[2023-03-14 10:56:00,326] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:56:00,326] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:56:00,326] [INFO] DQC Reference Directory: /var/lib/cwl/stgb74d4fd3-2ca3-43f1-bb8d-f3e283e8c09c/dqc_reference
[2023-03-14 10:56:01,485] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:01,485] [INFO] Task started: Prodigal
[2023-03-14 10:56:01,485] [INFO] Running command: cat /var/lib/cwl/stgd843b091-65b3-4d54-98cd-345337140b60/OceanDNA-b22443.fa | prodigal -d OceanDNA-b22443/cds.fna -a OceanDNA-b22443/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:28,228] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:28,229] [INFO] Task started: HMMsearch
[2023-03-14 10:56:28,229] [INFO] Running command: hmmsearch --tblout OceanDNA-b22443/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb74d4fd3-2ca3-43f1-bb8d-f3e283e8c09c/dqc_reference/reference_markers.hmm OceanDNA-b22443/protein.faa > /dev/null
[2023-03-14 10:56:28,575] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:28,576] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd843b091-65b3-4d54-98cd-345337140b60/OceanDNA-b22443.fa]
[2023-03-14 10:56:28,607] [INFO] Query marker FASTA was written to OceanDNA-b22443/markers.fasta
[2023-03-14 10:56:28,607] [INFO] Task started: Blastn
[2023-03-14 10:56:28,607] [INFO] Running command: blastn -query OceanDNA-b22443/markers.fasta -db /var/lib/cwl/stgb74d4fd3-2ca3-43f1-bb8d-f3e283e8c09c/dqc_reference/reference_markers.fasta -out OceanDNA-b22443/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:29,179] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:29,180] [INFO] Selected 18 target genomes.
[2023-03-14 10:56:29,180] [INFO] Target genome list was writen to OceanDNA-b22443/target_genomes.txt
[2023-03-14 10:56:29,192] [INFO] Task started: fastANI
[2023-03-14 10:56:29,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgd843b091-65b3-4d54-98cd-345337140b60/OceanDNA-b22443.fa --refList OceanDNA-b22443/target_genomes.txt --output OceanDNA-b22443/fastani_result.tsv --threads 1
[2023-03-14 10:56:45,882] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:45,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb74d4fd3-2ca3-43f1-bb8d-f3e283e8c09c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:45,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb74d4fd3-2ca3-43f1-bb8d-f3e283e8c09c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:45,882] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:45,882] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:45,882] [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 10:56:45,883] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22443/tc_result.tsv
[2023-03-14 10:56:45,883] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:45,883] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:45,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb74d4fd3-2ca3-43f1-bb8d-f3e283e8c09c/dqc_reference/checkm_data
[2023-03-14 10:56:45,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:45,892] [INFO] Task started: CheckM
[2023-03-14 10:56:45,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22443/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22443/checkm_input OceanDNA-b22443/checkm_result
[2023-03-14 10:57:51,562] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:51,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:51,565] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:51,565] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:51,566] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22443/markers.fasta)
[2023-03-14 10:57:51,566] [INFO] Task started: Blastn
[2023-03-14 10:57:51,566] [INFO] Running command: blastn -query OceanDNA-b22443/markers.fasta -db /var/lib/cwl/stgb74d4fd3-2ca3-43f1-bb8d-f3e283e8c09c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22443/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:52,441] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:52,442] [INFO] Selected 23 target genomes.
[2023-03-14 10:57:52,442] [INFO] Target genome list was writen to OceanDNA-b22443/target_genomes_gtdb.txt
[2023-03-14 10:57:52,467] [INFO] Task started: fastANI
[2023-03-14 10:57:52,467] [INFO] Running command: fastANI --query /var/lib/cwl/stgd843b091-65b3-4d54-98cd-345337140b60/OceanDNA-b22443.fa --refList OceanDNA-b22443/target_genomes_gtdb.txt --output OceanDNA-b22443/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:58:09,743] [INFO] Task succeeded: fastANI
[2023-03-14 10:58:09,745] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:58:09,745] [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_002862225.1	s__GCA-2862225 sp002862225	98.6713	1017	1401	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__GCA-2862225	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-14 10:58:09,745] [INFO] GTDB search result was written to OceanDNA-b22443/result_gtdb.tsv
[2023-03-14 10:58:09,746] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:58:09,746] [INFO] DFAST_QC result json was written to OceanDNA-b22443/dqc_result.json
[2023-03-14 10:58:09,746] [INFO] DFAST_QC completed!
[2023-03-14 10:58:09,746] [INFO] Total running time: 0h2m9s