[2023-03-18 04:38:00,488] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:38:00,488] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:38:00,488] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1d9a035-221a-49c3-864d-6654a03eccd2/dqc_reference
[2023-03-18 04:38:01,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:38:01,597] [INFO] Task started: Prodigal
[2023-03-18 04:38:01,597] [INFO] Running command: cat /var/lib/cwl/stgc776970a-ba62-496a-a424-6abb9a9290fb/OceanDNA-b7560.fa | prodigal -d OceanDNA-b7560/cds.fna -a OceanDNA-b7560/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:38:08,058] [INFO] Task succeeded: Prodigal
[2023-03-18 04:38:08,058] [INFO] Task started: HMMsearch
[2023-03-18 04:38:08,058] [INFO] Running command: hmmsearch --tblout OceanDNA-b7560/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1d9a035-221a-49c3-864d-6654a03eccd2/dqc_reference/reference_markers.hmm OceanDNA-b7560/protein.faa > /dev/null
[2023-03-18 04:38:08,202] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:38:08,203] [INFO] Found 6/6 markers.
[2023-03-18 04:38:08,215] [INFO] Query marker FASTA was written to OceanDNA-b7560/markers.fasta
[2023-03-18 04:38:08,216] [INFO] Task started: Blastn
[2023-03-18 04:38:08,216] [INFO] Running command: blastn -query OceanDNA-b7560/markers.fasta -db /var/lib/cwl/stgd1d9a035-221a-49c3-864d-6654a03eccd2/dqc_reference/reference_markers.fasta -out OceanDNA-b7560/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:08,786] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:08,788] [INFO] Selected 28 target genomes.
[2023-03-18 04:38:08,788] [INFO] Target genome list was writen to OceanDNA-b7560/target_genomes.txt
[2023-03-18 04:38:08,803] [INFO] Task started: fastANI
[2023-03-18 04:38:08,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgc776970a-ba62-496a-a424-6abb9a9290fb/OceanDNA-b7560.fa --refList OceanDNA-b7560/target_genomes.txt --output OceanDNA-b7560/fastani_result.tsv --threads 1
[2023-03-18 04:38:23,701] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:23,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1d9a035-221a-49c3-864d-6654a03eccd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:38:23,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1d9a035-221a-49c3-864d-6654a03eccd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:38:23,702] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:38:23,702] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:38:23,702] [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
--------------------------------------------------------------------------------
[2023-03-18 04:38:23,703] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7560/tc_result.tsv
[2023-03-18 04:38:23,703] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:38:23,704] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:38:23,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1d9a035-221a-49c3-864d-6654a03eccd2/dqc_reference/checkm_data
[2023-03-18 04:38:23,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:38:23,710] [INFO] Task started: CheckM
[2023-03-18 04:38:23,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7560/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7560/checkm_input OceanDNA-b7560/checkm_result
[2023-03-18 04:38:45,721] [INFO] Task succeeded: CheckM
[2023-03-18 04:38:45,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:38:45,724] [INFO] ===== Completeness check finished =====
[2023-03-18 04:38:45,724] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:38:45,724] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7560/markers.fasta)
[2023-03-18 04:38:45,726] [INFO] Task started: Blastn
[2023-03-18 04:38:45,726] [INFO] Running command: blastn -query OceanDNA-b7560/markers.fasta -db /var/lib/cwl/stgd1d9a035-221a-49c3-864d-6654a03eccd2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7560/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:46,493] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:46,494] [INFO] Selected 17 target genomes.
[2023-03-18 04:38:46,494] [INFO] Target genome list was writen to OceanDNA-b7560/target_genomes_gtdb.txt
[2023-03-18 04:38:46,506] [INFO] Task started: fastANI
[2023-03-18 04:38:46,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgc776970a-ba62-496a-a424-6abb9a9290fb/OceanDNA-b7560.fa --refList OceanDNA-b7560/target_genomes_gtdb.txt --output OceanDNA-b7560/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:38:54,771] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:54,774] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:38:54,775] [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_018401115.1	s__MAG-120531 sp018401115	92.895	188	190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182295.1	s__MAG-120531 sp905182295	87.2997	123	190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173115.1	s__MAG-120531 sp000173115	86.6558	146	190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	99.02	98.72	0.73	0.67	33	-
GCA_018500065.1	s__MAG-120531 sp018500065	78.5607	85	190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:38:54,776] [INFO] GTDB search result was written to OceanDNA-b7560/result_gtdb.tsv
[2023-03-18 04:38:54,776] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:38:54,778] [INFO] DFAST_QC result json was written to OceanDNA-b7560/dqc_result.json
[2023-03-18 04:38:54,778] [INFO] DFAST_QC completed!
[2023-03-18 04:38:54,778] [INFO] Total running time: 0h0m54s