[2023-03-15 12:44:24,482] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,482] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgf378f3f7-2e32-40c7-9272-3437ca54a876/dqc_reference
[2023-03-15 12:44:26,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,208] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,208] [INFO] Running command: cat /var/lib/cwl/stg63d9d425-ba71-407b-b53c-b75188d3fd18/OceanDNA-b11976.fa | prodigal -d OceanDNA-b11976/cds.fna -a OceanDNA-b11976/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:46,628] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:46,629] [INFO] Task started: HMMsearch
[2023-03-15 12:44:46,629] [INFO] Running command: hmmsearch --tblout OceanDNA-b11976/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf378f3f7-2e32-40c7-9272-3437ca54a876/dqc_reference/reference_markers.hmm OceanDNA-b11976/protein.faa > /dev/null
[2023-03-15 12:44:46,850] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:46,850] [INFO] Found 6/6 markers.
[2023-03-15 12:44:46,865] [INFO] Query marker FASTA was written to OceanDNA-b11976/markers.fasta
[2023-03-15 12:44:46,865] [INFO] Task started: Blastn
[2023-03-15 12:44:46,865] [INFO] Running command: blastn -query OceanDNA-b11976/markers.fasta -db /var/lib/cwl/stgf378f3f7-2e32-40c7-9272-3437ca54a876/dqc_reference/reference_markers.fasta -out OceanDNA-b11976/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:47,416] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:47,417] [INFO] Selected 22 target genomes.
[2023-03-15 12:44:47,417] [INFO] Target genome list was writen to OceanDNA-b11976/target_genomes.txt
[2023-03-15 12:44:47,429] [INFO] Task started: fastANI
[2023-03-15 12:44:47,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg63d9d425-ba71-407b-b53c-b75188d3fd18/OceanDNA-b11976.fa --refList OceanDNA-b11976/target_genomes.txt --output OceanDNA-b11976/fastani_result.tsv --threads 1
[2023-03-15 12:44:59,968] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:59,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf378f3f7-2e32-40c7-9272-3437ca54a876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:59,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf378f3f7-2e32-40c7-9272-3437ca54a876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:59,969] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:59,969] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:44:59,969] [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 12:44:59,969] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11976/tc_result.tsv
[2023-03-15 12:44:59,969] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:59,969] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:59,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf378f3f7-2e32-40c7-9272-3437ca54a876/dqc_reference/checkm_data
[2023-03-15 12:44:59,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:45:00,017] [INFO] Task started: CheckM
[2023-03-15 12:45:00,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11976/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11976/checkm_input OceanDNA-b11976/checkm_result
[2023-03-15 12:45:54,386] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:54,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:54,389] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:54,389] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:54,389] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11976/markers.fasta)
[2023-03-15 12:45:54,390] [INFO] Task started: Blastn
[2023-03-15 12:45:54,391] [INFO] Running command: blastn -query OceanDNA-b11976/markers.fasta -db /var/lib/cwl/stgf378f3f7-2e32-40c7-9272-3437ca54a876/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11976/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:55,232] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:55,233] [INFO] Selected 29 target genomes.
[2023-03-15 12:45:55,233] [INFO] Target genome list was writen to OceanDNA-b11976/target_genomes_gtdb.txt
[2023-03-15 12:45:55,453] [INFO] Task started: fastANI
[2023-03-15 12:45:55,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg63d9d425-ba71-407b-b53c-b75188d3fd18/OceanDNA-b11976.fa --refList OceanDNA-b11976/target_genomes_gtdb.txt --output OceanDNA-b11976/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:46:08,507] [INFO] Task succeeded: fastANI
[2023-03-15 12:46:08,512] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:46:08,512] [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_905478795.1	s__UBA8752 sp905478795	78.1881	160	581	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336475.1	s__UBA8752 sp002336475	77.8044	143	581	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.51	99.51	0.88	0.88	2	-
GCA_002172485.2	s__UBA8752 sp002172485	77.7942	121	581	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862785.1	s__UBA8752 sp002862785	77.7786	161	581	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389295.1	s__UBA8752 sp002389295	77.748	150	581	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.36	99.34	0.83	0.82	3	-
GCA_902535565.1	s__UBA8752 sp902535565	77.4662	67	581	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522855.1	s__UBA8752 sp011522855	77.2375	91	581	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720375.1	s__UBA8752 sp002720375	77.1238	78	581	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 12:46:08,513] [INFO] GTDB search result was written to OceanDNA-b11976/result_gtdb.tsv
[2023-03-15 12:46:08,513] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:46:08,514] [INFO] DFAST_QC result json was written to OceanDNA-b11976/dqc_result.json
[2023-03-15 12:46:08,514] [INFO] DFAST_QC completed!
[2023-03-15 12:46:08,514] [INFO] Total running time: 0h1m44s