[2023-03-18 22:09:38,388] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:09:38,388] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:09:38,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg05483a50-f0ed-4f7d-a0ac-33876447d3f1/dqc_reference
[2023-03-18 22:09:40,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:09:40,574] [INFO] Task started: Prodigal
[2023-03-18 22:09:40,574] [INFO] Running command: cat /var/lib/cwl/stgc2e30ad1-88cd-4cd1-b829-8d638fcb9f30/OceanDNA-b17555.fa | prodigal -d OceanDNA-b17555/cds.fna -a OceanDNA-b17555/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:10:00,399] [INFO] Task succeeded: Prodigal
[2023-03-18 22:10:00,399] [INFO] Task started: HMMsearch
[2023-03-18 22:10:00,399] [INFO] Running command: hmmsearch --tblout OceanDNA-b17555/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05483a50-f0ed-4f7d-a0ac-33876447d3f1/dqc_reference/reference_markers.hmm OceanDNA-b17555/protein.faa > /dev/null
[2023-03-18 22:10:00,614] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:10:00,615] [INFO] Found 6/6 markers.
[2023-03-18 22:10:00,636] [INFO] Query marker FASTA was written to OceanDNA-b17555/markers.fasta
[2023-03-18 22:10:00,637] [INFO] Task started: Blastn
[2023-03-18 22:10:00,637] [INFO] Running command: blastn -query OceanDNA-b17555/markers.fasta -db /var/lib/cwl/stg05483a50-f0ed-4f7d-a0ac-33876447d3f1/dqc_reference/reference_markers.fasta -out OceanDNA-b17555/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:10:01,190] [INFO] Task succeeded: Blastn
[2023-03-18 22:10:01,191] [INFO] Selected 22 target genomes.
[2023-03-18 22:10:01,191] [INFO] Target genome list was writen to OceanDNA-b17555/target_genomes.txt
[2023-03-18 22:10:01,204] [INFO] Task started: fastANI
[2023-03-18 22:10:01,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2e30ad1-88cd-4cd1-b829-8d638fcb9f30/OceanDNA-b17555.fa --refList OceanDNA-b17555/target_genomes.txt --output OceanDNA-b17555/fastani_result.tsv --threads 1
[2023-03-18 22:10:17,367] [INFO] Task succeeded: fastANI
[2023-03-18 22:10:17,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05483a50-f0ed-4f7d-a0ac-33876447d3f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:10:17,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05483a50-f0ed-4f7d-a0ac-33876447d3f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:10:17,372] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:10:17,372] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:10:17,372] [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
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	74.8129	57	1054	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	74.6488	62	1054	95	below_threshold
Burkholderia plantarii	strain=ATCC 43733	GCA_001411805.1	41899	41899	type	True	74.645	63	1054	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:10:17,372] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17555/tc_result.tsv
[2023-03-18 22:10:17,372] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:10:17,372] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:10:17,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05483a50-f0ed-4f7d-a0ac-33876447d3f1/dqc_reference/checkm_data
[2023-03-18 22:10:17,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:10:17,378] [INFO] Task started: CheckM
[2023-03-18 22:10:17,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17555/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17555/checkm_input OceanDNA-b17555/checkm_result
[2023-03-18 22:11:08,694] [INFO] Task succeeded: CheckM
[2023-03-18 22:11:08,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:11:08,705] [INFO] ===== Completeness check finished =====
[2023-03-18 22:11:08,705] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:11:08,705] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17555/markers.fasta)
[2023-03-18 22:11:08,706] [INFO] Task started: Blastn
[2023-03-18 22:11:08,706] [INFO] Running command: blastn -query OceanDNA-b17555/markers.fasta -db /var/lib/cwl/stg05483a50-f0ed-4f7d-a0ac-33876447d3f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17555/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:11:09,700] [INFO] Task succeeded: Blastn
[2023-03-18 22:11:09,717] [INFO] Selected 16 target genomes.
[2023-03-18 22:11:09,717] [INFO] Target genome list was writen to OceanDNA-b17555/target_genomes_gtdb.txt
[2023-03-18 22:11:09,729] [INFO] Task started: fastANI
[2023-03-18 22:11:09,730] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2e30ad1-88cd-4cd1-b829-8d638fcb9f30/OceanDNA-b17555.fa --refList OceanDNA-b17555/target_genomes_gtdb.txt --output OceanDNA-b17555/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:11:20,793] [INFO] Task succeeded: fastANI
[2023-03-18 22:11:20,799] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:11:20,799] [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_013824755.1	s__PNOJ01 sp013824755	78.5414	301	1054	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__PNOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719645.1	s__PNOJ01 sp016719645	78.4961	378	1054	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__PNOJ01	95.0	96.99	95.77	0.87	0.87	3	-
GCA_018814885.1	s__JAHIYU01 sp018814885	78.2828	325	1054	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__JAHIYU01	95.0	99.82	99.76	0.96	0.95	3	-
GCA_014859985.1	s__LZORAL124-64-63 sp014859985	77.7728	217	1054	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__LZORAL124-64-63	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829565.1	s__LZORAL124-64-63 sp018829565	77.2938	207	1054	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__LZORAL124-64-63	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847545.1	s__CAINDZ01 sp903847545	76.8531	127	1054	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	98.70	98.54	0.79	0.77	4	-
GCA_014730255.1	s__Glo-17 sp014730255	76.7878	154	1054	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__Glo-17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712675.1	s__CAINDZ01 sp016712675	76.7548	180	1054	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003353795.1	s__Glo-17 sp003353795	76.6694	182	1054	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__Glo-17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:11:20,799] [INFO] GTDB search result was written to OceanDNA-b17555/result_gtdb.tsv
[2023-03-18 22:11:20,799] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:11:20,800] [INFO] DFAST_QC result json was written to OceanDNA-b17555/dqc_result.json
[2023-03-18 22:11:20,800] [INFO] DFAST_QC completed!
[2023-03-18 22:11:20,800] [INFO] Total running time: 0h1m42s