[2023-03-18 02:53:05,583] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:53:05,583] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:53:05,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg14e8ef55-5a2b-46cc-b74f-de2cbd4fe1c8/dqc_reference
[2023-03-18 02:53:07,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:53:07,191] [INFO] Task started: Prodigal
[2023-03-18 02:53:07,191] [INFO] Running command: cat /var/lib/cwl/stg45c80e70-57d6-41d5-961e-13fbcd72bb7b/OceanDNA-b4155.fa | prodigal -d OceanDNA-b4155/cds.fna -a OceanDNA-b4155/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:53:18,656] [INFO] Task succeeded: Prodigal
[2023-03-18 02:53:18,656] [INFO] Task started: HMMsearch
[2023-03-18 02:53:18,656] [INFO] Running command: hmmsearch --tblout OceanDNA-b4155/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14e8ef55-5a2b-46cc-b74f-de2cbd4fe1c8/dqc_reference/reference_markers.hmm OceanDNA-b4155/protein.faa > /dev/null
[2023-03-18 02:53:18,827] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:53:18,827] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg45c80e70-57d6-41d5-961e-13fbcd72bb7b/OceanDNA-b4155.fa]
[2023-03-18 02:53:18,843] [INFO] Query marker FASTA was written to OceanDNA-b4155/markers.fasta
[2023-03-18 02:53:18,843] [INFO] Task started: Blastn
[2023-03-18 02:53:18,843] [INFO] Running command: blastn -query OceanDNA-b4155/markers.fasta -db /var/lib/cwl/stg14e8ef55-5a2b-46cc-b74f-de2cbd4fe1c8/dqc_reference/reference_markers.fasta -out OceanDNA-b4155/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:53:19,335] [INFO] Task succeeded: Blastn
[2023-03-18 02:53:19,336] [INFO] Selected 21 target genomes.
[2023-03-18 02:53:19,336] [INFO] Target genome list was writen to OceanDNA-b4155/target_genomes.txt
[2023-03-18 02:53:19,347] [INFO] Task started: fastANI
[2023-03-18 02:53:19,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg45c80e70-57d6-41d5-961e-13fbcd72bb7b/OceanDNA-b4155.fa --refList OceanDNA-b4155/target_genomes.txt --output OceanDNA-b4155/fastani_result.tsv --threads 1
[2023-03-18 02:53:33,319] [INFO] Task succeeded: fastANI
[2023-03-18 02:53:33,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14e8ef55-5a2b-46cc-b74f-de2cbd4fe1c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:53:33,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14e8ef55-5a2b-46cc-b74f-de2cbd4fe1c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:53:33,323] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:53:33,323] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:53:33,323] [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
Fulvivirga lutea	strain=S481	GCA_017068455.1	2810512	2810512	type	True	78.2537	145	512	95	below_threshold
Fulvivirga lutimaris	strain=KCTC 42720	GCA_009711525.1	1819566	1819566	type	True	77.1282	96	512	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:53:33,323] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4155/tc_result.tsv
[2023-03-18 02:53:33,324] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:53:33,324] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:53:33,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14e8ef55-5a2b-46cc-b74f-de2cbd4fe1c8/dqc_reference/checkm_data
[2023-03-18 02:53:33,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:53:33,328] [INFO] Task started: CheckM
[2023-03-18 02:53:33,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4155/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4155/checkm_input OceanDNA-b4155/checkm_result
[2023-03-18 02:54:06,230] [INFO] Task succeeded: CheckM
[2023-03-18 02:54:06,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:54:06,233] [INFO] ===== Completeness check finished =====
[2023-03-18 02:54:06,233] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:54:06,233] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4155/markers.fasta)
[2023-03-18 02:54:06,233] [INFO] Task started: Blastn
[2023-03-18 02:54:06,233] [INFO] Running command: blastn -query OceanDNA-b4155/markers.fasta -db /var/lib/cwl/stg14e8ef55-5a2b-46cc-b74f-de2cbd4fe1c8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4155/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:54:06,896] [INFO] Task succeeded: Blastn
[2023-03-18 02:54:06,897] [INFO] Selected 25 target genomes.
[2023-03-18 02:54:06,897] [INFO] Target genome list was writen to OceanDNA-b4155/target_genomes_gtdb.txt
[2023-03-18 02:54:07,018] [INFO] Task started: fastANI
[2023-03-18 02:54:07,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg45c80e70-57d6-41d5-961e-13fbcd72bb7b/OceanDNA-b4155.fa --refList OceanDNA-b4155/target_genomes_gtdb.txt --output OceanDNA-b4155/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:54:23,390] [INFO] Task succeeded: fastANI
[2023-03-18 02:54:23,393] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:54:23,393] [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_017068455.1	s__Fulvivirga sp017068455	78.2537	145	512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711525.1	s__Fulvivirga lutimaris	77.1282	96	512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338655.1	s__Fulvivirga sp002338655	76.8039	61	512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:54:23,394] [INFO] GTDB search result was written to OceanDNA-b4155/result_gtdb.tsv
[2023-03-18 02:54:23,394] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:54:23,394] [INFO] DFAST_QC result json was written to OceanDNA-b4155/dqc_result.json
[2023-03-18 02:54:23,394] [INFO] DFAST_QC completed!
[2023-03-18 02:54:23,394] [INFO] Total running time: 0h1m18s