[2023-03-15 03:56:21,752] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,752] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e1408de-0299-4c16-85ca-c1d776c3f1fe/dqc_reference
[2023-03-15 03:56:23,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,406] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,406] [INFO] Running command: cat /var/lib/cwl/stg90ed57af-0d94-4f91-8d36-a3335a288668/OceanDNA-b24966.fa | prodigal -d OceanDNA-b24966/cds.fna -a OceanDNA-b24966/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:32,040] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:32,040] [INFO] Task started: HMMsearch
[2023-03-15 03:56:32,040] [INFO] Running command: hmmsearch --tblout OceanDNA-b24966/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e1408de-0299-4c16-85ca-c1d776c3f1fe/dqc_reference/reference_markers.hmm OceanDNA-b24966/protein.faa > /dev/null
[2023-03-15 03:56:32,219] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:32,220] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg90ed57af-0d94-4f91-8d36-a3335a288668/OceanDNA-b24966.fa]
[2023-03-15 03:56:32,237] [INFO] Query marker FASTA was written to OceanDNA-b24966/markers.fasta
[2023-03-15 03:56:32,237] [INFO] Task started: Blastn
[2023-03-15 03:56:32,237] [INFO] Running command: blastn -query OceanDNA-b24966/markers.fasta -db /var/lib/cwl/stg2e1408de-0299-4c16-85ca-c1d776c3f1fe/dqc_reference/reference_markers.fasta -out OceanDNA-b24966/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:32,766] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:32,767] [INFO] Selected 14 target genomes.
[2023-03-15 03:56:32,767] [INFO] Target genome list was writen to OceanDNA-b24966/target_genomes.txt
[2023-03-15 03:56:32,775] [INFO] Task started: fastANI
[2023-03-15 03:56:32,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ed57af-0d94-4f91-8d36-a3335a288668/OceanDNA-b24966.fa --refList OceanDNA-b24966/target_genomes.txt --output OceanDNA-b24966/fastani_result.tsv --threads 1
[2023-03-15 03:56:42,208] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:42,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e1408de-0299-4c16-85ca-c1d776c3f1fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:56:42,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e1408de-0299-4c16-85ca-c1d776c3f1fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:56:42,212] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:56:42,213] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:56:42,213] [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
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	77.9426	99	258	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	77.9378	99	258	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	77.9316	100	258	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:56:42,213] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24966/tc_result.tsv
[2023-03-15 03:56:42,213] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:56:42,213] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:42,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e1408de-0299-4c16-85ca-c1d776c3f1fe/dqc_reference/checkm_data
[2023-03-15 03:56:42,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:42,218] [INFO] Task started: CheckM
[2023-03-15 03:56:42,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24966/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24966/checkm_input OceanDNA-b24966/checkm_result
[2023-03-15 03:57:10,085] [INFO] Task succeeded: CheckM
[2023-03-15 03:57:10,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.52%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:57:10,089] [INFO] ===== Completeness check finished =====
[2023-03-15 03:57:10,089] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:57:10,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24966/markers.fasta)
[2023-03-15 03:57:10,100] [INFO] Task started: Blastn
[2023-03-15 03:57:10,100] [INFO] Running command: blastn -query OceanDNA-b24966/markers.fasta -db /var/lib/cwl/stg2e1408de-0299-4c16-85ca-c1d776c3f1fe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24966/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:57:10,838] [INFO] Task succeeded: Blastn
[2023-03-15 03:57:10,839] [INFO] Selected 15 target genomes.
[2023-03-15 03:57:10,839] [INFO] Target genome list was writen to OceanDNA-b24966/target_genomes_gtdb.txt
[2023-03-15 03:57:10,852] [INFO] Task started: fastANI
[2023-03-15 03:57:10,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ed57af-0d94-4f91-8d36-a3335a288668/OceanDNA-b24966.fa --refList OceanDNA-b24966/target_genomes_gtdb.txt --output OceanDNA-b24966/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:57:21,031] [INFO] Task succeeded: fastANI
[2023-03-15 03:57:21,034] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:57:21,034] [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_000689395.1	s__Pyruvatibacter ectocarpi	88.7513	214	258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848855.1	s__Pyruvatibacter mobilis	77.9316	100	258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-15 03:57:21,035] [INFO] GTDB search result was written to OceanDNA-b24966/result_gtdb.tsv
[2023-03-15 03:57:21,035] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:57:21,035] [INFO] DFAST_QC result json was written to OceanDNA-b24966/dqc_result.json
[2023-03-15 03:57:21,036] [INFO] DFAST_QC completed!
[2023-03-15 03:57:21,036] [INFO] Total running time: 0h0m59s