[2023-03-14 11:40:05,646] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,647] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fafc461-49d8-40b2-98b1-9e1884018560/dqc_reference
[2023-03-14 11:40:06,765] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,765] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,765] [INFO] Running command: cat /var/lib/cwl/stgcc525866-fdce-4fe3-b4d8-9dcc8842b46e/OceanDNA-b4030.fa | prodigal -d OceanDNA-b4030/cds.fna -a OceanDNA-b4030/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:42,916] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:42,916] [INFO] Task started: HMMsearch
[2023-03-14 11:40:42,916] [INFO] Running command: hmmsearch --tblout OceanDNA-b4030/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fafc461-49d8-40b2-98b1-9e1884018560/dqc_reference/reference_markers.hmm OceanDNA-b4030/protein.faa > /dev/null
[2023-03-14 11:40:43,141] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:43,141] [INFO] Found 6/6 markers.
[2023-03-14 11:40:43,185] [INFO] Query marker FASTA was written to OceanDNA-b4030/markers.fasta
[2023-03-14 11:40:43,186] [INFO] Task started: Blastn
[2023-03-14 11:40:43,186] [INFO] Running command: blastn -query OceanDNA-b4030/markers.fasta -db /var/lib/cwl/stg1fafc461-49d8-40b2-98b1-9e1884018560/dqc_reference/reference_markers.fasta -out OceanDNA-b4030/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:43,718] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:43,722] [INFO] Selected 29 target genomes.
[2023-03-14 11:40:43,723] [INFO] Target genome list was writen to OceanDNA-b4030/target_genomes.txt
[2023-03-14 11:40:43,740] [INFO] Task started: fastANI
[2023-03-14 11:40:43,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc525866-fdce-4fe3-b4d8-9dcc8842b46e/OceanDNA-b4030.fa --refList OceanDNA-b4030/target_genomes.txt --output OceanDNA-b4030/fastani_result.tsv --threads 1
[2023-03-14 11:41:05,254] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:05,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fafc461-49d8-40b2-98b1-9e1884018560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:41:05,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fafc461-49d8-40b2-98b1-9e1884018560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:41:05,255] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:41:05,255] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:41:05,255] [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
--------------------------------------------------------------------------------
[2023-03-14 11:41:05,257] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4030/tc_result.tsv
[2023-03-14 11:41:05,262] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:41:05,262] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:41:05,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fafc461-49d8-40b2-98b1-9e1884018560/dqc_reference/checkm_data
[2023-03-14 11:41:05,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:41:05,275] [INFO] Task started: CheckM
[2023-03-14 11:41:05,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4030/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4030/checkm_input OceanDNA-b4030/checkm_result
[2023-03-14 11:42:34,406] [INFO] Task succeeded: CheckM
[2023-03-14 11:42:34,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:42:34,440] [INFO] ===== Completeness check finished =====
[2023-03-14 11:42:34,440] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:42:34,440] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4030/markers.fasta)
[2023-03-14 11:42:34,441] [INFO] Task started: Blastn
[2023-03-14 11:42:34,442] [INFO] Running command: blastn -query OceanDNA-b4030/markers.fasta -db /var/lib/cwl/stg1fafc461-49d8-40b2-98b1-9e1884018560/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4030/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:42:35,168] [INFO] Task succeeded: Blastn
[2023-03-14 11:42:35,177] [INFO] Selected 27 target genomes.
[2023-03-14 11:42:35,178] [INFO] Target genome list was writen to OceanDNA-b4030/target_genomes_gtdb.txt
[2023-03-14 11:42:35,242] [INFO] Task started: fastANI
[2023-03-14 11:42:35,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc525866-fdce-4fe3-b4d8-9dcc8842b46e/OceanDNA-b4030.fa --refList OceanDNA-b4030/target_genomes_gtdb.txt --output OceanDNA-b4030/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:42:54,773] [INFO] Task succeeded: fastANI
[2023-03-14 11:42:54,779] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:42:54,780] [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_002344795.1	s__ELB16-189 sp002344795	79.001	264	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345965.1	s__ELB16-189 sp002345965	77.489	245	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	99.88	99.88	0.94	0.94	2	-
GCA_016709845.1	s__ELB16-189 sp016709845	76.844	73	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425185.1	s__UBA2336 sp002425185	76.7841	57	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA2336	95.0	99.97	99.94	0.98	0.97	4	-
GCA_016787725.1	s__ELB16-189 sp016787725	76.382	69	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303805.1	s__ELB16-189 sp017303805	75.9543	55	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001567185.1	s__ELB16-189 sp001567185	75.6764	50	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	98.67	98.67	0.88	0.88	2	-
GCA_013141055.1	s__ELB16-189 sp013141055	75.6615	52	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303795.1	s__ELB16-189 sp017303795	75.4637	63	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140555.1	s__ELB16-189 sp013140555	75.4092	51	1549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:42:54,785] [INFO] GTDB search result was written to OceanDNA-b4030/result_gtdb.tsv
[2023-03-14 11:42:54,790] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:42:54,795] [INFO] DFAST_QC result json was written to OceanDNA-b4030/dqc_result.json
[2023-03-14 11:42:54,795] [INFO] DFAST_QC completed!
[2023-03-14 11:42:54,795] [INFO] Total running time: 0h2m49s