[2023-03-18 10:46:22,261] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:46:22,261] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:46:22,261] [INFO] DQC Reference Directory: /var/lib/cwl/stgddae9c53-bd36-4e74-9185-a77d48c72bf5/dqc_reference
[2023-03-18 10:46:23,374] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:46:23,374] [INFO] Task started: Prodigal
[2023-03-18 10:46:23,375] [INFO] Running command: cat /var/lib/cwl/stge159fe56-2ac6-478d-8248-46431acb6e5b/OceanDNA-b14654.fa | prodigal -d OceanDNA-b14654/cds.fna -a OceanDNA-b14654/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:46:29,776] [INFO] Task succeeded: Prodigal
[2023-03-18 10:46:29,777] [INFO] Task started: HMMsearch
[2023-03-18 10:46:29,777] [INFO] Running command: hmmsearch --tblout OceanDNA-b14654/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddae9c53-bd36-4e74-9185-a77d48c72bf5/dqc_reference/reference_markers.hmm OceanDNA-b14654/protein.faa > /dev/null
[2023-03-18 10:46:29,924] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:46:29,924] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge159fe56-2ac6-478d-8248-46431acb6e5b/OceanDNA-b14654.fa]
[2023-03-18 10:46:29,954] [INFO] Query marker FASTA was written to OceanDNA-b14654/markers.fasta
[2023-03-18 10:46:29,955] [INFO] Task started: Blastn
[2023-03-18 10:46:29,955] [INFO] Running command: blastn -query OceanDNA-b14654/markers.fasta -db /var/lib/cwl/stgddae9c53-bd36-4e74-9185-a77d48c72bf5/dqc_reference/reference_markers.fasta -out OceanDNA-b14654/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:46:30,401] [INFO] Task succeeded: Blastn
[2023-03-18 10:46:30,405] [INFO] Selected 13 target genomes.
[2023-03-18 10:46:30,405] [INFO] Target genome list was writen to OceanDNA-b14654/target_genomes.txt
[2023-03-18 10:46:30,412] [INFO] Task started: fastANI
[2023-03-18 10:46:30,412] [INFO] Running command: fastANI --query /var/lib/cwl/stge159fe56-2ac6-478d-8248-46431acb6e5b/OceanDNA-b14654.fa --refList OceanDNA-b14654/target_genomes.txt --output OceanDNA-b14654/fastani_result.tsv --threads 1
[2023-03-18 10:46:40,171] [INFO] Task succeeded: fastANI
[2023-03-18 10:46:40,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddae9c53-bd36-4e74-9185-a77d48c72bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:46:40,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddae9c53-bd36-4e74-9185-a77d48c72bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:46:40,172] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:46:40,172] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:46:40,172] [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 10:46:40,174] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14654/tc_result.tsv
[2023-03-18 10:46:40,174] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:46:40,174] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:46:40,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddae9c53-bd36-4e74-9185-a77d48c72bf5/dqc_reference/checkm_data
[2023-03-18 10:46:40,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:46:40,192] [INFO] Task started: CheckM
[2023-03-18 10:46:40,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14654/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14654/checkm_input OceanDNA-b14654/checkm_result
[2023-03-18 10:47:02,002] [INFO] Task succeeded: CheckM
[2023-03-18 10:47:02,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:47:02,020] [INFO] ===== Completeness check finished =====
[2023-03-18 10:47:02,020] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:47:02,021] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14654/markers.fasta)
[2023-03-18 10:47:02,022] [INFO] Task started: Blastn
[2023-03-18 10:47:02,022] [INFO] Running command: blastn -query OceanDNA-b14654/markers.fasta -db /var/lib/cwl/stgddae9c53-bd36-4e74-9185-a77d48c72bf5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14654/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:47:02,477] [INFO] Task succeeded: Blastn
[2023-03-18 10:47:02,482] [INFO] Selected 21 target genomes.
[2023-03-18 10:47:02,482] [INFO] Target genome list was writen to OceanDNA-b14654/target_genomes_gtdb.txt
[2023-03-18 10:47:02,547] [INFO] Task started: fastANI
[2023-03-18 10:47:02,547] [INFO] Running command: fastANI --query /var/lib/cwl/stge159fe56-2ac6-478d-8248-46431acb6e5b/OceanDNA-b14654.fa --refList OceanDNA-b14654/target_genomes_gtdb.txt --output OceanDNA-b14654/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:47:13,227] [INFO] Task succeeded: fastANI
[2023-03-18 10:47:13,229] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:47:13,229] [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_002313245.1	s__UBA9455 sp002313245	77.6827	81	261	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA9455	95.0	97.93	97.22	0.78	0.67	5	-
GCA_012959765.1	s__UBA1328 sp012959765	76.9202	61	261	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.88	99.88	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-18 10:47:13,232] [INFO] GTDB search result was written to OceanDNA-b14654/result_gtdb.tsv
[2023-03-18 10:47:13,234] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:47:13,236] [INFO] DFAST_QC result json was written to OceanDNA-b14654/dqc_result.json
[2023-03-18 10:47:13,236] [INFO] DFAST_QC completed!
[2023-03-18 10:47:13,236] [INFO] Total running time: 0h0m51s