[2023-03-17 11:36:53,898] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:36:53,899] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:36:53,899] [INFO] DQC Reference Directory: /var/lib/cwl/stga5d1baf9-0fe0-4249-849d-c961ce862efa/dqc_reference
[2023-03-17 11:36:55,024] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:36:55,025] [INFO] Task started: Prodigal
[2023-03-17 11:36:55,025] [INFO] Running command: cat /var/lib/cwl/stgfc481dd5-35cd-4a18-a800-5b28636489d4/OceanDNA-b30785.fa | prodigal -d OceanDNA-b30785/cds.fna -a OceanDNA-b30785/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:37:03,469] [INFO] Task succeeded: Prodigal
[2023-03-17 11:37:03,470] [INFO] Task started: HMMsearch
[2023-03-17 11:37:03,470] [INFO] Running command: hmmsearch --tblout OceanDNA-b30785/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5d1baf9-0fe0-4249-849d-c961ce862efa/dqc_reference/reference_markers.hmm OceanDNA-b30785/protein.faa > /dev/null
[2023-03-17 11:37:03,627] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:37:03,628] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfc481dd5-35cd-4a18-a800-5b28636489d4/OceanDNA-b30785.fa]
[2023-03-17 11:37:03,648] [INFO] Query marker FASTA was written to OceanDNA-b30785/markers.fasta
[2023-03-17 11:37:03,649] [INFO] Task started: Blastn
[2023-03-17 11:37:03,649] [INFO] Running command: blastn -query OceanDNA-b30785/markers.fasta -db /var/lib/cwl/stga5d1baf9-0fe0-4249-849d-c961ce862efa/dqc_reference/reference_markers.fasta -out OceanDNA-b30785/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:04,106] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:04,107] [INFO] Selected 24 target genomes.
[2023-03-17 11:37:04,108] [INFO] Target genome list was writen to OceanDNA-b30785/target_genomes.txt
[2023-03-17 11:37:04,123] [INFO] Task started: fastANI
[2023-03-17 11:37:04,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc481dd5-35cd-4a18-a800-5b28636489d4/OceanDNA-b30785.fa --refList OceanDNA-b30785/target_genomes.txt --output OceanDNA-b30785/fastani_result.tsv --threads 1
[2023-03-17 11:37:20,495] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:20,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5d1baf9-0fe0-4249-849d-c961ce862efa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:37:20,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5d1baf9-0fe0-4249-849d-c961ce862efa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:37:20,496] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:37:20,496] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:37:20,496] [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
--------------------------------------------------------------------------------
[2023-03-17 11:37:20,498] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30785/tc_result.tsv
[2023-03-17 11:37:20,499] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:37:20,499] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:37:20,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5d1baf9-0fe0-4249-849d-c961ce862efa/dqc_reference/checkm_data
[2023-03-17 11:37:20,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:37:20,564] [INFO] Task started: CheckM
[2023-03-17 11:37:20,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30785/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30785/checkm_input OceanDNA-b30785/checkm_result
[2023-03-17 11:37:46,611] [INFO] Task succeeded: CheckM
[2023-03-17 11:37:46,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.37%
Contamintation: 12.50%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-17 11:37:46,633] [INFO] ===== Completeness check finished =====
[2023-03-17 11:37:46,633] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:37:46,633] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30785/markers.fasta)
[2023-03-17 11:37:46,634] [INFO] Task started: Blastn
[2023-03-17 11:37:46,634] [INFO] Running command: blastn -query OceanDNA-b30785/markers.fasta -db /var/lib/cwl/stga5d1baf9-0fe0-4249-849d-c961ce862efa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30785/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:47,115] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:47,118] [INFO] Selected 14 target genomes.
[2023-03-17 11:37:47,118] [INFO] Target genome list was writen to OceanDNA-b30785/target_genomes_gtdb.txt
[2023-03-17 11:37:47,132] [INFO] Task started: fastANI
[2023-03-17 11:37:47,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc481dd5-35cd-4a18-a800-5b28636489d4/OceanDNA-b30785.fa --refList OceanDNA-b30785/target_genomes_gtdb.txt --output OceanDNA-b30785/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:37:55,387] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:55,393] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:37:55,393] [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_016763915.1	s__Casp-alpha2 sp016763915	82.5445	175	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	80.5248	260	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	80.3284	257	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	78.3676	174	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	78.2578	129	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_002938315.1	s__Casp-alpha2 sp002938315	77.6785	152	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.33	99.24	0.87	0.79	4	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	77.6502	117	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187325.1	s__JACPJY01 sp016187325	76.7036	71	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706405.1	s__UBA1479 sp002706405	76.4221	61	408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:37:55,394] [INFO] GTDB search result was written to OceanDNA-b30785/result_gtdb.tsv
[2023-03-17 11:37:55,395] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:37:55,397] [INFO] DFAST_QC result json was written to OceanDNA-b30785/dqc_result.json
[2023-03-17 11:37:55,397] [INFO] DFAST_QC completed!
[2023-03-17 11:37:55,397] [INFO] Total running time: 0h1m1s