[2023-06-07 22:55:00,323] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:55:00,325] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:55:00,325] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbe0dd10-fef8-4357-b6ca-80a81033e819/dqc_reference
[2023-06-07 22:55:01,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:55:01,589] [INFO] Task started: Prodigal
[2023-06-07 22:55:01,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg581d39bc-c04f-4ffd-89d7-a3294b48ad8a/GCA_902616635.1_AG-919-K15_genomic.fna.gz | prodigal -d GCA_902616635.1_AG-919-K15_genomic.fna/cds.fna -a GCA_902616635.1_AG-919-K15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:55:04,306] [INFO] Task succeeded: Prodigal
[2023-06-07 22:55:04,306] [INFO] Task started: HMMsearch
[2023-06-07 22:55:04,306] [INFO] Running command: hmmsearch --tblout GCA_902616635.1_AG-919-K15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbe0dd10-fef8-4357-b6ca-80a81033e819/dqc_reference/reference_markers.hmm GCA_902616635.1_AG-919-K15_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:55:04,555] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:55:04,557] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg581d39bc-c04f-4ffd-89d7-a3294b48ad8a/GCA_902616635.1_AG-919-K15_genomic.fna.gz]
[2023-06-07 22:55:04,582] [INFO] Query marker FASTA was written to GCA_902616635.1_AG-919-K15_genomic.fna/markers.fasta
[2023-06-07 22:55:04,583] [INFO] Task started: Blastn
[2023-06-07 22:55:04,583] [INFO] Running command: blastn -query GCA_902616635.1_AG-919-K15_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbe0dd10-fef8-4357-b6ca-80a81033e819/dqc_reference/reference_markers.fasta -out GCA_902616635.1_AG-919-K15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:05,190] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:05,195] [INFO] Selected 25 target genomes.
[2023-06-07 22:55:05,196] [INFO] Target genome list was writen to GCA_902616635.1_AG-919-K15_genomic.fna/target_genomes.txt
[2023-06-07 22:55:05,199] [INFO] Task started: fastANI
[2023-06-07 22:55:05,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg581d39bc-c04f-4ffd-89d7-a3294b48ad8a/GCA_902616635.1_AG-919-K15_genomic.fna.gz --refList GCA_902616635.1_AG-919-K15_genomic.fna/target_genomes.txt --output GCA_902616635.1_AG-919-K15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:55:18,564] [INFO] Task succeeded: fastANI
[2023-06-07 22:55:18,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbe0dd10-fef8-4357-b6ca-80a81033e819/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:55:18,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbe0dd10-fef8-4357-b6ca-80a81033e819/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:55:18,567] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:55:18,567] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 22:55:18,567] [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
--------------------------------------------------------------------------------
[2023-06-07 22:55:18,570] [INFO] DFAST Taxonomy check result was written to GCA_902616635.1_AG-919-K15_genomic.fna/tc_result.tsv
[2023-06-07 22:55:18,571] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:55:18,571] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:55:18,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbe0dd10-fef8-4357-b6ca-80a81033e819/dqc_reference/checkm_data
[2023-06-07 22:55:18,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:55:18,589] [INFO] Task started: CheckM
[2023-06-07 22:55:18,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902616635.1_AG-919-K15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902616635.1_AG-919-K15_genomic.fna/checkm_input GCA_902616635.1_AG-919-K15_genomic.fna/checkm_result
[2023-06-07 22:55:34,561] [INFO] Task succeeded: CheckM
[2023-06-07 22:55:34,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:55:34,580] [INFO] ===== Completeness check finished =====
[2023-06-07 22:55:34,580] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:55:34,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902616635.1_AG-919-K15_genomic.fna/markers.fasta)
[2023-06-07 22:55:34,581] [INFO] Task started: Blastn
[2023-06-07 22:55:34,581] [INFO] Running command: blastn -query GCA_902616635.1_AG-919-K15_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbe0dd10-fef8-4357-b6ca-80a81033e819/dqc_reference/reference_markers_gtdb.fasta -out GCA_902616635.1_AG-919-K15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:35,429] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:35,437] [INFO] Selected 8 target genomes.
[2023-06-07 22:55:35,437] [INFO] Target genome list was writen to GCA_902616635.1_AG-919-K15_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:55:35,439] [INFO] Task started: fastANI
[2023-06-07 22:55:35,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg581d39bc-c04f-4ffd-89d7-a3294b48ad8a/GCA_902616635.1_AG-919-K15_genomic.fna.gz --refList GCA_902616635.1_AG-919-K15_genomic.fna/target_genomes_gtdb.txt --output GCA_902616635.1_AG-919-K15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:55:37,315] [INFO] Task succeeded: fastANI
[2023-06-07 22:55:37,324] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:55:37,324] [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_902554655.1	s__MED-G14 sp902554655	99.5909	192	308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.59	99.59	0.62	0.62	2	conclusive
GCA_902520835.1	s__MED-G14 sp902520835	94.0991	234	308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457715.1	s__MED-G14 sp002457715	92.9692	185	308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	98.34	98.31	0.91	0.89	3	-
GCA_002693085.1	s__MED-G14 sp002693085	87.5877	144	308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702385.1	s__MED-G14 sp002702385	85.3213	155	308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587325.1	s__MED-G14 sp902587325	81.8008	180	308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.53	95.17	0.82	0.78	10	-
GCA_004321735.1	s__MED-G14 sp004321735	77.6186	101	308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.77	95.40	0.78	0.75	4	-
GCA_003331885.1	s__MED-G14 sp003331885	76.8615	70	308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.85	96.85	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-07 22:55:37,326] [INFO] GTDB search result was written to GCA_902616635.1_AG-919-K15_genomic.fna/result_gtdb.tsv
[2023-06-07 22:55:37,327] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:55:37,330] [INFO] DFAST_QC result json was written to GCA_902616635.1_AG-919-K15_genomic.fna/dqc_result.json
[2023-06-07 22:55:37,330] [INFO] DFAST_QC completed!
[2023-06-07 22:55:37,330] [INFO] Total running time: 0h0m37s