[2023-06-30 22:12:46,062] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:12:46,066] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:12:46,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg050d9106-6b71-4e64-bc1d-7145869ea006/dqc_reference
[2023-06-30 22:12:48,286] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:12:48,287] [INFO] Task started: Prodigal
[2023-06-30 22:12:48,288] [INFO] Running command: gunzip -c /var/lib/cwl/stg328b01a2-cfd5-4dcd-be91-2d0540a063c0/GCA_016708105.1_ASM1670810v1_genomic.fna.gz | prodigal -d GCA_016708105.1_ASM1670810v1_genomic.fna/cds.fna -a GCA_016708105.1_ASM1670810v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:13:07,601] [INFO] Task succeeded: Prodigal
[2023-06-30 22:13:07,602] [INFO] Task started: HMMsearch
[2023-06-30 22:13:07,602] [INFO] Running command: hmmsearch --tblout GCA_016708105.1_ASM1670810v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg050d9106-6b71-4e64-bc1d-7145869ea006/dqc_reference/reference_markers.hmm GCA_016708105.1_ASM1670810v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:13:07,872] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:13:07,874] [INFO] Found 6/6 markers.
[2023-06-30 22:13:07,912] [INFO] Query marker FASTA was written to GCA_016708105.1_ASM1670810v1_genomic.fna/markers.fasta
[2023-06-30 22:13:07,913] [INFO] Task started: Blastn
[2023-06-30 22:13:07,913] [INFO] Running command: blastn -query GCA_016708105.1_ASM1670810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg050d9106-6b71-4e64-bc1d-7145869ea006/dqc_reference/reference_markers.fasta -out GCA_016708105.1_ASM1670810v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:13:08,504] [INFO] Task succeeded: Blastn
[2023-06-30 22:13:08,509] [INFO] Selected 31 target genomes.
[2023-06-30 22:13:08,510] [INFO] Target genome list was writen to GCA_016708105.1_ASM1670810v1_genomic.fna/target_genomes.txt
[2023-06-30 22:13:08,512] [INFO] Task started: fastANI
[2023-06-30 22:13:08,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg328b01a2-cfd5-4dcd-be91-2d0540a063c0/GCA_016708105.1_ASM1670810v1_genomic.fna.gz --refList GCA_016708105.1_ASM1670810v1_genomic.fna/target_genomes.txt --output GCA_016708105.1_ASM1670810v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:13:25,482] [INFO] Task succeeded: fastANI
[2023-06-30 22:13:25,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg050d9106-6b71-4e64-bc1d-7145869ea006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:13:25,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg050d9106-6b71-4e64-bc1d-7145869ea006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:13:25,489] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:13:25,489] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 22:13:25,489] [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
Crocinitomix algicola	strain=0182	GCA_001661595.2	1740263	1740263	type	True	75.962	52	1416	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 22:13:25,492] [INFO] DFAST Taxonomy check result was written to GCA_016708105.1_ASM1670810v1_genomic.fna/tc_result.tsv
[2023-06-30 22:13:25,492] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:13:25,493] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:13:25,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg050d9106-6b71-4e64-bc1d-7145869ea006/dqc_reference/checkm_data
[2023-06-30 22:13:25,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:13:25,540] [INFO] Task started: CheckM
[2023-06-30 22:13:25,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708105.1_ASM1670810v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708105.1_ASM1670810v1_genomic.fna/checkm_input GCA_016708105.1_ASM1670810v1_genomic.fna/checkm_result
[2023-06-30 22:14:25,509] [INFO] Task succeeded: CheckM
[2023-06-30 22:14:25,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:14:25,533] [INFO] ===== Completeness check finished =====
[2023-06-30 22:14:25,534] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:14:25,534] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708105.1_ASM1670810v1_genomic.fna/markers.fasta)
[2023-06-30 22:14:25,535] [INFO] Task started: Blastn
[2023-06-30 22:14:25,535] [INFO] Running command: blastn -query GCA_016708105.1_ASM1670810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg050d9106-6b71-4e64-bc1d-7145869ea006/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708105.1_ASM1670810v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:14:26,298] [INFO] Task succeeded: Blastn
[2023-06-30 22:14:26,316] [INFO] Selected 25 target genomes.
[2023-06-30 22:14:26,316] [INFO] Target genome list was writen to GCA_016708105.1_ASM1670810v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:14:26,346] [INFO] Task started: fastANI
[2023-06-30 22:14:26,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg328b01a2-cfd5-4dcd-be91-2d0540a063c0/GCA_016708105.1_ASM1670810v1_genomic.fna.gz --refList GCA_016708105.1_ASM1670810v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708105.1_ASM1670810v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:14:41,131] [INFO] Task succeeded: fastANI
[2023-06-30 22:14:41,140] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:14:41,140] [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_016708105.1	s__JADJGJ01 sp016708105	100.0	1414	1416	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	99.76	99.76	0.97	0.97	2	conclusive
GCA_016719925.1	s__JADJGJ01 sp016719925	77.7702	351	1416	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709005.1	s__JADJGJ01 sp016709005	77.5313	306	1416	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	98.05	97.64	0.91	0.88	3	-
GCA_016192075.1	s__JADJGJ01 sp016192075	77.3776	287	1416	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661595.2	s__Crocinitomix algicola	75.962	52	1416	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:14:41,143] [INFO] GTDB search result was written to GCA_016708105.1_ASM1670810v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:14:41,143] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:14:41,146] [INFO] DFAST_QC result json was written to GCA_016708105.1_ASM1670810v1_genomic.fna/dqc_result.json
[2023-06-30 22:14:41,146] [INFO] DFAST_QC completed!
[2023-06-30 22:14:41,146] [INFO] Total running time: 0h1m55s