[2023-03-18 03:09:35,473] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:35,474] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:35,474] [INFO] DQC Reference Directory: /var/lib/cwl/stga3b4a2ec-374b-4ac9-b669-07c138f18d9a/dqc_reference
[2023-03-18 03:09:36,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:36,619] [INFO] Task started: Prodigal
[2023-03-18 03:09:36,619] [INFO] Running command: cat /var/lib/cwl/stgf395fbd9-5781-4004-945b-620c22428292/OceanDNA-b41459.fa | prodigal -d OceanDNA-b41459/cds.fna -a OceanDNA-b41459/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:58,204] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:58,204] [INFO] Task started: HMMsearch
[2023-03-18 03:09:58,204] [INFO] Running command: hmmsearch --tblout OceanDNA-b41459/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3b4a2ec-374b-4ac9-b669-07c138f18d9a/dqc_reference/reference_markers.hmm OceanDNA-b41459/protein.faa > /dev/null
[2023-03-18 03:09:58,441] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:58,441] [INFO] Found 6/6 markers.
[2023-03-18 03:09:58,464] [INFO] Query marker FASTA was written to OceanDNA-b41459/markers.fasta
[2023-03-18 03:09:58,464] [INFO] Task started: Blastn
[2023-03-18 03:09:58,464] [INFO] Running command: blastn -query OceanDNA-b41459/markers.fasta -db /var/lib/cwl/stga3b4a2ec-374b-4ac9-b669-07c138f18d9a/dqc_reference/reference_markers.fasta -out OceanDNA-b41459/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:59,080] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:59,081] [INFO] Selected 25 target genomes.
[2023-03-18 03:09:59,082] [INFO] Target genome list was writen to OceanDNA-b41459/target_genomes.txt
[2023-03-18 03:09:59,095] [INFO] Task started: fastANI
[2023-03-18 03:09:59,095] [INFO] Running command: fastANI --query /var/lib/cwl/stgf395fbd9-5781-4004-945b-620c22428292/OceanDNA-b41459.fa --refList OceanDNA-b41459/target_genomes.txt --output OceanDNA-b41459/fastani_result.tsv --threads 1
[2023-03-18 03:10:16,228] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:16,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3b4a2ec-374b-4ac9-b669-07c138f18d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:16,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3b4a2ec-374b-4ac9-b669-07c138f18d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:16,233] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 03:10:16,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 03:10:16,233] [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
Dasania marina	strain=DSM 21967	GCA_000373485.1	471499	471499	type	True	96.2699	1105	1283	95	conclusive
Oceanicoccus sagamiensis	strain=NBRC 107125	GCA_002117105.1	716816	716816	type	True	76.4919	93	1283	95	below_threshold
Zhongshania aliphaticivorans	strain=SM-2	GCA_001586255.1	1470434	1470434	type	True	76.2246	69	1283	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:16,233] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41459/tc_result.tsv
[2023-03-18 03:10:16,233] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:16,233] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:16,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3b4a2ec-374b-4ac9-b669-07c138f18d9a/dqc_reference/checkm_data
[2023-03-18 03:10:16,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:16,239] [INFO] Task started: CheckM
[2023-03-18 03:10:16,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41459/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41459/checkm_input OceanDNA-b41459/checkm_result
[2023-03-18 03:11:09,749] [INFO] Task succeeded: CheckM
[2023-03-18 03:11:09,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:11:09,752] [INFO] ===== Completeness check finished =====
[2023-03-18 03:11:09,752] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:11:09,752] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41459/markers.fasta)
[2023-03-18 03:11:09,752] [INFO] Task started: Blastn
[2023-03-18 03:11:09,752] [INFO] Running command: blastn -query OceanDNA-b41459/markers.fasta -db /var/lib/cwl/stga3b4a2ec-374b-4ac9-b669-07c138f18d9a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41459/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:11:10,731] [INFO] Task succeeded: Blastn
[2023-03-18 03:11:10,732] [INFO] Selected 22 target genomes.
[2023-03-18 03:11:10,732] [INFO] Target genome list was writen to OceanDNA-b41459/target_genomes_gtdb.txt
[2023-03-18 03:11:10,795] [INFO] Task started: fastANI
[2023-03-18 03:11:10,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgf395fbd9-5781-4004-945b-620c22428292/OceanDNA-b41459.fa --refList OceanDNA-b41459/target_genomes_gtdb.txt --output OceanDNA-b41459/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:11:23,902] [INFO] Task succeeded: fastANI
[2023-03-18 03:11:23,905] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:11:23,905] [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_000373485.1	s__Dasania marina	96.283	1104	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-21967;g__Dasania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900120175.1	s__Oceanicoccus sp900120175	77.1926	81	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-21967;g__Oceanicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117105.1	s__Oceanicoccus sagamiensis	76.4919	93	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-21967;g__Oceanicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:11:23,905] [INFO] GTDB search result was written to OceanDNA-b41459/result_gtdb.tsv
[2023-03-18 03:11:23,906] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:11:23,906] [INFO] DFAST_QC result json was written to OceanDNA-b41459/dqc_result.json
[2023-03-18 03:11:23,906] [INFO] DFAST_QC completed!
[2023-03-18 03:11:23,906] [INFO] Total running time: 0h1m48s