[2023-03-16 17:03:59,008] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:03:59,009] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:03:59,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg671d727d-1c12-42c7-9121-04b4fa5043e3/dqc_reference
[2023-03-16 17:04:00,110] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:04:00,110] [INFO] Task started: Prodigal
[2023-03-16 17:04:00,110] [INFO] Running command: cat /var/lib/cwl/stg11d9b6da-e8da-40b2-99b4-97f1f444abe9/OceanDNA-b7098.fa | prodigal -d OceanDNA-b7098/cds.fna -a OceanDNA-b7098/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:04:04,564] [INFO] Task succeeded: Prodigal
[2023-03-16 17:04:04,564] [INFO] Task started: HMMsearch
[2023-03-16 17:04:04,565] [INFO] Running command: hmmsearch --tblout OceanDNA-b7098/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg671d727d-1c12-42c7-9121-04b4fa5043e3/dqc_reference/reference_markers.hmm OceanDNA-b7098/protein.faa > /dev/null
[2023-03-16 17:04:04,723] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:04:04,724] [INFO] Found 6/6 markers.
[2023-03-16 17:04:04,731] [INFO] Query marker FASTA was written to OceanDNA-b7098/markers.fasta
[2023-03-16 17:04:04,733] [INFO] Task started: Blastn
[2023-03-16 17:04:04,733] [INFO] Running command: blastn -query OceanDNA-b7098/markers.fasta -db /var/lib/cwl/stg671d727d-1c12-42c7-9121-04b4fa5043e3/dqc_reference/reference_markers.fasta -out OceanDNA-b7098/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:04:05,256] [INFO] Task succeeded: Blastn
[2023-03-16 17:04:05,257] [INFO] Selected 29 target genomes.
[2023-03-16 17:04:05,258] [INFO] Target genome list was writen to OceanDNA-b7098/target_genomes.txt
[2023-03-16 17:04:05,290] [INFO] Task started: fastANI
[2023-03-16 17:04:05,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d9b6da-e8da-40b2-99b4-97f1f444abe9/OceanDNA-b7098.fa --refList OceanDNA-b7098/target_genomes.txt --output OceanDNA-b7098/fastani_result.tsv --threads 1
[2023-03-16 17:04:20,907] [INFO] Task succeeded: fastANI
[2023-03-16 17:04:20,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg671d727d-1c12-42c7-9121-04b4fa5043e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:04:20,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg671d727d-1c12-42c7-9121-04b4fa5043e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:04:20,908] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:04:20,908] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:04:20,908] [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
--------------------------------------------------------------------------------
[2023-03-16 17:04:20,908] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7098/tc_result.tsv
[2023-03-16 17:04:20,908] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:04:20,908] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:04:20,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg671d727d-1c12-42c7-9121-04b4fa5043e3/dqc_reference/checkm_data
[2023-03-16 17:04:20,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:04:20,936] [INFO] Task started: CheckM
[2023-03-16 17:04:20,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7098/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7098/checkm_input OceanDNA-b7098/checkm_result
[2023-03-16 17:04:42,874] [INFO] Task succeeded: CheckM
[2023-03-16 17:04:42,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:04:42,875] [INFO] ===== Completeness check finished =====
[2023-03-16 17:04:42,876] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:04:42,876] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7098/markers.fasta)
[2023-03-16 17:04:42,877] [INFO] Task started: Blastn
[2023-03-16 17:04:42,877] [INFO] Running command: blastn -query OceanDNA-b7098/markers.fasta -db /var/lib/cwl/stg671d727d-1c12-42c7-9121-04b4fa5043e3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7098/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:04:43,757] [INFO] Task succeeded: Blastn
[2023-03-16 17:04:43,758] [INFO] Selected 12 target genomes.
[2023-03-16 17:04:43,758] [INFO] Target genome list was writen to OceanDNA-b7098/target_genomes_gtdb.txt
[2023-03-16 17:04:43,866] [INFO] Task started: fastANI
[2023-03-16 17:04:43,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d9b6da-e8da-40b2-99b4-97f1f444abe9/OceanDNA-b7098.fa --refList OceanDNA-b7098/target_genomes_gtdb.txt --output OceanDNA-b7098/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:04:46,868] [INFO] Task succeeded: fastANI
[2023-03-16 17:04:46,873] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 17:04:46,873] [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_004213965.1	s__GCA-2700405 sp004213965	99.0639	203	254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902512065.1	s__GCA-2700405 sp902512065	95.025	191	254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002700405.1	s__GCA-2700405 sp002700405	92.3446	192	254	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_014239895.1	s__GCA-2700405 sp014239895	82.2954	168	254	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	82.0891	213	254	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_002702745.1	s__MED-G13 sp002702745	76.6991	50	254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697255.1	s__MED-G13 sp002697255	76.5528	67	254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:04:46,873] [INFO] GTDB search result was written to OceanDNA-b7098/result_gtdb.tsv
[2023-03-16 17:04:46,874] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:04:46,874] [INFO] DFAST_QC result json was written to OceanDNA-b7098/dqc_result.json
[2023-03-16 17:04:46,874] [INFO] DFAST_QC completed!
[2023-03-16 17:04:46,875] [INFO] Total running time: 0h0m48s