[2023-03-15 23:38:54,779] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:38:54,782] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:38:54,783] [INFO] DQC Reference Directory: /var/lib/cwl/stge9474799-bfb6-4d9c-81f4-9e660ca6391e/dqc_reference
[2023-03-15 23:38:55,875] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:38:55,876] [INFO] Task started: Prodigal
[2023-03-15 23:38:55,876] [INFO] Running command: cat /var/lib/cwl/stgcae1153d-50a5-409a-af07-7b6e40554487/OceanDNA-b11621.fa | prodigal -d OceanDNA-b11621/cds.fna -a OceanDNA-b11621/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:39:15,063] [INFO] Task succeeded: Prodigal
[2023-03-15 23:39:15,063] [INFO] Task started: HMMsearch
[2023-03-15 23:39:15,063] [INFO] Running command: hmmsearch --tblout OceanDNA-b11621/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9474799-bfb6-4d9c-81f4-9e660ca6391e/dqc_reference/reference_markers.hmm OceanDNA-b11621/protein.faa > /dev/null
[2023-03-15 23:39:15,239] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:39:15,240] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcae1153d-50a5-409a-af07-7b6e40554487/OceanDNA-b11621.fa]
[2023-03-15 23:39:15,355] [INFO] Query marker FASTA was written to OceanDNA-b11621/markers.fasta
[2023-03-15 23:39:15,356] [INFO] Task started: Blastn
[2023-03-15 23:39:15,356] [INFO] Running command: blastn -query OceanDNA-b11621/markers.fasta -db /var/lib/cwl/stge9474799-bfb6-4d9c-81f4-9e660ca6391e/dqc_reference/reference_markers.fasta -out OceanDNA-b11621/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:15,897] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:15,930] [INFO] Selected 20 target genomes.
[2023-03-15 23:39:15,931] [INFO] Target genome list was writen to OceanDNA-b11621/target_genomes.txt
[2023-03-15 23:39:15,941] [INFO] Task started: fastANI
[2023-03-15 23:39:15,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgcae1153d-50a5-409a-af07-7b6e40554487/OceanDNA-b11621.fa --refList OceanDNA-b11621/target_genomes.txt --output OceanDNA-b11621/fastani_result.tsv --threads 1
[2023-03-15 23:39:30,506] [INFO] Task succeeded: fastANI
[2023-03-15 23:39:30,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9474799-bfb6-4d9c-81f4-9e660ca6391e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:39:30,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9474799-bfb6-4d9c-81f4-9e660ca6391e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:39:30,507] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:39:30,507] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:39:30,507] [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
--------------------------------------------------------------------------------
[2023-03-15 23:39:30,518] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11621/tc_result.tsv
[2023-03-15 23:39:30,539] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:39:30,540] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:39:30,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9474799-bfb6-4d9c-81f4-9e660ca6391e/dqc_reference/checkm_data
[2023-03-15 23:39:30,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:39:30,552] [INFO] Task started: CheckM
[2023-03-15 23:39:30,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11621/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11621/checkm_input OceanDNA-b11621/checkm_result
[2023-03-15 23:40:21,480] [INFO] Task succeeded: CheckM
[2023-03-15 23:40:21,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:40:21,626] [INFO] ===== Completeness check finished =====
[2023-03-15 23:40:21,626] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:40:21,627] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11621/markers.fasta)
[2023-03-15 23:40:21,627] [INFO] Task started: Blastn
[2023-03-15 23:40:21,628] [INFO] Running command: blastn -query OceanDNA-b11621/markers.fasta -db /var/lib/cwl/stge9474799-bfb6-4d9c-81f4-9e660ca6391e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11621/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:40:22,358] [INFO] Task succeeded: Blastn
[2023-03-15 23:40:22,371] [INFO] Selected 29 target genomes.
[2023-03-15 23:40:22,371] [INFO] Target genome list was writen to OceanDNA-b11621/target_genomes_gtdb.txt
[2023-03-15 23:40:22,436] [INFO] Task started: fastANI
[2023-03-15 23:40:22,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgcae1153d-50a5-409a-af07-7b6e40554487/OceanDNA-b11621.fa --refList OceanDNA-b11621/target_genomes_gtdb.txt --output OceanDNA-b11621/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:40:38,972] [INFO] Task succeeded: fastANI
[2023-03-15 23:40:38,975] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:40:38,975] [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_002862785.1	s__UBA8752 sp002862785	76.4918	64	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478795.1	s__UBA8752 sp905478795	76.056	52	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:40:38,988] [INFO] GTDB search result was written to OceanDNA-b11621/result_gtdb.tsv
[2023-03-15 23:40:39,015] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:40:39,033] [INFO] DFAST_QC result json was written to OceanDNA-b11621/dqc_result.json
[2023-03-15 23:40:39,033] [INFO] DFAST_QC completed!
[2023-03-15 23:40:39,033] [INFO] Total running time: 0h1m44s