[2023-03-14 13:36:05,711] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:36:05,711] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:36:05,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg25fb2f0a-79cd-4d48-9281-6348ff6b388d/dqc_reference
[2023-03-14 13:36:06,784] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:36:06,784] [INFO] Task started: Prodigal
[2023-03-14 13:36:06,784] [INFO] Running command: cat /var/lib/cwl/stgdd69752a-027a-4799-8192-75aef3157036/OceanDNA-b15080.fa | prodigal -d OceanDNA-b15080/cds.fna -a OceanDNA-b15080/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:36:15,608] [INFO] Task succeeded: Prodigal
[2023-03-14 13:36:15,608] [INFO] Task started: HMMsearch
[2023-03-14 13:36:15,608] [INFO] Running command: hmmsearch --tblout OceanDNA-b15080/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25fb2f0a-79cd-4d48-9281-6348ff6b388d/dqc_reference/reference_markers.hmm OceanDNA-b15080/protein.faa > /dev/null
[2023-03-14 13:36:15,755] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:36:15,756] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdd69752a-027a-4799-8192-75aef3157036/OceanDNA-b15080.fa]
[2023-03-14 13:36:15,767] [INFO] Query marker FASTA was written to OceanDNA-b15080/markers.fasta
[2023-03-14 13:36:15,768] [INFO] Task started: Blastn
[2023-03-14 13:36:15,768] [INFO] Running command: blastn -query OceanDNA-b15080/markers.fasta -db /var/lib/cwl/stg25fb2f0a-79cd-4d48-9281-6348ff6b388d/dqc_reference/reference_markers.fasta -out OceanDNA-b15080/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:36:16,285] [INFO] Task succeeded: Blastn
[2023-03-14 13:36:16,286] [INFO] Selected 13 target genomes.
[2023-03-14 13:36:16,286] [INFO] Target genome list was writen to OceanDNA-b15080/target_genomes.txt
[2023-03-14 13:36:16,292] [INFO] Task started: fastANI
[2023-03-14 13:36:16,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd69752a-027a-4799-8192-75aef3157036/OceanDNA-b15080.fa --refList OceanDNA-b15080/target_genomes.txt --output OceanDNA-b15080/fastani_result.tsv --threads 1
[2023-03-14 13:36:23,927] [INFO] Task succeeded: fastANI
[2023-03-14 13:36:23,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25fb2f0a-79cd-4d48-9281-6348ff6b388d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:36:23,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25fb2f0a-79cd-4d48-9281-6348ff6b388d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:36:23,928] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:36:23,928] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:36:23,928] [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 13:36:23,943] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15080/tc_result.tsv
[2023-03-14 13:36:23,943] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:36:23,943] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:36:23,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25fb2f0a-79cd-4d48-9281-6348ff6b388d/dqc_reference/checkm_data
[2023-03-14 13:36:23,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:36:23,950] [INFO] Task started: CheckM
[2023-03-14 13:36:23,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15080/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15080/checkm_input OceanDNA-b15080/checkm_result
[2023-03-14 13:37:01,139] [INFO] Task succeeded: CheckM
[2023-03-14 13:37:01,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:37:01,142] [INFO] ===== Completeness check finished =====
[2023-03-14 13:37:01,142] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:37:01,142] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15080/markers.fasta)
[2023-03-14 13:37:01,143] [INFO] Task started: Blastn
[2023-03-14 13:37:01,143] [INFO] Running command: blastn -query OceanDNA-b15080/markers.fasta -db /var/lib/cwl/stg25fb2f0a-79cd-4d48-9281-6348ff6b388d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15080/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:37:01,928] [INFO] Task succeeded: Blastn
[2023-03-14 13:37:01,929] [INFO] Selected 11 target genomes.
[2023-03-14 13:37:01,929] [INFO] Target genome list was writen to OceanDNA-b15080/target_genomes_gtdb.txt
[2023-03-14 13:37:01,934] [INFO] Task started: fastANI
[2023-03-14 13:37:01,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd69752a-027a-4799-8192-75aef3157036/OceanDNA-b15080.fa --refList OceanDNA-b15080/target_genomes_gtdb.txt --output OceanDNA-b15080/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:37:07,321] [INFO] Task succeeded: fastANI
[2023-03-14 13:37:07,324] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:37:07,324] [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_014239685.1	s__GCA-2730555 sp014239685	89.9199	330	422	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730555.1	s__GCA-2730555 sp002730555	79.4187	277	422	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.68	99.68	0.93	0.93	2	-
GCA_018650185.1	s__GCA-2730555 sp018650185	78.5166	196	422	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.67	99.66	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-14 13:37:07,324] [INFO] GTDB search result was written to OceanDNA-b15080/result_gtdb.tsv
[2023-03-14 13:37:07,324] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:37:07,325] [INFO] DFAST_QC result json was written to OceanDNA-b15080/dqc_result.json
[2023-03-14 13:37:07,325] [INFO] DFAST_QC completed!
[2023-03-14 13:37:07,325] [INFO] Total running time: 0h1m2s