[2023-03-19 02:34:18,441] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:34:18,441] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:34:18,441] [INFO] DQC Reference Directory: /var/lib/cwl/stgf81ab9bc-af4e-49fe-9bc2-f39a604e676c/dqc_reference
[2023-03-19 02:34:19,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:34:19,542] [INFO] Task started: Prodigal
[2023-03-19 02:34:19,542] [INFO] Running command: cat /var/lib/cwl/stg6e82a2e6-5167-44ce-b9c4-e37bf9748bdf/OceanDNA-b35253.fa | prodigal -d OceanDNA-b35253/cds.fna -a OceanDNA-b35253/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:34:45,543] [INFO] Task succeeded: Prodigal
[2023-03-19 02:34:45,544] [INFO] Task started: HMMsearch
[2023-03-19 02:34:45,544] [INFO] Running command: hmmsearch --tblout OceanDNA-b35253/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf81ab9bc-af4e-49fe-9bc2-f39a604e676c/dqc_reference/reference_markers.hmm OceanDNA-b35253/protein.faa > /dev/null
[2023-03-19 02:34:45,772] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:34:45,772] [INFO] Found 6/6 markers.
[2023-03-19 02:34:45,797] [INFO] Query marker FASTA was written to OceanDNA-b35253/markers.fasta
[2023-03-19 02:34:45,798] [INFO] Task started: Blastn
[2023-03-19 02:34:45,798] [INFO] Running command: blastn -query OceanDNA-b35253/markers.fasta -db /var/lib/cwl/stgf81ab9bc-af4e-49fe-9bc2-f39a604e676c/dqc_reference/reference_markers.fasta -out OceanDNA-b35253/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:34:46,481] [INFO] Task succeeded: Blastn
[2023-03-19 02:34:46,482] [INFO] Selected 11 target genomes.
[2023-03-19 02:34:46,482] [INFO] Target genome list was writen to OceanDNA-b35253/target_genomes.txt
[2023-03-19 02:34:46,489] [INFO] Task started: fastANI
[2023-03-19 02:34:46,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e82a2e6-5167-44ce-b9c4-e37bf9748bdf/OceanDNA-b35253.fa --refList OceanDNA-b35253/target_genomes.txt --output OceanDNA-b35253/fastani_result.tsv --threads 1
[2023-03-19 02:34:58,023] [INFO] Task succeeded: fastANI
[2023-03-19 02:34:58,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf81ab9bc-af4e-49fe-9bc2-f39a604e676c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:34:58,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf81ab9bc-af4e-49fe-9bc2-f39a604e676c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:34:58,031] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 02:34:58,031] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 02:34:58,031] [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
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	96.4419	1363	1483	95	conclusive
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	94.7886	1253	1483	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	91.1716	1290	1483	95	below_threshold
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	85.48	954	1483	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	85.4779	1033	1483	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	85.2051	1081	1483	95	below_threshold
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	84.6794	1007	1483	95	below_threshold
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	84.6677	993	1483	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	84.4681	1022	1483	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	81.4391	936	1483	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	81.2096	944	1483	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:34:58,032] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35253/tc_result.tsv
[2023-03-19 02:34:58,032] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:34:58,032] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:34:58,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf81ab9bc-af4e-49fe-9bc2-f39a604e676c/dqc_reference/checkm_data
[2023-03-19 02:34:58,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:34:58,039] [INFO] Task started: CheckM
[2023-03-19 02:34:58,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35253/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35253/checkm_input OceanDNA-b35253/checkm_result
[2023-03-19 02:36:00,645] [INFO] Task succeeded: CheckM
[2023-03-19 02:36:00,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:36:00,652] [INFO] ===== Completeness check finished =====
[2023-03-19 02:36:00,652] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:36:00,652] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35253/markers.fasta)
[2023-03-19 02:36:00,653] [INFO] Task started: Blastn
[2023-03-19 02:36:00,653] [INFO] Running command: blastn -query OceanDNA-b35253/markers.fasta -db /var/lib/cwl/stgf81ab9bc-af4e-49fe-9bc2-f39a604e676c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35253/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:36:01,702] [INFO] Task succeeded: Blastn
[2023-03-19 02:36:01,704] [INFO] Selected 8 target genomes.
[2023-03-19 02:36:01,704] [INFO] Target genome list was writen to OceanDNA-b35253/target_genomes_gtdb.txt
[2023-03-19 02:36:01,711] [INFO] Task started: fastANI
[2023-03-19 02:36:01,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e82a2e6-5167-44ce-b9c4-e37bf9748bdf/OceanDNA-b35253.fa --refList OceanDNA-b35253/target_genomes_gtdb.txt --output OceanDNA-b35253/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:36:11,123] [INFO] Task succeeded: fastANI
[2023-03-19 02:36:11,129] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:36:11,129] [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_900456975.1	s__Shewanella baltica	96.4419	1363	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	conclusive
GCF_002838165.1	s__Shewanella sp002838165	94.6632	1304	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_002966515.1	s__Shewanella sp002966515	91.2291	1273	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCA_002783505.1	s__Shewanella sp002783505	85.6285	1080	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156405.1	s__Shewanella morhuae	85.1852	1083	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_000217915.1	s__Shewanella sp000217915	84.7637	1035	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406325.1	s__Shewanella putrefaciens	84.6541	1010	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCF_000014665.1	s__Shewanella sp000014665	81.4877	967	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:36:11,132] [INFO] GTDB search result was written to OceanDNA-b35253/result_gtdb.tsv
[2023-03-19 02:36:11,137] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:36:11,143] [INFO] DFAST_QC result json was written to OceanDNA-b35253/dqc_result.json
[2023-03-19 02:36:11,143] [INFO] DFAST_QC completed!
[2023-03-19 02:36:11,143] [INFO] Total running time: 0h1m53s