[2023-03-17 03:29:19,761] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:29:19,761] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:29:19,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c05fbe5-e769-47f7-9f0f-8508452a5072/dqc_reference
[2023-03-17 03:29:21,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:29:21,321] [INFO] Task started: Prodigal
[2023-03-17 03:29:21,322] [INFO] Running command: cat /var/lib/cwl/stga4f86b25-0453-4d92-a409-51f0550fb9f8/OceanDNA-b31431.fa | prodigal -d OceanDNA-b31431/cds.fna -a OceanDNA-b31431/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:29:43,554] [INFO] Task succeeded: Prodigal
[2023-03-17 03:29:43,554] [INFO] Task started: HMMsearch
[2023-03-17 03:29:43,554] [INFO] Running command: hmmsearch --tblout OceanDNA-b31431/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c05fbe5-e769-47f7-9f0f-8508452a5072/dqc_reference/reference_markers.hmm OceanDNA-b31431/protein.faa > /dev/null
[2023-03-17 03:29:43,757] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:29:43,758] [INFO] Found 6/6 markers.
[2023-03-17 03:29:43,780] [INFO] Query marker FASTA was written to OceanDNA-b31431/markers.fasta
[2023-03-17 03:29:43,781] [INFO] Task started: Blastn
[2023-03-17 03:29:43,781] [INFO] Running command: blastn -query OceanDNA-b31431/markers.fasta -db /var/lib/cwl/stg7c05fbe5-e769-47f7-9f0f-8508452a5072/dqc_reference/reference_markers.fasta -out OceanDNA-b31431/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:44,486] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:44,487] [INFO] Selected 15 target genomes.
[2023-03-17 03:29:44,487] [INFO] Target genome list was writen to OceanDNA-b31431/target_genomes.txt
[2023-03-17 03:29:44,494] [INFO] Task started: fastANI
[2023-03-17 03:29:44,494] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f86b25-0453-4d92-a409-51f0550fb9f8/OceanDNA-b31431.fa --refList OceanDNA-b31431/target_genomes.txt --output OceanDNA-b31431/fastani_result.tsv --threads 1
[2023-03-17 03:29:54,015] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:54,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c05fbe5-e769-47f7-9f0f-8508452a5072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:29:54,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c05fbe5-e769-47f7-9f0f-8508452a5072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:29:54,021] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:29:54,021] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:29:54,021] [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=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	80.5598	605	1223	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	80.5058	620	1223	95	below_threshold
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	79.7423	539	1223	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	79.427	479	1223	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	77.125	179	1223	95	below_threshold
Sneathiella limimaris	strain=KCTC 52846	GCA_012932565.1	1964213	1964213	type	True	76.5269	71	1223	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	76.2922	96	1223	95	below_threshold
Sneathiella glossodoripedis	strain=JCM 23214	GCA_000616095.1	418853	418853	type	True	76.1309	63	1223	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:29:54,021] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31431/tc_result.tsv
[2023-03-17 03:29:54,021] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:29:54,021] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:29:54,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c05fbe5-e769-47f7-9f0f-8508452a5072/dqc_reference/checkm_data
[2023-03-17 03:29:54,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:29:54,027] [INFO] Task started: CheckM
[2023-03-17 03:29:54,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31431/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31431/checkm_input OceanDNA-b31431/checkm_result
[2023-03-17 03:30:49,369] [INFO] Task succeeded: CheckM
[2023-03-17 03:30:49,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:30:49,372] [INFO] ===== Completeness check finished =====
[2023-03-17 03:30:49,372] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:30:49,372] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31431/markers.fasta)
[2023-03-17 03:30:49,372] [INFO] Task started: Blastn
[2023-03-17 03:30:49,372] [INFO] Running command: blastn -query OceanDNA-b31431/markers.fasta -db /var/lib/cwl/stg7c05fbe5-e769-47f7-9f0f-8508452a5072/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31431/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:30:50,703] [INFO] Task succeeded: Blastn
[2023-03-17 03:30:50,703] [INFO] Selected 8 target genomes.
[2023-03-17 03:30:50,703] [INFO] Target genome list was writen to OceanDNA-b31431/target_genomes_gtdb.txt
[2023-03-17 03:30:50,737] [INFO] Task started: fastANI
[2023-03-17 03:30:50,737] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f86b25-0453-4d92-a409-51f0550fb9f8/OceanDNA-b31431.fa --refList OceanDNA-b31431/target_genomes_gtdb.txt --output OceanDNA-b31431/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:30:56,756] [INFO] Task succeeded: fastANI
[2023-03-17 03:30:56,761] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:30:56,761] [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	91.9051	926	1223	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	80.496	621	1223	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	79.7423	539	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882915.1	s__Sneathiella litorea	79.4262	479	1223	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	79.399	469	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	95.34	95.31	0.92	0.91	3	-
GCF_900172325.1	s__Oceanibacterium hippocampi	76.2736	97	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000616095.1	s__Sneathiella glossodoripedis	76.1309	63	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:30:56,761] [INFO] GTDB search result was written to OceanDNA-b31431/result_gtdb.tsv
[2023-03-17 03:30:56,761] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:30:56,762] [INFO] DFAST_QC result json was written to OceanDNA-b31431/dqc_result.json
[2023-03-17 03:30:56,763] [INFO] DFAST_QC completed!
[2023-03-17 03:30:56,763] [INFO] Total running time: 0h1m37s