[2023-03-18 20:40:39,439] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,440] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,440] [INFO] DQC Reference Directory: /var/lib/cwl/stge5647cab-3a39-450b-8af9-0b4e3ec6f888/dqc_reference
[2023-03-18 20:40:41,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,210] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,210] [INFO] Running command: cat /var/lib/cwl/stg3ff1c7da-75af-4b4c-a8bc-cb8945381d0e/OceanDNA-b3920.fa | prodigal -d OceanDNA-b3920/cds.fna -a OceanDNA-b3920/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:41:30,818] [INFO] Task succeeded: Prodigal
[2023-03-18 20:41:30,818] [INFO] Task started: HMMsearch
[2023-03-18 20:41:30,819] [INFO] Running command: hmmsearch --tblout OceanDNA-b3920/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5647cab-3a39-450b-8af9-0b4e3ec6f888/dqc_reference/reference_markers.hmm OceanDNA-b3920/protein.faa > /dev/null
[2023-03-18 20:41:31,074] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:41:31,074] [INFO] Found 6/6 markers.
[2023-03-18 20:41:31,111] [INFO] Query marker FASTA was written to OceanDNA-b3920/markers.fasta
[2023-03-18 20:41:31,111] [INFO] Task started: Blastn
[2023-03-18 20:41:31,111] [INFO] Running command: blastn -query OceanDNA-b3920/markers.fasta -db /var/lib/cwl/stge5647cab-3a39-450b-8af9-0b4e3ec6f888/dqc_reference/reference_markers.fasta -out OceanDNA-b3920/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:31,648] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:31,649] [INFO] Selected 27 target genomes.
[2023-03-18 20:41:31,649] [INFO] Target genome list was writen to OceanDNA-b3920/target_genomes.txt
[2023-03-18 20:41:31,660] [INFO] Task started: fastANI
[2023-03-18 20:41:31,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff1c7da-75af-4b4c-a8bc-cb8945381d0e/OceanDNA-b3920.fa --refList OceanDNA-b3920/target_genomes.txt --output OceanDNA-b3920/fastani_result.tsv --threads 1
[2023-03-18 20:41:52,204] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:52,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5647cab-3a39-450b-8af9-0b4e3ec6f888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:52,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5647cab-3a39-450b-8af9-0b4e3ec6f888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:52,205] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:52,205] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:41:52,205] [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
--------------------------------------------------------------------------------
[2023-03-18 20:41:52,205] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3920/tc_result.tsv
[2023-03-18 20:41:52,205] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:52,205] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:52,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5647cab-3a39-450b-8af9-0b4e3ec6f888/dqc_reference/checkm_data
[2023-03-18 20:41:52,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:52,219] [INFO] Task started: CheckM
[2023-03-18 20:41:52,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3920/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3920/checkm_input OceanDNA-b3920/checkm_result
[2023-03-18 20:43:49,489] [INFO] Task succeeded: CheckM
[2023-03-18 20:43:49,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:43:49,494] [INFO] ===== Completeness check finished =====
[2023-03-18 20:43:49,494] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:43:49,494] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3920/markers.fasta)
[2023-03-18 20:43:49,494] [INFO] Task started: Blastn
[2023-03-18 20:43:49,494] [INFO] Running command: blastn -query OceanDNA-b3920/markers.fasta -db /var/lib/cwl/stge5647cab-3a39-450b-8af9-0b4e3ec6f888/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3920/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:43:50,214] [INFO] Task succeeded: Blastn
[2023-03-18 20:43:50,214] [INFO] Selected 24 target genomes.
[2023-03-18 20:43:50,215] [INFO] Target genome list was writen to OceanDNA-b3920/target_genomes_gtdb.txt
[2023-03-18 20:43:50,242] [INFO] Task started: fastANI
[2023-03-18 20:43:50,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff1c7da-75af-4b4c-a8bc-cb8945381d0e/OceanDNA-b3920.fa --refList OceanDNA-b3920/target_genomes_gtdb.txt --output OceanDNA-b3920/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:44:07,550] [INFO] Task succeeded: fastANI
[2023-03-18 20:44:07,552] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:44:07,552] [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
GCF_902498805.1	s__Imperialibacter sp902498805	91.5846	1771	2038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Imperialibacter	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-18 20:44:07,552] [INFO] GTDB search result was written to OceanDNA-b3920/result_gtdb.tsv
[2023-03-18 20:44:07,552] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:44:07,552] [INFO] DFAST_QC result json was written to OceanDNA-b3920/dqc_result.json
[2023-03-18 20:44:07,553] [INFO] DFAST_QC completed!
[2023-03-18 20:44:07,553] [INFO] Total running time: 0h3m28s