[2023-03-17 05:26:45,827] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,827] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f2c36fe-95b1-4ece-8fac-bb971b4933b2/dqc_reference
[2023-03-17 05:26:46,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:46,936] [INFO] Task started: Prodigal
[2023-03-17 05:26:46,936] [INFO] Running command: cat /var/lib/cwl/stg55ac0384-b3e6-4859-8322-3947ec448397/OceanDNA-b7090.fa | prodigal -d OceanDNA-b7090/cds.fna -a OceanDNA-b7090/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:26:52,628] [INFO] Task succeeded: Prodigal
[2023-03-17 05:26:52,629] [INFO] Task started: HMMsearch
[2023-03-17 05:26:52,629] [INFO] Running command: hmmsearch --tblout OceanDNA-b7090/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f2c36fe-95b1-4ece-8fac-bb971b4933b2/dqc_reference/reference_markers.hmm OceanDNA-b7090/protein.faa > /dev/null
[2023-03-17 05:26:52,804] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:26:52,805] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg55ac0384-b3e6-4859-8322-3947ec448397/OceanDNA-b7090.fa]
[2023-03-17 05:26:52,812] [INFO] Query marker FASTA was written to OceanDNA-b7090/markers.fasta
[2023-03-17 05:26:52,813] [INFO] Task started: Blastn
[2023-03-17 05:26:52,813] [INFO] Running command: blastn -query OceanDNA-b7090/markers.fasta -db /var/lib/cwl/stg3f2c36fe-95b1-4ece-8fac-bb971b4933b2/dqc_reference/reference_markers.fasta -out OceanDNA-b7090/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:26:53,319] [INFO] Task succeeded: Blastn
[2023-03-17 05:26:53,320] [INFO] Selected 25 target genomes.
[2023-03-17 05:26:53,320] [INFO] Target genome list was writen to OceanDNA-b7090/target_genomes.txt
[2023-03-17 05:26:53,335] [INFO] Task started: fastANI
[2023-03-17 05:26:53,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg55ac0384-b3e6-4859-8322-3947ec448397/OceanDNA-b7090.fa --refList OceanDNA-b7090/target_genomes.txt --output OceanDNA-b7090/fastani_result.tsv --threads 1
[2023-03-17 05:27:07,225] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:07,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f2c36fe-95b1-4ece-8fac-bb971b4933b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:27:07,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f2c36fe-95b1-4ece-8fac-bb971b4933b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:27:07,226] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:27:07,226] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:27:07,226] [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 05:27:07,226] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7090/tc_result.tsv
[2023-03-17 05:27:07,226] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:27:07,226] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:27:07,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f2c36fe-95b1-4ece-8fac-bb971b4933b2/dqc_reference/checkm_data
[2023-03-17 05:27:07,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:27:07,232] [INFO] Task started: CheckM
[2023-03-17 05:27:07,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7090/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7090/checkm_input OceanDNA-b7090/checkm_result
[2023-03-17 05:27:26,977] [INFO] Task succeeded: CheckM
[2023-03-17 05:27:26,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:27:26,979] [INFO] ===== Completeness check finished =====
[2023-03-17 05:27:26,979] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:27:26,979] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7090/markers.fasta)
[2023-03-17 05:27:26,979] [INFO] Task started: Blastn
[2023-03-17 05:27:26,979] [INFO] Running command: blastn -query OceanDNA-b7090/markers.fasta -db /var/lib/cwl/stg3f2c36fe-95b1-4ece-8fac-bb971b4933b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7090/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:27,688] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:27,689] [INFO] Selected 15 target genomes.
[2023-03-17 05:27:27,689] [INFO] Target genome list was writen to OceanDNA-b7090/target_genomes_gtdb.txt
[2023-03-17 05:27:27,816] [INFO] Task started: fastANI
[2023-03-17 05:27:27,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg55ac0384-b3e6-4859-8322-3947ec448397/OceanDNA-b7090.fa --refList OceanDNA-b7090/target_genomes_gtdb.txt --output OceanDNA-b7090/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:27:31,737] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:31,742] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:27:31,742] [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_014239895.1	s__GCA-2700405 sp014239895	92.6534	216	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018657955.1	s__GCA-2700405 sp018657955	89.304	291	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	99.95	99.87	0.95	0.89	9	-
GCA_902512065.1	s__GCA-2700405 sp902512065	82.6195	216	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213965.1	s__GCA-2700405 sp004213965	82.2647	219	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518355.1	s__MED-G13 sp902518355	76.9375	52	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_902510415.1	s__MED-G13 sp902510415	76.5396	53	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_002697255.1	s__MED-G13 sp002697255	76.5197	54	321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:27:31,742] [INFO] GTDB search result was written to OceanDNA-b7090/result_gtdb.tsv
[2023-03-17 05:27:31,742] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:27:31,743] [INFO] DFAST_QC result json was written to OceanDNA-b7090/dqc_result.json
[2023-03-17 05:27:31,743] [INFO] DFAST_QC completed!
[2023-03-17 05:27:31,743] [INFO] Total running time: 0h0m46s