[2023-03-17 11:25:37,401] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:37,402] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:37,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg760d48d8-16f5-455a-abaa-2dd7e25f230e/dqc_reference
[2023-03-17 11:25:38,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,524] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,524] [INFO] Running command: cat /var/lib/cwl/stgffb40a56-0a6e-4a1e-8584-a2de959b605b/OceanDNA-b22766.fa | prodigal -d OceanDNA-b22766/cds.fna -a OceanDNA-b22766/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:25:46,850] [INFO] Task succeeded: Prodigal
[2023-03-17 11:25:46,850] [INFO] Task started: HMMsearch
[2023-03-17 11:25:46,850] [INFO] Running command: hmmsearch --tblout OceanDNA-b22766/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg760d48d8-16f5-455a-abaa-2dd7e25f230e/dqc_reference/reference_markers.hmm OceanDNA-b22766/protein.faa > /dev/null
[2023-03-17 11:25:47,002] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:25:47,002] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgffb40a56-0a6e-4a1e-8584-a2de959b605b/OceanDNA-b22766.fa]
[2023-03-17 11:25:47,021] [INFO] Query marker FASTA was written to OceanDNA-b22766/markers.fasta
[2023-03-17 11:25:47,021] [INFO] Task started: Blastn
[2023-03-17 11:25:47,021] [INFO] Running command: blastn -query OceanDNA-b22766/markers.fasta -db /var/lib/cwl/stg760d48d8-16f5-455a-abaa-2dd7e25f230e/dqc_reference/reference_markers.fasta -out OceanDNA-b22766/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:25:47,484] [INFO] Task succeeded: Blastn
[2023-03-17 11:25:47,489] [INFO] Selected 5 target genomes.
[2023-03-17 11:25:47,489] [INFO] Target genome list was writen to OceanDNA-b22766/target_genomes.txt
[2023-03-17 11:25:47,492] [INFO] Task started: fastANI
[2023-03-17 11:25:47,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgffb40a56-0a6e-4a1e-8584-a2de959b605b/OceanDNA-b22766.fa --refList OceanDNA-b22766/target_genomes.txt --output OceanDNA-b22766/fastani_result.tsv --threads 1
[2023-03-17 11:25:49,738] [INFO] Task succeeded: fastANI
[2023-03-17 11:25:49,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg760d48d8-16f5-455a-abaa-2dd7e25f230e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:25:49,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg760d48d8-16f5-455a-abaa-2dd7e25f230e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:25:49,739] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:25:49,739] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:25:49,739] [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 11:25:49,740] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22766/tc_result.tsv
[2023-03-17 11:25:49,741] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:25:49,741] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:25:49,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg760d48d8-16f5-455a-abaa-2dd7e25f230e/dqc_reference/checkm_data
[2023-03-17 11:25:49,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:25:49,749] [INFO] Task started: CheckM
[2023-03-17 11:25:49,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22766/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22766/checkm_input OceanDNA-b22766/checkm_result
[2023-03-17 11:26:15,729] [INFO] Task succeeded: CheckM
[2023-03-17 11:26:15,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:26:16,045] [INFO] ===== Completeness check finished =====
[2023-03-17 11:26:16,045] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:26:16,045] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22766/markers.fasta)
[2023-03-17 11:26:16,046] [INFO] Task started: Blastn
[2023-03-17 11:26:16,047] [INFO] Running command: blastn -query OceanDNA-b22766/markers.fasta -db /var/lib/cwl/stg760d48d8-16f5-455a-abaa-2dd7e25f230e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22766/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:26:16,598] [INFO] Task succeeded: Blastn
[2023-03-17 11:26:16,604] [INFO] Selected 5 target genomes.
[2023-03-17 11:26:16,604] [INFO] Target genome list was writen to OceanDNA-b22766/target_genomes_gtdb.txt
[2023-03-17 11:26:16,609] [INFO] Task started: fastANI
[2023-03-17 11:26:16,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgffb40a56-0a6e-4a1e-8584-a2de959b605b/OceanDNA-b22766.fa --refList OceanDNA-b22766/target_genomes_gtdb.txt --output OceanDNA-b22766/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:26:19,351] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:19,353] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:26:19,353] [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_014237955.1	s__UBA7805 sp014237955	78.3641	84	348	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA7805;g__UBA7805	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:26:19,357] [INFO] GTDB search result was written to OceanDNA-b22766/result_gtdb.tsv
[2023-03-17 11:26:19,360] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:26:19,365] [INFO] DFAST_QC result json was written to OceanDNA-b22766/dqc_result.json
[2023-03-17 11:26:19,365] [INFO] DFAST_QC completed!
[2023-03-17 11:26:19,365] [INFO] Total running time: 0h0m42s