[2023-03-14 12:48:35,623] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:48:35,624] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:48:35,625] [INFO] DQC Reference Directory: /var/lib/cwl/stga86e15ee-8782-47f1-b720-6e504d19444c/dqc_reference
[2023-03-14 12:48:37,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:48:37,138] [INFO] Task started: Prodigal
[2023-03-14 12:48:37,138] [INFO] Running command: cat /var/lib/cwl/stgdd15aa23-0ad1-4039-bf16-a65cb2567f9f/OceanDNA-b4244.fa | prodigal -d OceanDNA-b4244/cds.fna -a OceanDNA-b4244/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:48:53,301] [INFO] Task succeeded: Prodigal
[2023-03-14 12:48:53,301] [INFO] Task started: HMMsearch
[2023-03-14 12:48:53,301] [INFO] Running command: hmmsearch --tblout OceanDNA-b4244/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga86e15ee-8782-47f1-b720-6e504d19444c/dqc_reference/reference_markers.hmm OceanDNA-b4244/protein.faa > /dev/null
[2023-03-14 12:48:53,496] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:48:53,497] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdd15aa23-0ad1-4039-bf16-a65cb2567f9f/OceanDNA-b4244.fa]
[2023-03-14 12:48:53,514] [INFO] Query marker FASTA was written to OceanDNA-b4244/markers.fasta
[2023-03-14 12:48:53,515] [INFO] Task started: Blastn
[2023-03-14 12:48:53,515] [INFO] Running command: blastn -query OceanDNA-b4244/markers.fasta -db /var/lib/cwl/stga86e15ee-8782-47f1-b720-6e504d19444c/dqc_reference/reference_markers.fasta -out OceanDNA-b4244/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:48:54,051] [INFO] Task succeeded: Blastn
[2023-03-14 12:48:54,052] [INFO] Selected 20 target genomes.
[2023-03-14 12:48:54,052] [INFO] Target genome list was writen to OceanDNA-b4244/target_genomes.txt
[2023-03-14 12:48:54,063] [INFO] Task started: fastANI
[2023-03-14 12:48:54,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd15aa23-0ad1-4039-bf16-a65cb2567f9f/OceanDNA-b4244.fa --refList OceanDNA-b4244/target_genomes.txt --output OceanDNA-b4244/fastani_result.tsv --threads 1
[2023-03-14 12:49:10,310] [INFO] Task succeeded: fastANI
[2023-03-14 12:49:10,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga86e15ee-8782-47f1-b720-6e504d19444c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:49:10,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga86e15ee-8782-47f1-b720-6e504d19444c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:49:10,311] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:49:10,311] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:49:10,311] [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 12:49:10,312] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4244/tc_result.tsv
[2023-03-14 12:49:10,312] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:49:10,312] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:49:10,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga86e15ee-8782-47f1-b720-6e504d19444c/dqc_reference/checkm_data
[2023-03-14 12:49:10,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:49:10,327] [INFO] Task started: CheckM
[2023-03-14 12:49:10,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4244/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4244/checkm_input OceanDNA-b4244/checkm_result
[2023-03-14 12:50:00,949] [INFO] Task succeeded: CheckM
[2023-03-14 12:50:00,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:50:00,961] [INFO] ===== Completeness check finished =====
[2023-03-14 12:50:00,961] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:50:00,961] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4244/markers.fasta)
[2023-03-14 12:50:00,964] [INFO] Task started: Blastn
[2023-03-14 12:50:00,965] [INFO] Running command: blastn -query OceanDNA-b4244/markers.fasta -db /var/lib/cwl/stga86e15ee-8782-47f1-b720-6e504d19444c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4244/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:50:01,857] [INFO] Task succeeded: Blastn
[2023-03-14 12:50:01,858] [INFO] Selected 9 target genomes.
[2023-03-14 12:50:01,858] [INFO] Target genome list was writen to OceanDNA-b4244/target_genomes_gtdb.txt
[2023-03-14 12:50:01,868] [INFO] Task started: fastANI
[2023-03-14 12:50:01,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd15aa23-0ad1-4039-bf16-a65cb2567f9f/OceanDNA-b4244.fa --refList OceanDNA-b4244/target_genomes_gtdb.txt --output OceanDNA-b4244/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:50:07,431] [INFO] Task succeeded: fastANI
[2023-03-14 12:50:07,435] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:50:07,436] [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_002691385.1	s__UBA4465 sp002691385	99.5271	686	783	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479015.1	s__UBA4465 sp002470835	83.9829	623	783	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.62	98.40	0.95	0.92	11	-
GCA_905182375.1	s__UBA4465 sp905182375	83.71	562	783	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292365.1	s__UBA4465 sp002292365	83.1226	523	783	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.58	99.58	0.82	0.82	2	-
GCA_905182655.1	s__UBA4465 sp905182655	82.5866	383	783	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902605755.1	s__UBA4465 sp902605755	81.7826	323	783	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:50:07,436] [INFO] GTDB search result was written to OceanDNA-b4244/result_gtdb.tsv
[2023-03-14 12:50:07,436] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:50:07,437] [INFO] DFAST_QC result json was written to OceanDNA-b4244/dqc_result.json
[2023-03-14 12:50:07,437] [INFO] DFAST_QC completed!
[2023-03-14 12:50:07,437] [INFO] Total running time: 0h1m32s