[2024-01-24 13:55:14,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:14,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:14,415] [INFO] DQC Reference Directory: /var/lib/cwl/stga22abf80-008d-43f6-acd5-43e183d0ab91/dqc_reference
[2024-01-24 13:55:15,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:15,757] [INFO] Task started: Prodigal
[2024-01-24 13:55:15,757] [INFO] Running command: gunzip -c /var/lib/cwl/stg482142f0-4d05-458f-bbd0-b1bc3bd83e19/GCF_000177335.1_ASM17733v1_genomic.fna.gz | prodigal -d GCF_000177335.1_ASM17733v1_genomic.fna/cds.fna -a GCF_000177335.1_ASM17733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:22,422] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:22,423] [INFO] Task started: HMMsearch
[2024-01-24 13:55:22,423] [INFO] Running command: hmmsearch --tblout GCF_000177335.1_ASM17733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga22abf80-008d-43f6-acd5-43e183d0ab91/dqc_reference/reference_markers.hmm GCF_000177335.1_ASM17733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:22,661] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:22,662] [INFO] Found 6/6 markers.
[2024-01-24 13:55:22,689] [INFO] Query marker FASTA was written to GCF_000177335.1_ASM17733v1_genomic.fna/markers.fasta
[2024-01-24 13:55:22,689] [INFO] Task started: Blastn
[2024-01-24 13:55:22,689] [INFO] Running command: blastn -query GCF_000177335.1_ASM17733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga22abf80-008d-43f6-acd5-43e183d0ab91/dqc_reference/reference_markers.fasta -out GCF_000177335.1_ASM17733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:23,327] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:23,330] [INFO] Selected 16 target genomes.
[2024-01-24 13:55:23,330] [INFO] Target genome list was writen to GCF_000177335.1_ASM17733v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:23,346] [INFO] Task started: fastANI
[2024-01-24 13:55:23,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg482142f0-4d05-458f-bbd0-b1bc3bd83e19/GCF_000177335.1_ASM17733v1_genomic.fna.gz --refList GCF_000177335.1_ASM17733v1_genomic.fna/target_genomes.txt --output GCF_000177335.1_ASM17733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:31,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:31,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga22abf80-008d-43f6-acd5-43e183d0ab91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:31,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga22abf80-008d-43f6-acd5-43e183d0ab91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:31,653] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:31,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:31,653] [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
Pyramidobacter piscolens	strain=W5455	GCA_000177335.1	638849	638849	type	True	100.0	790	793	95	conclusive
Pyramidobacter porci	strain=SM-530-WT-4B	GCA_009695745.1	2605789	2605789	type	True	92.2806	662	793	95	below_threshold
Jonquetella anthropi	strain=DSM 22815	GCA_000237805.1	428712	428712	type	True	76.7332	63	793	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.8675	64	793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:31,655] [INFO] DFAST Taxonomy check result was written to GCF_000177335.1_ASM17733v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:31,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:31,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:31,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga22abf80-008d-43f6-acd5-43e183d0ab91/dqc_reference/checkm_data
[2024-01-24 13:55:31,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:31,685] [INFO] Task started: CheckM
[2024-01-24 13:55:31,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000177335.1_ASM17733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000177335.1_ASM17733v1_genomic.fna/checkm_input GCF_000177335.1_ASM17733v1_genomic.fna/checkm_result
[2024-01-24 13:55:57,055] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:57,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:57,073] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:57,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:57,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000177335.1_ASM17733v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:57,074] [INFO] Task started: Blastn
[2024-01-24 13:55:57,074] [INFO] Running command: blastn -query GCF_000177335.1_ASM17733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga22abf80-008d-43f6-acd5-43e183d0ab91/dqc_reference/reference_markers_gtdb.fasta -out GCF_000177335.1_ASM17733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:58,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:58,053] [INFO] Selected 8 target genomes.
[2024-01-24 13:55:58,053] [INFO] Target genome list was writen to GCF_000177335.1_ASM17733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:58,066] [INFO] Task started: fastANI
[2024-01-24 13:55:58,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg482142f0-4d05-458f-bbd0-b1bc3bd83e19/GCF_000177335.1_ASM17733v1_genomic.fna.gz --refList GCF_000177335.1_ASM17733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000177335.1_ASM17733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:03,023] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:03,033] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:03,033] [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
GCF_000177335.1	s__Pyramidobacter piscolens	100.0	790	793	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	98.74	98.74	0.86	0.86	2	conclusive
GCF_002007215.1	s__Pyramidobacter sp002007215	93.22	653	793	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	97.07	95.83	0.85	0.81	3	-
GCF_009695745.1	s__Pyramidobacter porci	92.3074	661	793	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286835.1	s__Pyramidobacter sp016286835	79.829	234	793	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	97.54	97.39	0.80	0.78	3	-
GCA_017940445.1	s__Pyramidobacter sp017940445	79.5176	203	793	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	96.84	96.36	0.70	0.63	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:03,035] [INFO] GTDB search result was written to GCF_000177335.1_ASM17733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:03,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:03,038] [INFO] DFAST_QC result json was written to GCF_000177335.1_ASM17733v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:03,038] [INFO] DFAST_QC completed!
[2024-01-24 13:56:03,038] [INFO] Total running time: 0h0m49s