[2023-03-18 03:45:10,236] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,236] [INFO] DQC Reference Directory: /var/lib/cwl/stgc85871cf-312e-4e68-9b70-c10943632dc6/dqc_reference
[2023-03-18 03:45:11,967] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:11,968] [INFO] Task started: Prodigal
[2023-03-18 03:45:11,968] [INFO] Running command: cat /var/lib/cwl/stgf35651e5-299d-4192-9683-92b1b8a79d67/OceanDNA-b38547.fa | prodigal -d OceanDNA-b38547/cds.fna -a OceanDNA-b38547/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:30,364] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:30,365] [INFO] Task started: HMMsearch
[2023-03-18 03:45:30,365] [INFO] Running command: hmmsearch --tblout OceanDNA-b38547/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc85871cf-312e-4e68-9b70-c10943632dc6/dqc_reference/reference_markers.hmm OceanDNA-b38547/protein.faa > /dev/null
[2023-03-18 03:45:30,570] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:30,570] [INFO] Found 6/6 markers.
[2023-03-18 03:45:30,589] [INFO] Query marker FASTA was written to OceanDNA-b38547/markers.fasta
[2023-03-18 03:45:30,589] [INFO] Task started: Blastn
[2023-03-18 03:45:30,589] [INFO] Running command: blastn -query OceanDNA-b38547/markers.fasta -db /var/lib/cwl/stgc85871cf-312e-4e68-9b70-c10943632dc6/dqc_reference/reference_markers.fasta -out OceanDNA-b38547/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:31,222] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:31,222] [INFO] Selected 13 target genomes.
[2023-03-18 03:45:31,223] [INFO] Target genome list was writen to OceanDNA-b38547/target_genomes.txt
[2023-03-18 03:45:31,228] [INFO] Task started: fastANI
[2023-03-18 03:45:31,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgf35651e5-299d-4192-9683-92b1b8a79d67/OceanDNA-b38547.fa --refList OceanDNA-b38547/target_genomes.txt --output OceanDNA-b38547/fastani_result.tsv --threads 1
[2023-03-18 03:45:41,622] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:41,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc85871cf-312e-4e68-9b70-c10943632dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:41,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc85871cf-312e-4e68-9b70-c10943632dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:41,630] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:41,630] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:41,631] [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
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	91.8765	963	1119	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	91.7441	939	1119	95	below_threshold
Acinetobacter guillouiae	strain=CCUG 2491	GCA_008802215.1	106649	106649	type	True	82.134	724	1119	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	82.0846	736	1119	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	82.0742	714	1119	95	below_threshold
Acinetobacter bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	81.6715	704	1119	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	81.1095	617	1119	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.2812	550	1119	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.0203	457	1119	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	79.5952	430	1119	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	78.9862	379	1119	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	78.924	393	1119	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.575	366	1119	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:41,631] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38547/tc_result.tsv
[2023-03-18 03:45:41,631] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:41,631] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:41,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc85871cf-312e-4e68-9b70-c10943632dc6/dqc_reference/checkm_data
[2023-03-18 03:45:41,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:41,636] [INFO] Task started: CheckM
[2023-03-18 03:45:41,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38547/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38547/checkm_input OceanDNA-b38547/checkm_result
[2023-03-18 03:46:29,286] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:29,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:29,289] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:29,289] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:29,289] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38547/markers.fasta)
[2023-03-18 03:46:29,289] [INFO] Task started: Blastn
[2023-03-18 03:46:29,289] [INFO] Running command: blastn -query OceanDNA-b38547/markers.fasta -db /var/lib/cwl/stgc85871cf-312e-4e68-9b70-c10943632dc6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38547/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:30,298] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:30,299] [INFO] Selected 11 target genomes.
[2023-03-18 03:46:30,299] [INFO] Target genome list was writen to OceanDNA-b38547/target_genomes_gtdb.txt
[2023-03-18 03:46:30,308] [INFO] Task started: fastANI
[2023-03-18 03:46:30,308] [INFO] Running command: fastANI --query /var/lib/cwl/stgf35651e5-299d-4192-9683-92b1b8a79d67/OceanDNA-b38547.fa --refList OceanDNA-b38547/target_genomes_gtdb.txt --output OceanDNA-b38547/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:40,248] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:40,255] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:46:40,255] [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_002233755.1	s__Acinetobacter piscicola	91.8785	962	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611475.1	s__Acinetobacter rongchengensis	91.7508	938	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214135.1	s__Acinetobacter sp000214135	88.3899	942	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368145.1	s__Acinetobacter guillouiae	82.0716	739	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	81.741	648	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368925.1	s__Acinetobacter bereziniae	81.6612	705	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.33	97.29	0.90	0.83	53	-
GCF_003024515.2	s__Acinetobacter sichuanensis	81.1202	616	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015218165.1	s__Acinetobacter piscicola_A	81.0947	588	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.43	98.21	0.96	0.90	7	-
GCF_003268395.1	s__Acinetobacter sp003268395	81.071	608	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902809855.1	s__Acinetobacter sp902809855	80.8262	591	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135235.1	s__Acinetobacter sp002135235	80.282	550	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:40,255] [INFO] GTDB search result was written to OceanDNA-b38547/result_gtdb.tsv
[2023-03-18 03:46:40,255] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:40,257] [INFO] DFAST_QC result json was written to OceanDNA-b38547/dqc_result.json
[2023-03-18 03:46:40,257] [INFO] DFAST_QC completed!
[2023-03-18 03:46:40,257] [INFO] Total running time: 0h1m30s