[2023-03-17 01:23:45,128] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,128] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,128] [INFO] DQC Reference Directory: /var/lib/cwl/stgeba069f0-8ea5-4c58-97e0-ada631cca492/dqc_reference
[2023-03-17 01:23:46,318] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,318] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,318] [INFO] Running command: cat /var/lib/cwl/stg201f9360-5025-4dfb-adcd-b9d941c23256/OceanDNA-b11462.fa | prodigal -d OceanDNA-b11462/cds.fna -a OceanDNA-b11462/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:24:02,292] [INFO] Task succeeded: Prodigal
[2023-03-17 01:24:02,293] [INFO] Task started: HMMsearch
[2023-03-17 01:24:02,293] [INFO] Running command: hmmsearch --tblout OceanDNA-b11462/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeba069f0-8ea5-4c58-97e0-ada631cca492/dqc_reference/reference_markers.hmm OceanDNA-b11462/protein.faa > /dev/null
[2023-03-17 01:24:02,465] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:24:02,465] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg201f9360-5025-4dfb-adcd-b9d941c23256/OceanDNA-b11462.fa]
[2023-03-17 01:24:02,479] [INFO] Query marker FASTA was written to OceanDNA-b11462/markers.fasta
[2023-03-17 01:24:02,479] [INFO] Task started: Blastn
[2023-03-17 01:24:02,479] [INFO] Running command: blastn -query OceanDNA-b11462/markers.fasta -db /var/lib/cwl/stgeba069f0-8ea5-4c58-97e0-ada631cca492/dqc_reference/reference_markers.fasta -out OceanDNA-b11462/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:03,016] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:03,016] [INFO] Selected 30 target genomes.
[2023-03-17 01:24:03,017] [INFO] Target genome list was writen to OceanDNA-b11462/target_genomes.txt
[2023-03-17 01:24:03,032] [INFO] Task started: fastANI
[2023-03-17 01:24:03,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg201f9360-5025-4dfb-adcd-b9d941c23256/OceanDNA-b11462.fa --refList OceanDNA-b11462/target_genomes.txt --output OceanDNA-b11462/fastani_result.tsv --threads 1
[2023-03-17 01:24:20,301] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:20,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeba069f0-8ea5-4c58-97e0-ada631cca492/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:24:20,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeba069f0-8ea5-4c58-97e0-ada631cca492/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:24:20,302] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:24:20,302] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 01:24:20,302] [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
--------------------------------------------------------------------------------
[2023-03-17 01:24:20,302] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11462/tc_result.tsv
[2023-03-17 01:24:20,302] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:24:20,302] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:24:20,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeba069f0-8ea5-4c58-97e0-ada631cca492/dqc_reference/checkm_data
[2023-03-17 01:24:20,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:24:20,308] [INFO] Task started: CheckM
[2023-03-17 01:24:20,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11462/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11462/checkm_input OceanDNA-b11462/checkm_result
[2023-03-17 01:25:03,596] [INFO] Task succeeded: CheckM
[2023-03-17 01:25:03,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:25:03,598] [INFO] ===== Completeness check finished =====
[2023-03-17 01:25:03,599] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:25:03,599] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11462/markers.fasta)
[2023-03-17 01:25:03,599] [INFO] Task started: Blastn
[2023-03-17 01:25:03,600] [INFO] Running command: blastn -query OceanDNA-b11462/markers.fasta -db /var/lib/cwl/stgeba069f0-8ea5-4c58-97e0-ada631cca492/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11462/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:25:04,387] [INFO] Task succeeded: Blastn
[2023-03-17 01:25:04,388] [INFO] Selected 26 target genomes.
[2023-03-17 01:25:04,388] [INFO] Target genome list was writen to OceanDNA-b11462/target_genomes_gtdb.txt
[2023-03-17 01:25:05,206] [INFO] Task started: fastANI
[2023-03-17 01:25:05,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg201f9360-5025-4dfb-adcd-b9d941c23256/OceanDNA-b11462.fa --refList OceanDNA-b11462/target_genomes_gtdb.txt --output OceanDNA-b11462/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:25:19,101] [INFO] Task succeeded: fastANI
[2023-03-17 01:25:19,104] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:25:19,104] [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_903825395.1	s__CAIKAF01 sp903825395	94.2853	604	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__CAIKAF01;g__CAIKAF01	95.0	99.98	99.96	0.99	0.99	7	-
GCA_016866335.1	s__CAIKAF01 sp016866335	78.2879	224	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__CAIKAF01;g__CAIKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837495.1	s__CAIKAF01 sp903837495	78.1147	264	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__CAIKAF01;g__CAIKAF01	95.0	97.84	97.84	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-17 01:25:19,104] [INFO] GTDB search result was written to OceanDNA-b11462/result_gtdb.tsv
[2023-03-17 01:25:19,104] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:25:19,105] [INFO] DFAST_QC result json was written to OceanDNA-b11462/dqc_result.json
[2023-03-17 01:25:19,105] [INFO] DFAST_QC completed!
[2023-03-17 01:25:19,105] [INFO] Total running time: 0h1m34s