53	818	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:14:57,161] [INFO] DFAST Taxonomy check result was written to GCA_022643535.1_ASM2264353v1_genomic.fna/tc_result.tsv
[2023-06-13 15:14:57,162] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:14:57,162] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:14:57,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f91a738-e18f-46da-bfcd-f4c7e93ecba3/dqc_reference/checkm_data
[2023-06-13 15:14:57,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:14:57,194] [INFO] Task started: CheckM
[2023-06-13 15:14:57,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022643535.1_ASM2264353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022643535.1_ASM2264353v1_genomic.fna/checkm_input GCA_022643535.1_ASM2264353v1_genomic.fna/checkm_result
[2023-06-13 15:15:22,756] [INFO] Task succeeded: CheckM
[2023-06-13 15:15:22,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:15:22,779] [INFO] ===== Completeness check finished =====
[2023-06-13 15:15:22,779] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:15:22,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022643535.1_ASM2264353v1_genomic.fna/markers.fasta)
[2023-06-13 15:15:22,780] [INFO] Task started: Blastn
[2023-06-13 15:15:22,781] [INFO] Running command: blastn -query GCA_022643535.1_ASM2264353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f91a738-e18f-46da-bfcd-f4c7e93ecba3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022643535.1_ASM2264353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:15:23,898] [INFO] Task succeeded: Blastn
[2023-06-13 15:15:23,903] [INFO] Selected 28 target genomes.
[2023-06-13 15:15:23,903] [INFO] Target genome list was writen to GCA_022643535.1_ASM2264353v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:15:23,904] [INFO] Task started: fastANI
[2023-06-13 15:15:23,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa9f1c4d-9e41-48ac-8e91-fec201633832/GCA_022643535.1_ASM2264353v1_genomic.fna.gz --refList GCA_022643535.1_ASM2264353v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022643535.1_ASM2264353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:15:36,520] [INFO] Task succeeded: fastANI
[2023-06-13 15:15:36,534] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:15:36,535] [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_900317475.1	s__CAG-791 sp900317475	98.8493	609	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.34	98.93	0.86	0.78	29	conclusive
GCA_902781655.1	s__CAG-791 sp902781655	78.3784	178	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431495.1	s__CAG-791 sp000431495	78.3726	87	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.54	97.54	0.90	0.90	2	-
GCA_900320025.1	s__CAG-791 sp900320025	78.2536	161	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.86	98.12	0.80	0.73	19	-
GCA_900315055.1	s__CAG-791 sp900315055	77.2436	107	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.03	98.45	0.88	0.84	8	-
GCA_017432565.1	s__CAG-791 sp017432565	76.7977	65	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449485.1	s__CAG-791 sp017449485	76.6246	58	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	96.27	96.27	0.75	0.75	2	-
GCF_900625025.1	s__CAG-791 sp900625025	76.524	104	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781215.1	s__CAG-791 sp902781215	76.4681	57	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	96.36	96.36	0.81	0.81	2	-
GCA_900107575.1	s__CAG-791 sp900107575	76.4209	78	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:15:36,537] [INFO] GTDB search result was written to GCA_022643535.1_ASM2264353v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:15:36,538] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:15:36,542] [INFO] DFAST_QC result json was written to GCA_022643535.1_ASM2264353v1_genomic.fna/dqc_result.json
[2023-06-13 15:15:36,542] [INFO] DFAST_QC completed!
[2023-06-13 15:15:36,542] [INFO] Total running time: 0h1m2s