[2023-03-19 04:29:38,146] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:38,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:38,147] [INFO] DQC Reference Directory: /var/lib/cwl/stgc66c01ec-7096-4f79-b2a4-adf15971bc94/dqc_reference
[2023-03-19 04:29:39,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:39,833] [INFO] Task started: Prodigal
[2023-03-19 04:29:39,833] [INFO] Running command: cat /var/lib/cwl/stg05653902-533a-43f0-9b19-0ca4a1b62d29/OceanDNA-b32999.fa | prodigal -d OceanDNA-b32999/cds.fna -a OceanDNA-b32999/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:30:06,211] [INFO] Task succeeded: Prodigal
[2023-03-19 04:30:06,211] [INFO] Task started: HMMsearch
[2023-03-19 04:30:06,211] [INFO] Running command: hmmsearch --tblout OceanDNA-b32999/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc66c01ec-7096-4f79-b2a4-adf15971bc94/dqc_reference/reference_markers.hmm OceanDNA-b32999/protein.faa > /dev/null
[2023-03-19 04:30:06,433] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:30:06,433] [INFO] Found 6/6 markers.
[2023-03-19 04:30:06,459] [INFO] Query marker FASTA was written to OceanDNA-b32999/markers.fasta
[2023-03-19 04:30:06,459] [INFO] Task started: Blastn
[2023-03-19 04:30:06,459] [INFO] Running command: blastn -query OceanDNA-b32999/markers.fasta -db /var/lib/cwl/stgc66c01ec-7096-4f79-b2a4-adf15971bc94/dqc_reference/reference_markers.fasta -out OceanDNA-b32999/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:07,112] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:07,113] [INFO] Selected 26 target genomes.
[2023-03-19 04:30:07,113] [INFO] Target genome list was writen to OceanDNA-b32999/target_genomes.txt
[2023-03-19 04:30:07,121] [INFO] Task started: fastANI
[2023-03-19 04:30:07,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg05653902-533a-43f0-9b19-0ca4a1b62d29/OceanDNA-b32999.fa --refList OceanDNA-b32999/target_genomes.txt --output OceanDNA-b32999/fastani_result.tsv --threads 1
[2023-03-19 04:30:23,773] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:23,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc66c01ec-7096-4f79-b2a4-adf15971bc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:23,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc66c01ec-7096-4f79-b2a4-adf15971bc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:23,779] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:23,780] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:30:23,780] [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
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	77.2154	301	1372	95	below_threshold
Hwanghaeella grinnelliae	strain=Gri0909	GCA_004005845.1	2500179	2500179	type	True	76.4383	98	1372	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.3862	106	1372	95	below_threshold
Aestuariispira insulae	strain=CECT 8488	GCA_003385955.1	1461337	1461337	type	True	76.2797	84	1372	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.0746	51	1372	95	below_threshold
Aestuariispira ectoiniformans	strain=SWCN16	GCA_025136295.1	2775080	2775080	type	True	75.9227	88	1372	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.5386	61	1372	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:30:23,780] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32999/tc_result.tsv
[2023-03-19 04:30:23,780] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:23,780] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:23,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc66c01ec-7096-4f79-b2a4-adf15971bc94/dqc_reference/checkm_data
[2023-03-19 04:30:23,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:23,881] [INFO] Task started: CheckM
[2023-03-19 04:30:23,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32999/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32999/checkm_input OceanDNA-b32999/checkm_result
[2023-03-19 04:31:29,341] [INFO] Task succeeded: CheckM
[2023-03-19 04:31:29,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:31:29,344] [INFO] ===== Completeness check finished =====
[2023-03-19 04:31:29,344] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:31:29,344] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32999/markers.fasta)
[2023-03-19 04:31:29,344] [INFO] Task started: Blastn
[2023-03-19 04:31:29,344] [INFO] Running command: blastn -query OceanDNA-b32999/markers.fasta -db /var/lib/cwl/stgc66c01ec-7096-4f79-b2a4-adf15971bc94/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32999/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:31:30,485] [INFO] Task succeeded: Blastn
[2023-03-19 04:31:30,486] [INFO] Selected 12 target genomes.
[2023-03-19 04:31:30,486] [INFO] Target genome list was writen to OceanDNA-b32999/target_genomes_gtdb.txt
[2023-03-19 04:31:30,554] [INFO] Task started: fastANI
[2023-03-19 04:31:30,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg05653902-533a-43f0-9b19-0ca4a1b62d29/OceanDNA-b32999.fa --refList OceanDNA-b32999/target_genomes_gtdb.txt --output OceanDNA-b32999/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:31:39,453] [INFO] Task succeeded: fastANI
[2023-03-19 04:31:39,458] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:31:39,458] [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_002696645.1	s__GCA-2696645 sp002696645	99.9486	1307	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	99.85	99.85	0.96	0.96	2	conclusive
GCA_002709955.1	s__GCA-2696645 sp002709955	91.0918	1178	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	99.86	99.71	0.96	0.91	10	-
GCA_017792345.1	s__GCA-2696645 sp017792345	77.2803	365	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	95.39	95.37	0.96	0.95	3	-
GCA_012926505.1	s__GCA-2696645 sp012926505	77.2246	300	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005845.1	s__Hwanghaeella grinnelliae	76.4383	98	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Hwanghaeella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006844765.1	s__SPJV01 sp006844765	76.3654	63	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__SPJV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012315.1	s__SSEL01 sp008012315	76.2249	55	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SSEL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:31:39,458] [INFO] GTDB search result was written to OceanDNA-b32999/result_gtdb.tsv
[2023-03-19 04:31:39,458] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:31:39,459] [INFO] DFAST_QC result json was written to OceanDNA-b32999/dqc_result.json
[2023-03-19 04:31:39,460] [INFO] DFAST_QC completed!
[2023-03-19 04:31:39,460] [INFO] Total running time: 0h2m1s