[2023-03-15 05:16:58,330] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:16:58,330] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:16:58,330] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ee3525c-cac3-4e38-831b-3b8864168a78/dqc_reference
[2023-03-15 05:16:59,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:16:59,421] [INFO] Task started: Prodigal
[2023-03-15 05:16:59,421] [INFO] Running command: cat /var/lib/cwl/stg8438f3d3-dc1c-4713-b460-09c67bd80216/OceanDNA-b9797.fa | prodigal -d OceanDNA-b9797/cds.fna -a OceanDNA-b9797/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:17:14,641] [INFO] Task succeeded: Prodigal
[2023-03-15 05:17:14,641] [INFO] Task started: HMMsearch
[2023-03-15 05:17:14,641] [INFO] Running command: hmmsearch --tblout OceanDNA-b9797/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ee3525c-cac3-4e38-831b-3b8864168a78/dqc_reference/reference_markers.hmm OceanDNA-b9797/protein.faa > /dev/null
[2023-03-15 05:17:14,830] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:17:14,830] [INFO] Found 6/6 markers.
[2023-03-15 05:17:14,853] [INFO] Query marker FASTA was written to OceanDNA-b9797/markers.fasta
[2023-03-15 05:17:14,853] [INFO] Task started: Blastn
[2023-03-15 05:17:14,854] [INFO] Running command: blastn -query OceanDNA-b9797/markers.fasta -db /var/lib/cwl/stg9ee3525c-cac3-4e38-831b-3b8864168a78/dqc_reference/reference_markers.fasta -out OceanDNA-b9797/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:17:15,419] [INFO] Task succeeded: Blastn
[2023-03-15 05:17:15,422] [INFO] Selected 15 target genomes.
[2023-03-15 05:17:15,423] [INFO] Target genome list was writen to OceanDNA-b9797/target_genomes.txt
[2023-03-15 05:17:15,433] [INFO] Task started: fastANI
[2023-03-15 05:17:15,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg8438f3d3-dc1c-4713-b460-09c67bd80216/OceanDNA-b9797.fa --refList OceanDNA-b9797/target_genomes.txt --output OceanDNA-b9797/fastani_result.tsv --threads 1
[2023-03-15 05:17:24,806] [INFO] Task succeeded: fastANI
[2023-03-15 05:17:24,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ee3525c-cac3-4e38-831b-3b8864168a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:17:24,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ee3525c-cac3-4e38-831b-3b8864168a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:17:24,813] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:17:24,813] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:17:24,813] [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 ulvanivorans	strain=PLR	GCA_000732625.1	906888	906888	type	True	91.9577	728	810	95	below_threshold
Nonlabens ulvanivorans	strain=DSM 22727	GCA_003001855.1	906888	906888	type	True	91.9284	726	810	95	below_threshold
Nonlabens arenilitoris	strain=KCTC 32109	GCA_002954765.1	1217969	1217969	type	True	89.4208	722	810	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002954345.1	191564	191564	type	True	79.3498	307	810	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002934445.1	191564	191564	type	True	79.1385	310	810	95	below_threshold
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	78.2983	271	810	95	below_threshold
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	78.243	267	810	95	below_threshold
Nonlabens tegetincola	strain=JCM 12886	GCA_002954355.1	323273	323273	type	True	76.7522	167	810	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	75.5534	54	810	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:17:24,815] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9797/tc_result.tsv
[2023-03-15 05:17:24,816] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:17:24,817] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:17:24,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ee3525c-cac3-4e38-831b-3b8864168a78/dqc_reference/checkm_data
[2023-03-15 05:17:24,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:17:24,890] [INFO] Task started: CheckM
[2023-03-15 05:17:24,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9797/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9797/checkm_input OceanDNA-b9797/checkm_result
[2023-03-15 05:18:06,141] [INFO] Task succeeded: CheckM
[2023-03-15 05:18:06,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:18:06,208] [INFO] ===== Completeness check finished =====
[2023-03-15 05:18:06,208] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:18:06,209] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9797/markers.fasta)
[2023-03-15 05:18:06,210] [INFO] Task started: Blastn
[2023-03-15 05:18:06,210] [INFO] Running command: blastn -query OceanDNA-b9797/markers.fasta -db /var/lib/cwl/stg9ee3525c-cac3-4e38-831b-3b8864168a78/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9797/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:18:06,987] [INFO] Task succeeded: Blastn
[2023-03-15 05:18:06,995] [INFO] Selected 9 target genomes.
[2023-03-15 05:18:06,996] [INFO] Target genome list was writen to OceanDNA-b9797/target_genomes_gtdb.txt
[2023-03-15 05:18:07,006] [INFO] Task started: fastANI
[2023-03-15 05:18:07,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg8438f3d3-dc1c-4713-b460-09c67bd80216/OceanDNA-b9797.fa --refList OceanDNA-b9797/target_genomes_gtdb.txt --output OceanDNA-b9797/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:18:12,545] [INFO] Task succeeded: fastANI
[2023-03-15 05:18:12,551] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:18:12,551] [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_000755285.1	s__Nonlabens ulvanivorans_A	96.1981	751	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	97.55	97.55	0.94	0.94	2	conclusive
GCF_000732625.1	s__Nonlabens ulvanivorans	91.9577	728	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	98.59	98.07	0.92	0.89	5	-
GCF_002954765.1	s__Nonlabens arenilitoris	89.4208	722	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153385.1	s__Nonlabens sp000153385	86.8868	701	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934445.1	s__Nonlabens xylanidelens	79.1385	310	810	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	78.5266	237	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332115.1	s__Nonlabens dokdonensis	78.243	267	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002831625.1	s__Nonlabens sp002831625	77.6176	204	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954355.1	s__Nonlabens tegetincola	76.7522	167	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	97.69	97.39	0.93	0.90	5	-
--------------------------------------------------------------------------------
[2023-03-15 05:18:12,553] [INFO] GTDB search result was written to OceanDNA-b9797/result_gtdb.tsv
[2023-03-15 05:18:12,555] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:18:12,559] [INFO] DFAST_QC result json was written to OceanDNA-b9797/dqc_result.json
[2023-03-15 05:18:12,559] [INFO] DFAST_QC completed!
[2023-03-15 05:18:12,559] [INFO] Total running time: 0h1m14s