[2023-06-08 06:51:29,220] [INFO] DFAST_QC pipeline started.
[2023-06-08 06:51:29,227] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 06:51:29,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg88a0da73-9cf8-4b1b-b5cf-77d1a6ecbe38/dqc_reference
[2023-06-08 06:51:30,814] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 06:51:30,814] [INFO] Task started: Prodigal
[2023-06-08 06:51:30,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a34f355-bece-4f81-b911-367988062821/GCA_902623155.1_AG-893-M13_genomic.fna.gz | prodigal -d GCA_902623155.1_AG-893-M13_genomic.fna/cds.fna -a GCA_902623155.1_AG-893-M13_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 06:51:32,337] [INFO] Task succeeded: Prodigal
[2023-06-08 06:51:32,337] [INFO] Task started: HMMsearch
[2023-06-08 06:51:32,337] [INFO] Running command: hmmsearch --tblout GCA_902623155.1_AG-893-M13_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88a0da73-9cf8-4b1b-b5cf-77d1a6ecbe38/dqc_reference/reference_markers.hmm GCA_902623155.1_AG-893-M13_genomic.fna/protein.faa > /dev/null
[2023-06-08 06:51:32,514] [INFO] Task succeeded: HMMsearch
[2023-06-08 06:51:32,516] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8a34f355-bece-4f81-b911-367988062821/GCA_902623155.1_AG-893-M13_genomic.fna.gz]
[2023-06-08 06:51:32,535] [INFO] Query marker FASTA was written to GCA_902623155.1_AG-893-M13_genomic.fna/markers.fasta
[2023-06-08 06:51:32,536] [INFO] Task started: Blastn
[2023-06-08 06:51:32,536] [INFO] Running command: blastn -query GCA_902623155.1_AG-893-M13_genomic.fna/markers.fasta -db /var/lib/cwl/stg88a0da73-9cf8-4b1b-b5cf-77d1a6ecbe38/dqc_reference/reference_markers.fasta -out GCA_902623155.1_AG-893-M13_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:51:33,061] [INFO] Task succeeded: Blastn
[2023-06-08 06:51:33,065] [INFO] Selected 15 target genomes.
[2023-06-08 06:51:33,065] [INFO] Target genome list was writen to GCA_902623155.1_AG-893-M13_genomic.fna/target_genomes.txt
[2023-06-08 06:51:33,069] [INFO] Task started: fastANI
[2023-06-08 06:51:33,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a34f355-bece-4f81-b911-367988062821/GCA_902623155.1_AG-893-M13_genomic.fna.gz --refList GCA_902623155.1_AG-893-M13_genomic.fna/target_genomes.txt --output GCA_902623155.1_AG-893-M13_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 06:51:42,825] [INFO] Task succeeded: fastANI
[2023-06-08 06:51:42,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88a0da73-9cf8-4b1b-b5cf-77d1a6ecbe38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 06:51:42,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88a0da73-9cf8-4b1b-b5cf-77d1a6ecbe38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 06:51:42,827] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 06:51:42,828] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 06:51:42,828] [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
--------------------------------------------------------------------------------
[2023-06-08 06:51:42,830] [INFO] DFAST Taxonomy check result was written to GCA_902623155.1_AG-893-M13_genomic.fna/tc_result.tsv
[2023-06-08 06:51:42,830] [INFO] ===== Taxonomy check completed =====
[2023-06-08 06:51:42,830] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 06:51:42,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88a0da73-9cf8-4b1b-b5cf-77d1a6ecbe38/dqc_reference/checkm_data
[2023-06-08 06:51:42,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 06:51:42,843] [INFO] Task started: CheckM
[2023-06-08 06:51:42,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902623155.1_AG-893-M13_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902623155.1_AG-893-M13_genomic.fna/checkm_input GCA_902623155.1_AG-893-M13_genomic.fna/checkm_result
[2023-06-08 06:51:56,682] [INFO] Task succeeded: CheckM
[2023-06-08 06:51:56,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.10%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 06:51:56,718] [INFO] ===== Completeness check finished =====
[2023-06-08 06:51:56,718] [INFO] ===== Start GTDB Search =====
[2023-06-08 06:51:56,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902623155.1_AG-893-M13_genomic.fna/markers.fasta)
[2023-06-08 06:51:56,719] [INFO] Task started: Blastn
[2023-06-08 06:51:56,719] [INFO] Running command: blastn -query GCA_902623155.1_AG-893-M13_genomic.fna/markers.fasta -db /var/lib/cwl/stg88a0da73-9cf8-4b1b-b5cf-77d1a6ecbe38/dqc_reference/reference_markers_gtdb.fasta -out GCA_902623155.1_AG-893-M13_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:51:57,346] [INFO] Task succeeded: Blastn
[2023-06-08 06:51:57,349] [INFO] Selected 8 target genomes.
[2023-06-08 06:51:57,350] [INFO] Target genome list was writen to GCA_902623155.1_AG-893-M13_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 06:51:57,354] [INFO] Task started: fastANI
[2023-06-08 06:51:57,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a34f355-bece-4f81-b911-367988062821/GCA_902623155.1_AG-893-M13_genomic.fna.gz --refList GCA_902623155.1_AG-893-M13_genomic.fna/target_genomes_gtdb.txt --output GCA_902623155.1_AG-893-M13_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 06:51:58,963] [INFO] Task succeeded: fastANI
[2023-06-08 06:51:58,972] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 06:51:58,972] [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_902583445.1	s__MED-G11 sp902583445	98.8111	115	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.54	95.81	0.70	0.67	3	conclusive
GCA_902617285.1	s__MED-G11 sp902617285	93.3506	118	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.97	95.44	0.83	0.80	4	-
GCA_016780245.1	s__MED-G11 sp016780245	91.45	106	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.94	99.94	0.84	0.84	2	-
GCA_902594745.1	s__MED-G11 sp902594745	90.8408	123	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.86	97.86	0.89	0.89	2	-
GCA_902560025.1	s__MED-G11 sp902560025	90.5797	89	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902577515.1	s__MED-G11 sp902577515	89.7269	108	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.13	99.13	0.84	0.84	2	-
GCA_017856235.1	s__MED-G11 sp017856235	87.9556	120	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.25	98.96	0.92	0.89	4	-
GCA_902598525.1	s__MED-G11 sp902598525	84.836	111	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.61	96.61	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-08 06:51:58,974] [INFO] GTDB search result was written to GCA_902623155.1_AG-893-M13_genomic.fna/result_gtdb.tsv
[2023-06-08 06:51:58,975] [INFO] ===== GTDB Search completed =====
[2023-06-08 06:51:58,978] [INFO] DFAST_QC result json was written to GCA_902623155.1_AG-893-M13_genomic.fna/dqc_result.json
[2023-06-08 06:51:58,979] [INFO] DFAST_QC completed!
[2023-06-08 06:51:58,979] [INFO] Total running time: 0h0m30s