[2023-06-17 06:00:21,895] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:00:21,900] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:00:21,901] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf5fd344-b74e-4afd-adde-4f4813759c72/dqc_reference
[2023-06-17 06:00:23,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:00:23,461] [INFO] Task started: Prodigal
[2023-06-17 06:00:23,461] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb9f5cbe-63ff-4e16-87de-74521175b11e/GCA_905182175.1_FRAM18_bin217_genomic.fna.gz | prodigal -d GCA_905182175.1_FRAM18_bin217_genomic.fna/cds.fna -a GCA_905182175.1_FRAM18_bin217_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:00:35,379] [INFO] Task succeeded: Prodigal
[2023-06-17 06:00:35,380] [INFO] Task started: HMMsearch
[2023-06-17 06:00:35,380] [INFO] Running command: hmmsearch --tblout GCA_905182175.1_FRAM18_bin217_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf5fd344-b74e-4afd-adde-4f4813759c72/dqc_reference/reference_markers.hmm GCA_905182175.1_FRAM18_bin217_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:00:35,669] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:00:35,671] [INFO] Found 6/6 markers.
[2023-06-17 06:00:35,703] [INFO] Query marker FASTA was written to GCA_905182175.1_FRAM18_bin217_genomic.fna/markers.fasta
[2023-06-17 06:00:35,704] [INFO] Task started: Blastn
[2023-06-17 06:00:35,704] [INFO] Running command: blastn -query GCA_905182175.1_FRAM18_bin217_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf5fd344-b74e-4afd-adde-4f4813759c72/dqc_reference/reference_markers.fasta -out GCA_905182175.1_FRAM18_bin217_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:00:36,383] [INFO] Task succeeded: Blastn
[2023-06-17 06:00:36,388] [INFO] Selected 25 target genomes.
[2023-06-17 06:00:36,389] [INFO] Target genome list was writen to GCA_905182175.1_FRAM18_bin217_genomic.fna/target_genomes.txt
[2023-06-17 06:00:36,400] [INFO] Task started: fastANI
[2023-06-17 06:00:36,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb9f5cbe-63ff-4e16-87de-74521175b11e/GCA_905182175.1_FRAM18_bin217_genomic.fna.gz --refList GCA_905182175.1_FRAM18_bin217_genomic.fna/target_genomes.txt --output GCA_905182175.1_FRAM18_bin217_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:00:53,522] [INFO] Task succeeded: fastANI
[2023-06-17 06:00:53,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf5fd344-b74e-4afd-adde-4f4813759c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:00:53,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf5fd344-b74e-4afd-adde-4f4813759c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:00:53,527] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:00:53,527] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 06:00:53,527] [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
Acidiluteibacter ferrifornacis	strain=S-15	GCA_009909615.1	2692424	2692424	type	True	75.7289	50	1089	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 06:00:53,529] [INFO] DFAST Taxonomy check result was written to GCA_905182175.1_FRAM18_bin217_genomic.fna/tc_result.tsv
[2023-06-17 06:00:53,530] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:00:53,530] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:00:53,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf5fd344-b74e-4afd-adde-4f4813759c72/dqc_reference/checkm_data
[2023-06-17 06:00:53,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:00:53,574] [INFO] Task started: CheckM
[2023-06-17 06:00:53,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905182175.1_FRAM18_bin217_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905182175.1_FRAM18_bin217_genomic.fna/checkm_input GCA_905182175.1_FRAM18_bin217_genomic.fna/checkm_result
[2023-06-17 06:01:31,890] [INFO] Task succeeded: CheckM
[2023-06-17 06:01:31,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 06:01:31,918] [INFO] ===== Completeness check finished =====
[2023-06-17 06:01:31,919] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:01:31,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905182175.1_FRAM18_bin217_genomic.fna/markers.fasta)
[2023-06-17 06:01:31,920] [INFO] Task started: Blastn
[2023-06-17 06:01:31,920] [INFO] Running command: blastn -query GCA_905182175.1_FRAM18_bin217_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf5fd344-b74e-4afd-adde-4f4813759c72/dqc_reference/reference_markers_gtdb.fasta -out GCA_905182175.1_FRAM18_bin217_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:01:32,753] [INFO] Task succeeded: Blastn
[2023-06-17 06:01:32,758] [INFO] Selected 22 target genomes.
[2023-06-17 06:01:32,758] [INFO] Target genome list was writen to GCA_905182175.1_FRAM18_bin217_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:01:32,781] [INFO] Task started: fastANI
[2023-06-17 06:01:32,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb9f5cbe-63ff-4e16-87de-74521175b11e/GCA_905182175.1_FRAM18_bin217_genomic.fna.gz --refList GCA_905182175.1_FRAM18_bin217_genomic.fna/target_genomes_gtdb.txt --output GCA_905182175.1_FRAM18_bin217_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:01:43,876] [INFO] Task succeeded: fastANI
[2023-06-17 06:01:43,889] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 06:01:43,889] [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_905182175.1	s__NORP294 sp905182175	100.0	1086	1089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479325.1	s__NORP294 sp905479325	78.2097	328	1089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608405.1	s__NORP294 sp018608405	77.9231	312	1089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763995.1	s__NORP294 sp016763995	77.2282	184	1089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013112545.1	s__BCD18 sp013112545	76.3062	99	1089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BCD18	95.0	99.98	99.95	0.99	0.99	3	-
GCA_002415785.1	s__UBA5081 sp002415785	76.0081	89	1089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__UBA5081	95.0	99.97	99.97	0.98	0.96	4	-
GCF_009909615.1	s__Acidiluteibacter ferrifornacis	75.7289	50	1089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Acidiluteibacter	95.0	97.97	97.97	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-17 06:01:43,891] [INFO] GTDB search result was written to GCA_905182175.1_FRAM18_bin217_genomic.fna/result_gtdb.tsv
[2023-06-17 06:01:43,892] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:01:43,896] [INFO] DFAST_QC result json was written to GCA_905182175.1_FRAM18_bin217_genomic.fna/dqc_result.json
[2023-06-17 06:01:43,896] [INFO] DFAST_QC completed!
[2023-06-17 06:01:43,896] [INFO] Total running time: 0h1m22s