[2023-03-17 01:44:57,164] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:44:57,164] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:44:57,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg9823348c-bdf3-4865-bca8-c9512f9fcf7d/dqc_reference
[2023-03-17 01:44:59,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:44:59,094] [INFO] Task started: Prodigal
[2023-03-17 01:44:59,094] [INFO] Running command: cat /var/lib/cwl/stg4cd3c4b4-52b6-4151-b7a1-3c053397abab/OceanDNA-b9793.fa | prodigal -d OceanDNA-b9793/cds.fna -a OceanDNA-b9793/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:45:16,978] [INFO] Task succeeded: Prodigal
[2023-03-17 01:45:16,979] [INFO] Task started: HMMsearch
[2023-03-17 01:45:16,979] [INFO] Running command: hmmsearch --tblout OceanDNA-b9793/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9823348c-bdf3-4865-bca8-c9512f9fcf7d/dqc_reference/reference_markers.hmm OceanDNA-b9793/protein.faa > /dev/null
[2023-03-17 01:45:17,169] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:45:17,170] [INFO] Found 6/6 markers.
[2023-03-17 01:45:17,186] [INFO] Query marker FASTA was written to OceanDNA-b9793/markers.fasta
[2023-03-17 01:45:17,186] [INFO] Task started: Blastn
[2023-03-17 01:45:17,186] [INFO] Running command: blastn -query OceanDNA-b9793/markers.fasta -db /var/lib/cwl/stg9823348c-bdf3-4865-bca8-c9512f9fcf7d/dqc_reference/reference_markers.fasta -out OceanDNA-b9793/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:17,755] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:17,756] [INFO] Selected 11 target genomes.
[2023-03-17 01:45:17,756] [INFO] Target genome list was writen to OceanDNA-b9793/target_genomes.txt
[2023-03-17 01:45:17,763] [INFO] Task started: fastANI
[2023-03-17 01:45:17,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cd3c4b4-52b6-4151-b7a1-3c053397abab/OceanDNA-b9793.fa --refList OceanDNA-b9793/target_genomes.txt --output OceanDNA-b9793/fastani_result.tsv --threads 1
[2023-03-17 01:45:24,549] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:24,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9823348c-bdf3-4865-bca8-c9512f9fcf7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:45:24,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9823348c-bdf3-4865-bca8-c9512f9fcf7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:45:24,555] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:45:24,555] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:45:24,555] [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
Nonlabens xylanidelens	strain=DSM 16809	GCA_002934445.1	191564	191564	type	True	79.6264	481	896	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002954345.1	191564	191564	type	True	79.5345	481	896	95	below_threshold
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	78.9145	458	896	95	below_threshold
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	78.9007	458	896	95	below_threshold
Nonlabens ulvanivorans	strain=PLR	GCA_000732625.1	906888	906888	type	True	77.4325	240	896	95	below_threshold
Nonlabens arenilitoris	strain=KCTC 32109	GCA_002954765.1	1217969	1217969	type	True	77.3276	233	896	95	below_threshold
Nonlabens xiamenensis	strain=1Q3	GCA_003865345.1	2341043	2341043	type	True	76.626	123	896	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:45:24,555] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9793/tc_result.tsv
[2023-03-17 01:45:24,555] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:45:24,555] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:45:24,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9823348c-bdf3-4865-bca8-c9512f9fcf7d/dqc_reference/checkm_data
[2023-03-17 01:45:24,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:45:24,560] [INFO] Task started: CheckM
[2023-03-17 01:45:24,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9793/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9793/checkm_input OceanDNA-b9793/checkm_result
[2023-03-17 01:46:10,931] [INFO] Task succeeded: CheckM
[2023-03-17 01:46:10,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:46:10,933] [INFO] ===== Completeness check finished =====
[2023-03-17 01:46:10,934] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:46:10,934] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9793/markers.fasta)
[2023-03-17 01:46:10,935] [INFO] Task started: Blastn
[2023-03-17 01:46:10,935] [INFO] Running command: blastn -query OceanDNA-b9793/markers.fasta -db /var/lib/cwl/stg9823348c-bdf3-4865-bca8-c9512f9fcf7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9793/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:46:11,729] [INFO] Task succeeded: Blastn
[2023-03-17 01:46:11,730] [INFO] Selected 6 target genomes.
[2023-03-17 01:46:11,730] [INFO] Target genome list was writen to OceanDNA-b9793/target_genomes_gtdb.txt
[2023-03-17 01:46:11,881] [INFO] Task started: fastANI
[2023-03-17 01:46:11,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cd3c4b4-52b6-4151-b7a1-3c053397abab/OceanDNA-b9793.fa --refList OceanDNA-b9793/target_genomes_gtdb.txt --output OceanDNA-b9793/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:46:16,295] [INFO] Task succeeded: fastANI
[2023-03-17 01:46:16,299] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 01:46:16,300] [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
GCF_002831625.1	s__Nonlabens sp002831625	98.9814	874	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012974865.1	s__Nonlabens sp012974865	88.7324	796	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401815.1	s__Nonlabens sp018401815	87.9175	720	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.14	99.12	0.97	0.97	3	-
GCF_002934445.1	s__Nonlabens xylanidelens	79.6368	480	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000332115.1	s__Nonlabens dokdonensis	78.8965	460	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002162835.1	s__Nonlabens dokdonensis_B	78.8533	388	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:46:16,300] [INFO] GTDB search result was written to OceanDNA-b9793/result_gtdb.tsv
[2023-03-17 01:46:16,300] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:46:16,301] [INFO] DFAST_QC result json was written to OceanDNA-b9793/dqc_result.json
[2023-03-17 01:46:16,301] [INFO] DFAST_QC completed!
[2023-03-17 01:46:16,301] [INFO] Total running time: 0h1m19s