[2023-03-18 03:27:00,921] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,921] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg83875479-43bd-46e1-af08-c8f5f8e0c9a8/dqc_reference
[2023-03-18 03:27:02,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,640] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,640] [INFO] Running command: cat /var/lib/cwl/stgde792196-0a68-4ea7-b6d9-86c12e7b6845/OceanDNA-b45804.fa | prodigal -d OceanDNA-b45804/cds.fna -a OceanDNA-b45804/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:22,994] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:22,995] [INFO] Task started: HMMsearch
[2023-03-18 03:27:22,995] [INFO] Running command: hmmsearch --tblout OceanDNA-b45804/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83875479-43bd-46e1-af08-c8f5f8e0c9a8/dqc_reference/reference_markers.hmm OceanDNA-b45804/protein.faa > /dev/null
[2023-03-18 03:27:23,185] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:23,186] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgde792196-0a68-4ea7-b6d9-86c12e7b6845/OceanDNA-b45804.fa]
[2023-03-18 03:27:23,208] [INFO] Query marker FASTA was written to OceanDNA-b45804/markers.fasta
[2023-03-18 03:27:23,208] [INFO] Task started: Blastn
[2023-03-18 03:27:23,208] [INFO] Running command: blastn -query OceanDNA-b45804/markers.fasta -db /var/lib/cwl/stg83875479-43bd-46e1-af08-c8f5f8e0c9a8/dqc_reference/reference_markers.fasta -out OceanDNA-b45804/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:23,653] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:23,653] [INFO] Selected 16 target genomes.
[2023-03-18 03:27:23,654] [INFO] Target genome list was writen to OceanDNA-b45804/target_genomes.txt
[2023-03-18 03:27:23,663] [INFO] Task started: fastANI
[2023-03-18 03:27:23,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgde792196-0a68-4ea7-b6d9-86c12e7b6845/OceanDNA-b45804.fa --refList OceanDNA-b45804/target_genomes.txt --output OceanDNA-b45804/fastani_result.tsv --threads 1
[2023-03-18 03:27:35,937] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:35,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83875479-43bd-46e1-af08-c8f5f8e0c9a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:35,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83875479-43bd-46e1-af08-c8f5f8e0c9a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:35,942] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:35,942] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:27:35,942] [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	76.6248	68	696	95	below_threshold
Pelagicoccus mobilis	strain=KCTC 13126	GCA_016595505.1	415221	415221	type	True	76.5059	55	696	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:27:35,942] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45804/tc_result.tsv
[2023-03-18 03:27:35,942] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:35,942] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:35,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83875479-43bd-46e1-af08-c8f5f8e0c9a8/dqc_reference/checkm_data
[2023-03-18 03:27:35,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:35,948] [INFO] Task started: CheckM
[2023-03-18 03:27:35,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45804/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45804/checkm_input OceanDNA-b45804/checkm_result
[2023-03-18 03:28:28,479] [INFO] Task succeeded: CheckM
[2023-03-18 03:28:28,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:28:28,481] [INFO] ===== Completeness check finished =====
[2023-03-18 03:28:28,482] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:28:28,482] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45804/markers.fasta)
[2023-03-18 03:28:28,482] [INFO] Task started: Blastn
[2023-03-18 03:28:28,482] [INFO] Running command: blastn -query OceanDNA-b45804/markers.fasta -db /var/lib/cwl/stg83875479-43bd-46e1-af08-c8f5f8e0c9a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45804/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:28,913] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:28,914] [INFO] Selected 19 target genomes.
[2023-03-18 03:28:28,914] [INFO] Target genome list was writen to OceanDNA-b45804/target_genomes_gtdb.txt
[2023-03-18 03:28:28,933] [INFO] Task started: fastANI
[2023-03-18 03:28:28,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgde792196-0a68-4ea7-b6d9-86c12e7b6845/OceanDNA-b45804.fa --refList OceanDNA-b45804/target_genomes_gtdb.txt --output OceanDNA-b45804/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:28:40,773] [INFO] Task succeeded: fastANI
[2023-03-18 03:28:40,776] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:28:40,777] [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	77.0475	105	696	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.68	99.65	0.95	0.94	5	-
GCF_014803405.1	s__Pelagicoccus sp014803405	76.6248	68	696	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595505.1	s__Pelagicoccus mobilis	76.5059	55	696	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	76.2784	55	696	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	96.17	95.09	0.91	0.87	4	-
--------------------------------------------------------------------------------
[2023-03-18 03:28:40,777] [INFO] GTDB search result was written to OceanDNA-b45804/result_gtdb.tsv
[2023-03-18 03:28:40,777] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:28:40,778] [INFO] DFAST_QC result json was written to OceanDNA-b45804/dqc_result.json
[2023-03-18 03:28:40,778] [INFO] DFAST_QC completed!
[2023-03-18 03:28:40,778] [INFO] Total running time: 0h1m40s