[2023-03-19 02:14:01,440] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:14:01,442] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:14:01,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg05cfb2ec-2f4c-4498-b3d7-a297db999035/dqc_reference
[2023-03-19 02:14:02,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:14:02,550] [INFO] Task started: Prodigal
[2023-03-19 02:14:02,551] [INFO] Running command: cat /var/lib/cwl/stgb4772811-1458-413b-943c-c7e5f088f279/OceanDNA-b31456.fa | prodigal -d OceanDNA-b31456/cds.fna -a OceanDNA-b31456/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:14:25,056] [INFO] Task succeeded: Prodigal
[2023-03-19 02:14:25,057] [INFO] Task started: HMMsearch
[2023-03-19 02:14:25,057] [INFO] Running command: hmmsearch --tblout OceanDNA-b31456/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05cfb2ec-2f4c-4498-b3d7-a297db999035/dqc_reference/reference_markers.hmm OceanDNA-b31456/protein.faa > /dev/null
[2023-03-19 02:14:25,259] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:14:25,259] [INFO] Found 6/6 markers.
[2023-03-19 02:14:25,301] [INFO] Query marker FASTA was written to OceanDNA-b31456/markers.fasta
[2023-03-19 02:14:25,302] [INFO] Task started: Blastn
[2023-03-19 02:14:25,302] [INFO] Running command: blastn -query OceanDNA-b31456/markers.fasta -db /var/lib/cwl/stg05cfb2ec-2f4c-4498-b3d7-a297db999035/dqc_reference/reference_markers.fasta -out OceanDNA-b31456/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:14:26,029] [INFO] Task succeeded: Blastn
[2023-03-19 02:14:26,057] [INFO] Selected 17 target genomes.
[2023-03-19 02:14:26,057] [INFO] Target genome list was writen to OceanDNA-b31456/target_genomes.txt
[2023-03-19 02:14:26,100] [INFO] Task started: fastANI
[2023-03-19 02:14:26,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4772811-1458-413b-943c-c7e5f088f279/OceanDNA-b31456.fa --refList OceanDNA-b31456/target_genomes.txt --output OceanDNA-b31456/fastani_result.tsv --threads 1
[2023-03-19 02:14:38,559] [INFO] Task succeeded: fastANI
[2023-03-19 02:14:38,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05cfb2ec-2f4c-4498-b3d7-a297db999035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:14:38,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05cfb2ec-2f4c-4498-b3d7-a297db999035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:14:38,567] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:14:38,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:14:38,567] [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
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	80.2606	609	1228	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	80.1751	608	1228	95	below_threshold
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	79.4238	581	1228	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	79.1792	518	1228	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	76.7859	198	1228	95	below_threshold
Sneathiella limimaris	strain=KCTC 52846	GCA_012932565.1	1964213	1964213	type	True	76.3813	74	1228	95	below_threshold
Sneathiella glossodoripedis	strain=JCM 23214	GCA_000616095.1	418853	418853	type	True	75.8547	58	1228	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:14:38,573] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31456/tc_result.tsv
[2023-03-19 02:14:38,573] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:14:38,573] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:14:38,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05cfb2ec-2f4c-4498-b3d7-a297db999035/dqc_reference/checkm_data
[2023-03-19 02:14:38,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:14:38,718] [INFO] Task started: CheckM
[2023-03-19 02:14:38,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31456/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31456/checkm_input OceanDNA-b31456/checkm_result
[2023-03-19 02:15:34,867] [INFO] Task succeeded: CheckM
[2023-03-19 02:15:34,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:15:34,903] [INFO] ===== Completeness check finished =====
[2023-03-19 02:15:34,903] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:15:34,904] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31456/markers.fasta)
[2023-03-19 02:15:34,905] [INFO] Task started: Blastn
[2023-03-19 02:15:34,905] [INFO] Running command: blastn -query OceanDNA-b31456/markers.fasta -db /var/lib/cwl/stg05cfb2ec-2f4c-4498-b3d7-a297db999035/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31456/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:15:36,250] [INFO] Task succeeded: Blastn
[2023-03-19 02:15:36,252] [INFO] Selected 10 target genomes.
[2023-03-19 02:15:36,252] [INFO] Target genome list was writen to OceanDNA-b31456/target_genomes_gtdb.txt
[2023-03-19 02:15:36,263] [INFO] Task started: fastANI
[2023-03-19 02:15:36,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4772811-1458-413b-943c-c7e5f088f279/OceanDNA-b31456.fa --refList OceanDNA-b31456/target_genomes_gtdb.txt --output OceanDNA-b31456/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:15:43,579] [INFO] Task succeeded: fastANI
[2023-03-19 02:15:43,585] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:15:43,585] [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_002706985.1	s__Sneathiella sp002706985	85.9961	870	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	-
GCF_009882935.1	s__Sneathiella chungangensis	80.2606	609	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017313765.1	s__Sneathiella sp017313765	79.4238	581	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694385.1	s__Sneathiella sp002694385	79.2009	449	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	95.34	95.31	0.92	0.91	3	-
GCF_009882915.1	s__Sneathiella litorea	79.1792	518	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226265.1	s__Sneathiella sp006226265	78.5284	246	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002732675.1	s__Sneathiella sp002732675	77.0603	148	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000616095.1	s__Sneathiella glossodoripedis	75.8718	59	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:15:43,585] [INFO] GTDB search result was written to OceanDNA-b31456/result_gtdb.tsv
[2023-03-19 02:15:43,586] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:15:43,587] [INFO] DFAST_QC result json was written to OceanDNA-b31456/dqc_result.json
[2023-03-19 02:15:43,587] [INFO] DFAST_QC completed!
[2023-03-19 02:15:43,587] [INFO] Total running time: 0h1m42s