[2023-03-17 04:48:54,016] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:54,016] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:54,016] [INFO] DQC Reference Directory: /var/lib/cwl/stg69dc3212-0dea-4c7c-aef1-2f08a25c3535/dqc_reference
[2023-03-17 04:48:55,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,155] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,156] [INFO] Running command: cat /var/lib/cwl/stgc3912f5c-6ce4-4b87-a70f-dc74b106f962/OceanDNA-b26567.fa | prodigal -d OceanDNA-b26567/cds.fna -a OceanDNA-b26567/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:07,692] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:07,692] [INFO] Task started: HMMsearch
[2023-03-17 04:49:07,692] [INFO] Running command: hmmsearch --tblout OceanDNA-b26567/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69dc3212-0dea-4c7c-aef1-2f08a25c3535/dqc_reference/reference_markers.hmm OceanDNA-b26567/protein.faa > /dev/null
[2023-03-17 04:49:07,857] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:07,857] [INFO] Found 6/6 markers.
[2023-03-17 04:49:07,871] [INFO] Query marker FASTA was written to OceanDNA-b26567/markers.fasta
[2023-03-17 04:49:07,871] [INFO] Task started: Blastn
[2023-03-17 04:49:07,871] [INFO] Running command: blastn -query OceanDNA-b26567/markers.fasta -db /var/lib/cwl/stg69dc3212-0dea-4c7c-aef1-2f08a25c3535/dqc_reference/reference_markers.fasta -out OceanDNA-b26567/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:08,417] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:08,418] [INFO] Selected 24 target genomes.
[2023-03-17 04:49:08,419] [INFO] Target genome list was writen to OceanDNA-b26567/target_genomes.txt
[2023-03-17 04:49:08,431] [INFO] Task started: fastANI
[2023-03-17 04:49:08,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3912f5c-6ce4-4b87-a70f-dc74b106f962/OceanDNA-b26567.fa --refList OceanDNA-b26567/target_genomes.txt --output OceanDNA-b26567/fastani_result.tsv --threads 1
[2023-03-17 04:49:25,634] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:25,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69dc3212-0dea-4c7c-aef1-2f08a25c3535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:25,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69dc3212-0dea-4c7c-aef1-2f08a25c3535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:25,635] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:25,635] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:25,635] [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 04:49:25,636] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26567/tc_result.tsv
[2023-03-17 04:49:25,636] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:25,636] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:25,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69dc3212-0dea-4c7c-aef1-2f08a25c3535/dqc_reference/checkm_data
[2023-03-17 04:49:25,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:25,641] [INFO] Task started: CheckM
[2023-03-17 04:49:25,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26567/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26567/checkm_input OceanDNA-b26567/checkm_result
[2023-03-17 04:50:00,358] [INFO] Task succeeded: CheckM
[2023-03-17 04:50:00,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.76%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 04:50:00,362] [INFO] ===== Completeness check finished =====
[2023-03-17 04:50:00,362] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:50:00,362] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26567/markers.fasta)
[2023-03-17 04:50:00,362] [INFO] Task started: Blastn
[2023-03-17 04:50:00,362] [INFO] Running command: blastn -query OceanDNA-b26567/markers.fasta -db /var/lib/cwl/stg69dc3212-0dea-4c7c-aef1-2f08a25c3535/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26567/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:50:01,186] [INFO] Task succeeded: Blastn
[2023-03-17 04:50:01,187] [INFO] Selected 19 target genomes.
[2023-03-17 04:50:01,187] [INFO] Target genome list was writen to OceanDNA-b26567/target_genomes_gtdb.txt
[2023-03-17 04:50:01,724] [INFO] Task started: fastANI
[2023-03-17 04:50:01,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3912f5c-6ce4-4b87-a70f-dc74b106f962/OceanDNA-b26567.fa --refList OceanDNA-b26567/target_genomes_gtdb.txt --output OceanDNA-b26567/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:50:10,831] [INFO] Task succeeded: fastANI
[2023-03-17 04:50:10,838] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:50:10,838] [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_002731315.1	s__UBA8309 sp002731315	99.5971	401	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002686685.1	s__UBA8309 sp002686685	91.0192	413	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_002683535.1	s__UBA8309 sp002683535	78.2625	174	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780765.1	s__UBA8309 sp016780765	78.2439	256	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCA_002457745.1	s__UBA8309 sp002457745	77.9404	155	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	77.5643	190	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_009920665.1	s__UBA8309 sp009920665	77.3004	222	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	77.2887	193	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524735.1	s__UBA8309 sp011524735	77.2541	112	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	76.1544	77	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:50:10,838] [INFO] GTDB search result was written to OceanDNA-b26567/result_gtdb.tsv
[2023-03-17 04:50:10,838] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:50:10,839] [INFO] DFAST_QC result json was written to OceanDNA-b26567/dqc_result.json
[2023-03-17 04:50:10,839] [INFO] DFAST_QC completed!
[2023-03-17 04:50:10,839] [INFO] Total running time: 0h1m17s