[2023-03-15 10:09:49,678] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:09:49,679] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:09:49,679] [INFO] DQC Reference Directory: /var/lib/cwl/stgb775a47b-acd7-43de-b84e-d69e394e2b1c/dqc_reference
[2023-03-15 10:09:51,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:09:51,537] [INFO] Task started: Prodigal
[2023-03-15 10:09:51,537] [INFO] Running command: cat /var/lib/cwl/stg9ef56481-784d-4d20-8c4d-faaf13711e89/OceanDNA-b11211.fa | prodigal -d OceanDNA-b11211/cds.fna -a OceanDNA-b11211/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:10:01,915] [INFO] Task succeeded: Prodigal
[2023-03-15 10:10:01,916] [INFO] Task started: HMMsearch
[2023-03-15 10:10:01,916] [INFO] Running command: hmmsearch --tblout OceanDNA-b11211/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb775a47b-acd7-43de-b84e-d69e394e2b1c/dqc_reference/reference_markers.hmm OceanDNA-b11211/protein.faa > /dev/null
[2023-03-15 10:10:02,107] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:10:02,108] [INFO] Found 6/6 markers.
[2023-03-15 10:10:02,118] [INFO] Query marker FASTA was written to OceanDNA-b11211/markers.fasta
[2023-03-15 10:10:02,118] [INFO] Task started: Blastn
[2023-03-15 10:10:02,118] [INFO] Running command: blastn -query OceanDNA-b11211/markers.fasta -db /var/lib/cwl/stgb775a47b-acd7-43de-b84e-d69e394e2b1c/dqc_reference/reference_markers.fasta -out OceanDNA-b11211/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:02,656] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:02,657] [INFO] Selected 29 target genomes.
[2023-03-15 10:10:02,657] [INFO] Target genome list was writen to OceanDNA-b11211/target_genomes.txt
[2023-03-15 10:10:02,700] [INFO] Task started: fastANI
[2023-03-15 10:10:02,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef56481-784d-4d20-8c4d-faaf13711e89/OceanDNA-b11211.fa --refList OceanDNA-b11211/target_genomes.txt --output OceanDNA-b11211/fastani_result.tsv --threads 1
[2023-03-15 10:10:18,916] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:18,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb775a47b-acd7-43de-b84e-d69e394e2b1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:10:18,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb775a47b-acd7-43de-b84e-d69e394e2b1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:10:18,917] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:10:18,917] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:10:18,917] [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 10:10:18,917] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11211/tc_result.tsv
[2023-03-15 10:10:18,917] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:10:18,917] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:10:18,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb775a47b-acd7-43de-b84e-d69e394e2b1c/dqc_reference/checkm_data
[2023-03-15 10:10:18,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:10:19,009] [INFO] Task started: CheckM
[2023-03-15 10:10:19,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11211/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11211/checkm_input OceanDNA-b11211/checkm_result
[2023-03-15 10:10:50,181] [INFO] Task succeeded: CheckM
[2023-03-15 10:10:50,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:10:50,223] [INFO] ===== Completeness check finished =====
[2023-03-15 10:10:50,223] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:10:50,224] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11211/markers.fasta)
[2023-03-15 10:10:50,225] [INFO] Task started: Blastn
[2023-03-15 10:10:50,225] [INFO] Running command: blastn -query OceanDNA-b11211/markers.fasta -db /var/lib/cwl/stgb775a47b-acd7-43de-b84e-d69e394e2b1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11211/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:50,983] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:50,987] [INFO] Selected 9 target genomes.
[2023-03-15 10:10:50,987] [INFO] Target genome list was writen to OceanDNA-b11211/target_genomes_gtdb.txt
[2023-03-15 10:10:51,055] [INFO] Task started: fastANI
[2023-03-15 10:10:51,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef56481-784d-4d20-8c4d-faaf13711e89/OceanDNA-b11211.fa --refList OceanDNA-b11211/target_genomes_gtdb.txt --output OceanDNA-b11211/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:10:54,223] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:54,229] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:10:54,229] [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_018623955.1	s__UBA8316 sp018623955	97.3623	195	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002364535.1	s__UBA8316 sp002364535	87.431	346	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_002687665.1	s__UBA8316 sp002687665	86.4514	244	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619315.1	s__UBA8316 sp902619315	85.7654	244	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	83.6384	277	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_002390455.1	s__UBA8316 sp002390455	82.8434	305	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_002336305.1	s__UBA8316 sp002336305	82.188	259	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647605.1	s__UBA8316 sp018647605	78.9181	212	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711215.1	s__UBA8316 sp002711215	77.7087	190	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	100.00	100.00	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:10:54,231] [INFO] GTDB search result was written to OceanDNA-b11211/result_gtdb.tsv
[2023-03-15 10:10:54,239] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:10:54,244] [INFO] DFAST_QC result json was written to OceanDNA-b11211/dqc_result.json
[2023-03-15 10:10:54,244] [INFO] DFAST_QC completed!
[2023-03-15 10:10:54,244] [INFO] Total running time: 0h1m5s