[2023-06-14 01:47:41,947] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:47:41,949] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:47:41,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg875470f0-5499-4390-950c-4423ba98d8db/dqc_reference
[2023-06-14 01:47:43,417] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:47:43,418] [INFO] Task started: Prodigal
[2023-06-14 01:47:43,418] [INFO] Running command: gunzip -c /var/lib/cwl/stg87de4542-0d19-4c96-a0e5-117452c74692/GCA_022787985.1_ASM2278798v1_genomic.fna.gz | prodigal -d GCA_022787985.1_ASM2278798v1_genomic.fna/cds.fna -a GCA_022787985.1_ASM2278798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:47:46,842] [INFO] Task succeeded: Prodigal
[2023-06-14 01:47:46,842] [INFO] Task started: HMMsearch
[2023-06-14 01:47:46,842] [INFO] Running command: hmmsearch --tblout GCA_022787985.1_ASM2278798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg875470f0-5499-4390-950c-4423ba98d8db/dqc_reference/reference_markers.hmm GCA_022787985.1_ASM2278798v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:47:47,070] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:47:47,071] [INFO] Found 6/6 markers.
[2023-06-14 01:47:47,112] [INFO] Query marker FASTA was written to GCA_022787985.1_ASM2278798v1_genomic.fna/markers.fasta
[2023-06-14 01:47:47,113] [INFO] Task started: Blastn
[2023-06-14 01:47:47,113] [INFO] Running command: blastn -query GCA_022787985.1_ASM2278798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg875470f0-5499-4390-950c-4423ba98d8db/dqc_reference/reference_markers.fasta -out GCA_022787985.1_ASM2278798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:47:47,738] [INFO] Task succeeded: Blastn
[2023-06-14 01:47:47,742] [INFO] Selected 23 target genomes.
[2023-06-14 01:47:47,743] [INFO] Target genome list was writen to GCA_022787985.1_ASM2278798v1_genomic.fna/target_genomes.txt
[2023-06-14 01:47:47,749] [INFO] Task started: fastANI
[2023-06-14 01:47:47,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg87de4542-0d19-4c96-a0e5-117452c74692/GCA_022787985.1_ASM2278798v1_genomic.fna.gz --refList GCA_022787985.1_ASM2278798v1_genomic.fna/target_genomes.txt --output GCA_022787985.1_ASM2278798v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:48:03,142] [INFO] Task succeeded: fastANI
[2023-06-14 01:48:03,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg875470f0-5499-4390-950c-4423ba98d8db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:48:03,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg875470f0-5499-4390-950c-4423ba98d8db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:48:03,152] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:48:03,152] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:48:03,152] [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
--------------------------------------------------------------------------------
[2023-06-14 01:48:03,155] [INFO] DFAST Taxonomy check result was written to GCA_022787985.1_ASM2278798v1_genomic.fna/tc_result.tsv
[2023-06-14 01:48:03,155] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:48:03,155] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:48:03,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg875470f0-5499-4390-950c-4423ba98d8db/dqc_reference/checkm_data
[2023-06-14 01:48:03,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:48:03,198] [INFO] Task started: CheckM
[2023-06-14 01:48:03,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022787985.1_ASM2278798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022787985.1_ASM2278798v1_genomic.fna/checkm_input GCA_022787985.1_ASM2278798v1_genomic.fna/checkm_result
[2023-06-14 01:48:21,241] [INFO] Task succeeded: CheckM
[2023-06-14 01:48:21,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:48:21,263] [INFO] ===== Completeness check finished =====
[2023-06-14 01:48:21,263] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:48:21,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022787985.1_ASM2278798v1_genomic.fna/markers.fasta)
[2023-06-14 01:48:21,264] [INFO] Task started: Blastn
[2023-06-14 01:48:21,264] [INFO] Running command: blastn -query GCA_022787985.1_ASM2278798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg875470f0-5499-4390-950c-4423ba98d8db/dqc_reference/reference_markers_gtdb.fasta -out GCA_022787985.1_ASM2278798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:48:22,099] [INFO] Task succeeded: Blastn
[2023-06-14 01:48:22,103] [INFO] Selected 21 target genomes.
[2023-06-14 01:48:22,103] [INFO] Target genome list was writen to GCA_022787985.1_ASM2278798v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:48:22,181] [INFO] Task started: fastANI
[2023-06-14 01:48:22,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg87de4542-0d19-4c96-a0e5-117452c74692/GCA_022787985.1_ASM2278798v1_genomic.fna.gz --refList GCA_022787985.1_ASM2278798v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022787985.1_ASM2278798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:48:29,366] [INFO] Task succeeded: fastANI
[2023-06-14 01:48:29,380] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:48:29,380] [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_004556165.1	s__PeH17 sp004556165	98.3878	362	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.62	98.21	0.87	0.80	6	conclusive
GCA_900542285.1	s__PeH17 sp900542285	79.0745	125	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.90	98.16	0.94	0.91	7	-
GCA_001940845.1	s__PeH17 sp001940845	78.9848	72	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794055.1	s__PeH17 sp902794055	78.0607	69	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017395105.1	s__PeH17 sp017395105	77.5677	61	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017523925.1	s__PeH17 sp017523925	77.5267	84	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016282255.1	s__PeH17 sp016282255	77.3186	66	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:48:29,382] [INFO] GTDB search result was written to GCA_022787985.1_ASM2278798v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:48:29,383] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:48:29,386] [INFO] DFAST_QC result json was written to GCA_022787985.1_ASM2278798v1_genomic.fna/dqc_result.json
[2023-06-14 01:48:29,387] [INFO] DFAST_QC completed!
[2023-06-14 01:48:29,387] [INFO] Total running time: 0h0m47s