[2023-06-08 03:14:37,325] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:14:37,328] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:14:37,328] [INFO] DQC Reference Directory: /var/lib/cwl/stg301715b9-17ae-4f0d-809e-1e0599de097c/dqc_reference
[2023-06-08 03:14:39,365] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:14:39,367] [INFO] Task started: Prodigal
[2023-06-08 03:14:39,367] [INFO] Running command: gunzip -c /var/lib/cwl/stgae5c9c4a-1ece-454c-9df7-af0f89733f66/GCA_902635205.1_AG-914-O16_genomic.fna.gz | prodigal -d GCA_902635205.1_AG-914-O16_genomic.fna/cds.fna -a GCA_902635205.1_AG-914-O16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:14:40,899] [INFO] Task succeeded: Prodigal
[2023-06-08 03:14:40,900] [INFO] Task started: HMMsearch
[2023-06-08 03:14:40,900] [INFO] Running command: hmmsearch --tblout GCA_902635205.1_AG-914-O16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg301715b9-17ae-4f0d-809e-1e0599de097c/dqc_reference/reference_markers.hmm GCA_902635205.1_AG-914-O16_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:14:41,102] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:14:41,104] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgae5c9c4a-1ece-454c-9df7-af0f89733f66/GCA_902635205.1_AG-914-O16_genomic.fna.gz]
[2023-06-08 03:14:41,125] [INFO] Query marker FASTA was written to GCA_902635205.1_AG-914-O16_genomic.fna/markers.fasta
[2023-06-08 03:14:41,125] [INFO] Task started: Blastn
[2023-06-08 03:14:41,125] [INFO] Running command: blastn -query GCA_902635205.1_AG-914-O16_genomic.fna/markers.fasta -db /var/lib/cwl/stg301715b9-17ae-4f0d-809e-1e0599de097c/dqc_reference/reference_markers.fasta -out GCA_902635205.1_AG-914-O16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:42,496] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:42,500] [INFO] Selected 10 target genomes.
[2023-06-08 03:14:42,501] [INFO] Target genome list was writen to GCA_902635205.1_AG-914-O16_genomic.fna/target_genomes.txt
[2023-06-08 03:14:42,503] [INFO] Task started: fastANI
[2023-06-08 03:14:42,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgae5c9c4a-1ece-454c-9df7-af0f89733f66/GCA_902635205.1_AG-914-O16_genomic.fna.gz --refList GCA_902635205.1_AG-914-O16_genomic.fna/target_genomes.txt --output GCA_902635205.1_AG-914-O16_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:14:46,459] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:46,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg301715b9-17ae-4f0d-809e-1e0599de097c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:14:46,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg301715b9-17ae-4f0d-809e-1e0599de097c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:14:46,462] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:14:46,462] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:14:46,462] [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 03:14:46,465] [INFO] DFAST Taxonomy check result was written to GCA_902635205.1_AG-914-O16_genomic.fna/tc_result.tsv
[2023-06-08 03:14:46,465] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:14:46,466] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:14:46,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg301715b9-17ae-4f0d-809e-1e0599de097c/dqc_reference/checkm_data
[2023-06-08 03:14:46,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:14:46,483] [INFO] Task started: CheckM
[2023-06-08 03:14:46,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902635205.1_AG-914-O16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902635205.1_AG-914-O16_genomic.fna/checkm_input GCA_902635205.1_AG-914-O16_genomic.fna/checkm_result
[2023-06-08 03:14:59,863] [INFO] Task succeeded: CheckM
[2023-06-08 03:14:59,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:14:59,893] [INFO] ===== Completeness check finished =====
[2023-06-08 03:14:59,894] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:14:59,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902635205.1_AG-914-O16_genomic.fna/markers.fasta)
[2023-06-08 03:14:59,895] [INFO] Task started: Blastn
[2023-06-08 03:14:59,895] [INFO] Running command: blastn -query GCA_902635205.1_AG-914-O16_genomic.fna/markers.fasta -db /var/lib/cwl/stg301715b9-17ae-4f0d-809e-1e0599de097c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902635205.1_AG-914-O16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:15:00,374] [INFO] Task succeeded: Blastn
[2023-06-08 03:15:00,378] [INFO] Selected 9 target genomes.
[2023-06-08 03:15:00,378] [INFO] Target genome list was writen to GCA_902635205.1_AG-914-O16_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:15:00,381] [INFO] Task started: fastANI
[2023-06-08 03:15:00,381] [INFO] Running command: fastANI --query /var/lib/cwl/stgae5c9c4a-1ece-454c-9df7-af0f89733f66/GCA_902635205.1_AG-914-O16_genomic.fna.gz --refList GCA_902635205.1_AG-914-O16_genomic.fna/target_genomes_gtdb.txt --output GCA_902635205.1_AG-914-O16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:15:02,599] [INFO] Task succeeded: fastANI
[2023-06-08 03:15:02,609] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:15:02,610] [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_902613455.1	s__AG-339-G14 sp902613455	97.0913	262	270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.22	96.70	0.93	0.90	20	conclusive
GCA_003282105.1	s__AG-339-G14 sp003282105	92.5752	183	270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	95.52	95.11	0.79	0.67	11	-
GCA_902616715.1	s__AG-339-G14 sp902616715	79.2328	127	270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.52	98.27	0.93	0.90	8	-
GCA_004213955.1	s__AG-339-G14 sp004213955	78.8939	125	270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902562135.1	s__AG-339-G14 sp902562135	78.7228	96	270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.66	97.66	0.82	0.82	2	-
GCA_902527995.1	s__AG-339-G14 sp902527995	78.0961	78	270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536295.1	s__AG-339-G14 sp902536295	77.879	106	270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	97.79	97.73	0.85	0.77	3	-
--------------------------------------------------------------------------------
[2023-06-08 03:15:02,612] [INFO] GTDB search result was written to GCA_902635205.1_AG-914-O16_genomic.fna/result_gtdb.tsv
[2023-06-08 03:15:02,613] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:15:02,616] [INFO] DFAST_QC result json was written to GCA_902635205.1_AG-914-O16_genomic.fna/dqc_result.json
[2023-06-08 03:15:02,616] [INFO] DFAST_QC completed!
[2023-06-08 03:15:02,616] [INFO] Total running time: 0h0m25s