[2023-03-17 23:09:44,538] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:09:44,538] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:09:44,538] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbbd2255-a841-4e79-ac2d-e300872090ea/dqc_reference
[2023-03-17 23:09:45,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:09:45,686] [INFO] Task started: Prodigal
[2023-03-17 23:09:45,686] [INFO] Running command: cat /var/lib/cwl/stg6353e6c6-e5a2-410f-ab0c-7e78e60dc328/OceanDNA-b45823.fa | prodigal -d OceanDNA-b45823/cds.fna -a OceanDNA-b45823/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:10:17,729] [INFO] Task succeeded: Prodigal
[2023-03-17 23:10:17,730] [INFO] Task started: HMMsearch
[2023-03-17 23:10:17,730] [INFO] Running command: hmmsearch --tblout OceanDNA-b45823/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbbd2255-a841-4e79-ac2d-e300872090ea/dqc_reference/reference_markers.hmm OceanDNA-b45823/protein.faa > /dev/null
[2023-03-17 23:10:17,947] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:10:17,948] [INFO] Found 6/6 markers.
[2023-03-17 23:10:17,985] [INFO] Query marker FASTA was written to OceanDNA-b45823/markers.fasta
[2023-03-17 23:10:17,986] [INFO] Task started: Blastn
[2023-03-17 23:10:17,986] [INFO] Running command: blastn -query OceanDNA-b45823/markers.fasta -db /var/lib/cwl/stgcbbd2255-a841-4e79-ac2d-e300872090ea/dqc_reference/reference_markers.fasta -out OceanDNA-b45823/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:10:18,565] [INFO] Task succeeded: Blastn
[2023-03-17 23:10:18,569] [INFO] Selected 20 target genomes.
[2023-03-17 23:10:18,569] [INFO] Target genome list was writen to OceanDNA-b45823/target_genomes.txt
[2023-03-17 23:10:18,580] [INFO] Task started: fastANI
[2023-03-17 23:10:18,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg6353e6c6-e5a2-410f-ab0c-7e78e60dc328/OceanDNA-b45823.fa --refList OceanDNA-b45823/target_genomes.txt --output OceanDNA-b45823/fastani_result.tsv --threads 1
[2023-03-17 23:10:32,426] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:32,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbbd2255-a841-4e79-ac2d-e300872090ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:10:32,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbbd2255-a841-4e79-ac2d-e300872090ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:10:32,430] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:10:32,430] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:10:32,430] [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
Pelagicoccus enzymogenes	strain=NFK12	GCA_014803405.1	2773457	2773457	type	True	76.2822	68	1352	95	below_threshold
Pelagicoccus mobilis	strain=KCTC 13126	GCA_016595505.1	415221	415221	type	True	75.7769	89	1352	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:10:32,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45823/tc_result.tsv
[2023-03-17 23:10:32,441] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:10:32,442] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:10:32,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbbd2255-a841-4e79-ac2d-e300872090ea/dqc_reference/checkm_data
[2023-03-17 23:10:32,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:10:32,489] [INFO] Task started: CheckM
[2023-03-17 23:10:32,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45823/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45823/checkm_input OceanDNA-b45823/checkm_result
[2023-03-17 23:11:51,052] [INFO] Task succeeded: CheckM
[2023-03-17 23:11:51,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:11:51,078] [INFO] ===== Completeness check finished =====
[2023-03-17 23:11:51,078] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:11:51,078] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45823/markers.fasta)
[2023-03-17 23:11:51,079] [INFO] Task started: Blastn
[2023-03-17 23:11:51,079] [INFO] Running command: blastn -query OceanDNA-b45823/markers.fasta -db /var/lib/cwl/stgcbbd2255-a841-4e79-ac2d-e300872090ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45823/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:11:52,011] [INFO] Task succeeded: Blastn
[2023-03-17 23:11:52,019] [INFO] Selected 26 target genomes.
[2023-03-17 23:11:52,019] [INFO] Target genome list was writen to OceanDNA-b45823/target_genomes_gtdb.txt
[2023-03-17 23:11:52,061] [INFO] Task started: fastANI
[2023-03-17 23:11:52,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg6353e6c6-e5a2-410f-ab0c-7e78e60dc328/OceanDNA-b45823.fa --refList OceanDNA-b45823/target_genomes_gtdb.txt --output OceanDNA-b45823/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:12:07,631] [INFO] Task succeeded: fastANI
[2023-03-17 23:12:07,636] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:12:07,637] [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_018700525.1	s__UBA5691 sp018700525	82.0732	847	1352	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.68	99.65	0.95	0.94	5	-
GCA_002420185.1	s__UBA5691 sp002420185	76.9266	95	1352	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000155695.1	s__Pelagicoccus sp000155695	76.4014	78	1352	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014529625.1	s__UBA5691 sp002420265	76.3612	141	1352	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	96.17	95.09	0.91	0.87	4	-
GCF_014803405.1	s__Pelagicoccus sp014803405	76.2822	68	1352	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694885.1	s__UBA5691 sp002694885	75.8747	90	1352	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.79	99.79	0.86	0.86	2	-
GCF_016595505.1	s__Pelagicoccus mobilis	75.7769	89	1352	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:12:07,637] [INFO] GTDB search result was written to OceanDNA-b45823/result_gtdb.tsv
[2023-03-17 23:12:07,637] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:12:07,638] [INFO] DFAST_QC result json was written to OceanDNA-b45823/dqc_result.json
[2023-03-17 23:12:07,638] [INFO] DFAST_QC completed!
[2023-03-17 23:12:07,638] [INFO] Total running time: 0h2m23s