[2023-03-16 03:23:48,509] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:48,509] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:48,509] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4b04b68-7aab-4a2f-a818-4ce153722663/dqc_reference
[2023-03-16 03:23:50,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,648] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,649] [INFO] Running command: cat /var/lib/cwl/stg3f1b1839-2ce3-46b8-adc4-2df2d5582b3c/OceanDNA-b33424.fa | prodigal -d OceanDNA-b33424/cds.fna -a OceanDNA-b33424/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:01,326] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:01,326] [INFO] Task started: HMMsearch
[2023-03-16 03:24:01,326] [INFO] Running command: hmmsearch --tblout OceanDNA-b33424/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4b04b68-7aab-4a2f-a818-4ce153722663/dqc_reference/reference_markers.hmm OceanDNA-b33424/protein.faa > /dev/null
[2023-03-16 03:24:01,570] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:01,571] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3f1b1839-2ce3-46b8-adc4-2df2d5582b3c/OceanDNA-b33424.fa]
[2023-03-16 03:24:01,588] [INFO] Query marker FASTA was written to OceanDNA-b33424/markers.fasta
[2023-03-16 03:24:01,588] [INFO] Task started: Blastn
[2023-03-16 03:24:01,588] [INFO] Running command: blastn -query OceanDNA-b33424/markers.fasta -db /var/lib/cwl/stgf4b04b68-7aab-4a2f-a818-4ce153722663/dqc_reference/reference_markers.fasta -out OceanDNA-b33424/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:02,193] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:02,193] [INFO] Selected 16 target genomes.
[2023-03-16 03:24:02,194] [INFO] Target genome list was writen to OceanDNA-b33424/target_genomes.txt
[2023-03-16 03:24:02,205] [INFO] Task started: fastANI
[2023-03-16 03:24:02,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1b1839-2ce3-46b8-adc4-2df2d5582b3c/OceanDNA-b33424.fa --refList OceanDNA-b33424/target_genomes.txt --output OceanDNA-b33424/fastani_result.tsv --threads 1
[2023-03-16 03:24:11,211] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:11,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4b04b68-7aab-4a2f-a818-4ce153722663/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:11,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4b04b68-7aab-4a2f-a818-4ce153722663/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:11,217] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:11,217] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:24:11,217] [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
Pusillimonas maritima	strain=17-4A	GCA_003576595.1	2026239	2026239	type	True	84.7036	386	514	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.1773	131	514	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_013416545.1	645616	645616	type	True	77.0659	61	514	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.0659	61	514	95	below_threshold
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	77.0227	62	514	95	below_threshold
Pusillimonas soli	strain=DSM 25264	GCA_013416335.1	659016	659016	type	True	76.3367	50	514	95	below_threshold
Pusillimonas soli	strain=KCTC 22455	GCA_004153445.1	659016	659016	type	True	76.3367	50	514	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:11,217] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33424/tc_result.tsv
[2023-03-16 03:24:11,217] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:11,218] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:11,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4b04b68-7aab-4a2f-a818-4ce153722663/dqc_reference/checkm_data
[2023-03-16 03:24:11,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:11,222] [INFO] Task started: CheckM
[2023-03-16 03:24:11,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33424/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33424/checkm_input OceanDNA-b33424/checkm_result
[2023-03-16 03:24:42,290] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:42,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:42,292] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:42,292] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:42,293] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33424/markers.fasta)
[2023-03-16 03:24:42,293] [INFO] Task started: Blastn
[2023-03-16 03:24:42,293] [INFO] Running command: blastn -query OceanDNA-b33424/markers.fasta -db /var/lib/cwl/stgf4b04b68-7aab-4a2f-a818-4ce153722663/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33424/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:43,283] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:43,284] [INFO] Selected 12 target genomes.
[2023-03-16 03:24:43,284] [INFO] Target genome list was writen to OceanDNA-b33424/target_genomes_gtdb.txt
[2023-03-16 03:24:43,407] [INFO] Task started: fastANI
[2023-03-16 03:24:43,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1b1839-2ce3-46b8-adc4-2df2d5582b3c/OceanDNA-b33424.fa --refList OceanDNA-b33424/target_genomes_gtdb.txt --output OceanDNA-b33424/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:50,896] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:50,902] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:24:50,902] [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_002694155.1	s__Pusillimonas_A sp002694155	99.8846	391	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003576595.1	s__Pusillimonas_A maritima	84.7036	386	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	96.55	95.88	0.88	0.85	8	-
GCF_011388195.1	s__Pusillimonas_A sp011388195	83.7376	369	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384935.1	s__Pusillimonas_A sp002384935	81.6953	340	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.90	98.23	0.90	0.79	9	-
GCF_014237865.1	s__Pusillimonas_A sp014237865	77.1566	132	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002236805.1	s__Pusillimonas_A sp002236805	77.122	116	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
GCF_004153445.1	s__Pusillimonas_B soli	76.3367	50	514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:50,902] [INFO] GTDB search result was written to OceanDNA-b33424/result_gtdb.tsv
[2023-03-16 03:24:50,902] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:50,903] [INFO] DFAST_QC result json was written to OceanDNA-b33424/dqc_result.json
[2023-03-16 03:24:50,903] [INFO] DFAST_QC completed!
[2023-03-16 03:24:50,903] [INFO] Total running time: 0h1m2s