[2023-03-15 09:25:29,097] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:25:29,097] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:25:29,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e20faf1-0198-4414-9fed-5ea30e9ee7d3/dqc_reference
[2023-03-15 09:25:30,383] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:25:30,384] [INFO] Task started: Prodigal
[2023-03-15 09:25:30,384] [INFO] Running command: cat /var/lib/cwl/stgc259c0e2-c495-4c4a-b13f-543111bd68ba/OceanDNA-b19554.fa | prodigal -d OceanDNA-b19554/cds.fna -a OceanDNA-b19554/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:25:34,746] [INFO] Task succeeded: Prodigal
[2023-03-15 09:25:34,746] [INFO] Task started: HMMsearch
[2023-03-15 09:25:34,746] [INFO] Running command: hmmsearch --tblout OceanDNA-b19554/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e20faf1-0198-4414-9fed-5ea30e9ee7d3/dqc_reference/reference_markers.hmm OceanDNA-b19554/protein.faa > /dev/null
[2023-03-15 09:25:34,931] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:25:34,931] [INFO] Found 6/6 markers.
[2023-03-15 09:25:34,942] [INFO] Query marker FASTA was written to OceanDNA-b19554/markers.fasta
[2023-03-15 09:25:34,942] [INFO] Task started: Blastn
[2023-03-15 09:25:34,942] [INFO] Running command: blastn -query OceanDNA-b19554/markers.fasta -db /var/lib/cwl/stg2e20faf1-0198-4414-9fed-5ea30e9ee7d3/dqc_reference/reference_markers.fasta -out OceanDNA-b19554/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:25:35,887] [INFO] Task succeeded: Blastn
[2023-03-15 09:25:35,888] [INFO] Selected 10 target genomes.
[2023-03-15 09:25:35,888] [INFO] Target genome list was writen to OceanDNA-b19554/target_genomes.txt
[2023-03-15 09:25:35,895] [INFO] Task started: fastANI
[2023-03-15 09:25:35,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgc259c0e2-c495-4c4a-b13f-543111bd68ba/OceanDNA-b19554.fa --refList OceanDNA-b19554/target_genomes.txt --output OceanDNA-b19554/fastani_result.tsv --threads 1
[2023-03-15 09:25:41,585] [INFO] Task succeeded: fastANI
[2023-03-15 09:25:41,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e20faf1-0198-4414-9fed-5ea30e9ee7d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:25:41,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e20faf1-0198-4414-9fed-5ea30e9ee7d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:25:41,586] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:25:41,586] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:25:41,586] [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 09:25:41,586] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19554/tc_result.tsv
[2023-03-15 09:25:41,586] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:25:41,586] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:25:41,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e20faf1-0198-4414-9fed-5ea30e9ee7d3/dqc_reference/checkm_data
[2023-03-15 09:25:41,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:25:41,888] [INFO] Task started: CheckM
[2023-03-15 09:25:41,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19554/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19554/checkm_input OceanDNA-b19554/checkm_result
[2023-03-15 09:26:06,520] [INFO] Task succeeded: CheckM
[2023-03-15 09:26:06,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 2.98%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 09:26:06,522] [INFO] ===== Completeness check finished =====
[2023-03-15 09:26:06,522] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:26:06,522] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19554/markers.fasta)
[2023-03-15 09:26:06,523] [INFO] Task started: Blastn
[2023-03-15 09:26:06,523] [INFO] Running command: blastn -query OceanDNA-b19554/markers.fasta -db /var/lib/cwl/stg2e20faf1-0198-4414-9fed-5ea30e9ee7d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19554/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:26:08,120] [INFO] Task succeeded: Blastn
[2023-03-15 09:26:08,121] [INFO] Selected 16 target genomes.
[2023-03-15 09:26:08,121] [INFO] Target genome list was writen to OceanDNA-b19554/target_genomes_gtdb.txt
[2023-03-15 09:26:08,477] [INFO] Task started: fastANI
[2023-03-15 09:26:08,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgc259c0e2-c495-4c4a-b13f-543111bd68ba/OceanDNA-b19554.fa --refList OceanDNA-b19554/target_genomes_gtdb.txt --output OceanDNA-b19554/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:26:15,040] [INFO] Task succeeded: fastANI
[2023-03-15 09:26:15,045] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:26:15,045] [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_002713385.1	s__UBA2126 sp002713385	98.7167	159	209	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	95.44	95.44	0.61	0.61	2	conclusive
GCA_004124535.1	s__UBA2126 sp004124535	94.2454	110	209	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	97.80	97.80	0.52	0.52	2	-
GCA_004124385.1	s__UBA2126 sp004124385	79.6981	119	209	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	99.49	99.49	0.93	0.93	2	-
GCA_002730315.1	s__UBA2126 sp002730315	79.1913	66	209	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	99.18	99.07	0.56	0.51	3	-
GCA_002436185.1	s__UBA2126 sp002436185	79.1567	107	209	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	99.90	99.88	0.91	0.83	5	-
GCA_014381755.1	s__UBA2126 sp014381755	78.4458	111	209	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256485.1	s__UBA2126 sp002256485	78.0334	97	209	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:26:15,046] [INFO] GTDB search result was written to OceanDNA-b19554/result_gtdb.tsv
[2023-03-15 09:26:15,046] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:26:15,047] [INFO] DFAST_QC result json was written to OceanDNA-b19554/dqc_result.json
[2023-03-15 09:26:15,047] [INFO] DFAST_QC completed!
[2023-03-15 09:26:15,047] [INFO] Total running time: 0h0m46s