[2023-03-17 09:51:05,535] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:51:05,537] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:51:05,537] [INFO] DQC Reference Directory: /var/lib/cwl/stgea1e4a29-5a65-4096-96ad-5ad78fe1290c/dqc_reference
[2023-03-17 09:51:06,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:51:06,628] [INFO] Task started: Prodigal
[2023-03-17 09:51:06,628] [INFO] Running command: cat /var/lib/cwl/stg1f2369a6-8213-4ed5-9f2e-74ce6e35168e/OceanDNA-b11464.fa | prodigal -d OceanDNA-b11464/cds.fna -a OceanDNA-b11464/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:51:14,025] [INFO] Task succeeded: Prodigal
[2023-03-17 09:51:14,025] [INFO] Task started: HMMsearch
[2023-03-17 09:51:14,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b11464/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea1e4a29-5a65-4096-96ad-5ad78fe1290c/dqc_reference/reference_markers.hmm OceanDNA-b11464/protein.faa > /dev/null
[2023-03-17 09:51:14,162] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:51:14,163] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1f2369a6-8213-4ed5-9f2e-74ce6e35168e/OceanDNA-b11464.fa]
[2023-03-17 09:51:14,184] [INFO] Query marker FASTA was written to OceanDNA-b11464/markers.fasta
[2023-03-17 09:51:14,186] [INFO] Task started: Blastn
[2023-03-17 09:51:14,186] [INFO] Running command: blastn -query OceanDNA-b11464/markers.fasta -db /var/lib/cwl/stgea1e4a29-5a65-4096-96ad-5ad78fe1290c/dqc_reference/reference_markers.fasta -out OceanDNA-b11464/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:51:14,655] [INFO] Task succeeded: Blastn
[2023-03-17 09:51:14,659] [INFO] Selected 10 target genomes.
[2023-03-17 09:51:14,659] [INFO] Target genome list was writen to OceanDNA-b11464/target_genomes.txt
[2023-03-17 09:51:14,665] [INFO] Task started: fastANI
[2023-03-17 09:51:14,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f2369a6-8213-4ed5-9f2e-74ce6e35168e/OceanDNA-b11464.fa --refList OceanDNA-b11464/target_genomes.txt --output OceanDNA-b11464/fastani_result.tsv --threads 1
[2023-03-17 09:51:20,883] [INFO] Task succeeded: fastANI
[2023-03-17 09:51:20,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea1e4a29-5a65-4096-96ad-5ad78fe1290c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:51:20,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea1e4a29-5a65-4096-96ad-5ad78fe1290c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:51:20,884] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:51:20,884] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:51:20,884] [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 09:51:20,886] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11464/tc_result.tsv
[2023-03-17 09:51:20,886] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:51:20,886] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:51:20,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea1e4a29-5a65-4096-96ad-5ad78fe1290c/dqc_reference/checkm_data
[2023-03-17 09:51:20,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:51:20,892] [INFO] Task started: CheckM
[2023-03-17 09:51:20,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11464/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11464/checkm_input OceanDNA-b11464/checkm_result
[2023-03-17 09:51:45,723] [INFO] Task succeeded: CheckM
[2023-03-17 09:51:45,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 09:51:45,725] [INFO] ===== Completeness check finished =====
[2023-03-17 09:51:45,725] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:51:45,725] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11464/markers.fasta)
[2023-03-17 09:51:45,726] [INFO] Task started: Blastn
[2023-03-17 09:51:45,727] [INFO] Running command: blastn -query OceanDNA-b11464/markers.fasta -db /var/lib/cwl/stgea1e4a29-5a65-4096-96ad-5ad78fe1290c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11464/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:51:46,250] [INFO] Task succeeded: Blastn
[2023-03-17 09:51:46,251] [INFO] Selected 8 target genomes.
[2023-03-17 09:51:46,251] [INFO] Target genome list was writen to OceanDNA-b11464/target_genomes_gtdb.txt
[2023-03-17 09:51:46,362] [INFO] Task started: fastANI
[2023-03-17 09:51:46,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f2369a6-8213-4ed5-9f2e-74ce6e35168e/OceanDNA-b11464.fa --refList OceanDNA-b11464/target_genomes_gtdb.txt --output OceanDNA-b11464/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:51:50,301] [INFO] Task succeeded: fastANI
[2023-03-17 09:51:50,304] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:51:50,304] [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_018669945.1	s__NORP312 sp018669945	88.8256	246	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-2746335;g__NORP312	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480125.1	s__NORP312 sp905480125	87.2066	253	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-2746335;g__NORP312	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763645.1	s__NORP312 sp016763645	76.9579	67	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-2746335;g__NORP312	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:51:50,304] [INFO] GTDB search result was written to OceanDNA-b11464/result_gtdb.tsv
[2023-03-17 09:51:50,304] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:51:50,305] [INFO] DFAST_QC result json was written to OceanDNA-b11464/dqc_result.json
[2023-03-17 09:51:50,305] [INFO] DFAST_QC completed!
[2023-03-17 09:51:50,305] [INFO] Total running time: 0h0m45s