[2023-03-16 04:05:20,417] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,417] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,417] [INFO] DQC Reference Directory: /var/lib/cwl/stgf48bd3c7-4350-4faf-b2a2-9e6d711cfb47/dqc_reference
[2023-03-16 04:05:22,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,126] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,126] [INFO] Running command: cat /var/lib/cwl/stg99a2c401-21c9-494f-847f-42f6438046c6/OceanDNA-b10097.fa | prodigal -d OceanDNA-b10097/cds.fna -a OceanDNA-b10097/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:40,502] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:40,502] [INFO] Task started: HMMsearch
[2023-03-16 04:05:40,502] [INFO] Running command: hmmsearch --tblout OceanDNA-b10097/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf48bd3c7-4350-4faf-b2a2-9e6d711cfb47/dqc_reference/reference_markers.hmm OceanDNA-b10097/protein.faa > /dev/null
[2023-03-16 04:05:40,682] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:40,683] [INFO] Found 6/6 markers.
[2023-03-16 04:05:40,702] [INFO] Query marker FASTA was written to OceanDNA-b10097/markers.fasta
[2023-03-16 04:05:40,703] [INFO] Task started: Blastn
[2023-03-16 04:05:40,703] [INFO] Running command: blastn -query OceanDNA-b10097/markers.fasta -db /var/lib/cwl/stgf48bd3c7-4350-4faf-b2a2-9e6d711cfb47/dqc_reference/reference_markers.fasta -out OceanDNA-b10097/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:41,262] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:41,263] [INFO] Selected 29 target genomes.
[2023-03-16 04:05:41,263] [INFO] Target genome list was writen to OceanDNA-b10097/target_genomes.txt
[2023-03-16 04:05:41,277] [INFO] Task started: fastANI
[2023-03-16 04:05:41,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg99a2c401-21c9-494f-847f-42f6438046c6/OceanDNA-b10097.fa --refList OceanDNA-b10097/target_genomes.txt --output OceanDNA-b10097/fastani_result.tsv --threads 1
[2023-03-16 04:05:57,921] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:57,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf48bd3c7-4350-4faf-b2a2-9e6d711cfb47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:57,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf48bd3c7-4350-4faf-b2a2-9e6d711cfb47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:57,925] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:57,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:05:57,925] [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
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	77.9572	213	743	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.8945	81	743	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	76.7208	62	743	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:05:57,926] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10097/tc_result.tsv
[2023-03-16 04:05:57,926] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:57,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:57,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf48bd3c7-4350-4faf-b2a2-9e6d711cfb47/dqc_reference/checkm_data
[2023-03-16 04:05:57,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:57,934] [INFO] Task started: CheckM
[2023-03-16 04:05:57,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10097/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10097/checkm_input OceanDNA-b10097/checkm_result
[2023-03-16 04:06:45,838] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:45,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.39%
Contamintation: 10.42%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 04:06:45,841] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:45,841] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:45,841] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10097/markers.fasta)
[2023-03-16 04:06:45,841] [INFO] Task started: Blastn
[2023-03-16 04:06:45,841] [INFO] Running command: blastn -query OceanDNA-b10097/markers.fasta -db /var/lib/cwl/stgf48bd3c7-4350-4faf-b2a2-9e6d711cfb47/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10097/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:46,700] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:46,700] [INFO] Selected 24 target genomes.
[2023-03-16 04:06:46,701] [INFO] Target genome list was writen to OceanDNA-b10097/target_genomes_gtdb.txt
[2023-03-16 04:06:46,746] [INFO] Task started: fastANI
[2023-03-16 04:06:46,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg99a2c401-21c9-494f-847f-42f6438046c6/OceanDNA-b10097.fa --refList OceanDNA-b10097/target_genomes_gtdb.txt --output OceanDNA-b10097/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:59,254] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:59,260] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:06:59,260] [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_013043685.1	s__Pukyongia sp013043685	78.0347	227	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	99.85	99.75	0.96	0.95	6	-
GCF_002966125.1	s__Pukyongia salina	77.9572	213	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501705.1	s__Pukyongia sp008501705	77.8903	188	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479745.1	s__Pukyongia sp905479745	77.687	185	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827225.1	s__SMXJ01 sp009827225	77.1406	87	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002065.1	s__SMXJ01 sp013002065	76.7895	63	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002379985.1	s__Marixanthomonas sp002379985	76.5811	54	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	99.95	99.94	0.93	0.86	4	-
GCA_013043825.1	s__SMXJ01 sp013043825	76.2226	66	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:59,260] [INFO] GTDB search result was written to OceanDNA-b10097/result_gtdb.tsv
[2023-03-16 04:06:59,260] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:59,261] [INFO] DFAST_QC result json was written to OceanDNA-b10097/dqc_result.json
[2023-03-16 04:06:59,261] [INFO] DFAST_QC completed!
[2023-03-16 04:06:59,261] [INFO] Total running time: 0h1m39s