[2023-06-08 08:29:35,370] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:29:35,372] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:29:35,372] [INFO] DQC Reference Directory: /var/lib/cwl/stga05e0ee8-430d-4ee9-8ddf-e76c71d80721/dqc_reference
[2023-06-08 08:29:37,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:29:37,607] [INFO] Task started: Prodigal
[2023-06-08 08:29:37,607] [INFO] Running command: gunzip -c /var/lib/cwl/stga557829c-798f-4ca2-b940-cb40487d62b1/GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna.gz | prodigal -d GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/cds.fna -a GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:29:46,155] [INFO] Task succeeded: Prodigal
[2023-06-08 08:29:46,156] [INFO] Task started: HMMsearch
[2023-06-08 08:29:46,156] [INFO] Running command: hmmsearch --tblout GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga05e0ee8-430d-4ee9-8ddf-e76c71d80721/dqc_reference/reference_markers.hmm GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:29:46,428] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:29:46,429] [INFO] Found 6/6 markers.
[2023-06-08 08:29:46,461] [INFO] Query marker FASTA was written to GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/markers.fasta
[2023-06-08 08:29:46,461] [INFO] Task started: Blastn
[2023-06-08 08:29:46,461] [INFO] Running command: blastn -query GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stga05e0ee8-430d-4ee9-8ddf-e76c71d80721/dqc_reference/reference_markers.fasta -out GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:29:47,085] [INFO] Task succeeded: Blastn
[2023-06-08 08:29:47,089] [INFO] Selected 22 target genomes.
[2023-06-08 08:29:47,090] [INFO] Target genome list was writen to GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-08 08:29:47,098] [INFO] Task started: fastANI
[2023-06-08 08:29:47,098] [INFO] Running command: fastANI --query /var/lib/cwl/stga557829c-798f-4ca2-b940-cb40487d62b1/GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna.gz --refList GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:30:02,417] [INFO] Task succeeded: fastANI
[2023-06-08 08:30:02,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga05e0ee8-430d-4ee9-8ddf-e76c71d80721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:30:02,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga05e0ee8-430d-4ee9-8ddf-e76c71d80721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:30:02,426] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:30:02,426] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:30:02,427] [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
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	74.8786	50	949	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	74.7958	54	949	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:30:02,429] [INFO] DFAST Taxonomy check result was written to GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-08 08:30:02,429] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:30:02,430] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:30:02,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga05e0ee8-430d-4ee9-8ddf-e76c71d80721/dqc_reference/checkm_data
[2023-06-08 08:30:02,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:30:02,464] [INFO] Task started: CheckM
[2023-06-08 08:30:02,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/checkm_input GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/checkm_result
[2023-06-08 08:30:32,526] [INFO] Task succeeded: CheckM
[2023-06-08 08:30:32,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:30:32,550] [INFO] ===== Completeness check finished =====
[2023-06-08 08:30:32,550] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:30:32,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/markers.fasta)
[2023-06-08 08:30:32,551] [INFO] Task started: Blastn
[2023-06-08 08:30:32,551] [INFO] Running command: blastn -query GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stga05e0ee8-430d-4ee9-8ddf-e76c71d80721/dqc_reference/reference_markers_gtdb.fasta -out GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:30:33,448] [INFO] Task succeeded: Blastn
[2023-06-08 08:30:33,453] [INFO] Selected 18 target genomes.
[2023-06-08 08:30:33,453] [INFO] Target genome list was writen to GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:30:33,570] [INFO] Task started: fastANI
[2023-06-08 08:30:33,570] [INFO] Running command: fastANI --query /var/lib/cwl/stga557829c-798f-4ca2-b940-cb40487d62b1/GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna.gz --refList GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:30:45,351] [INFO] Task succeeded: fastANI
[2023-06-08 08:30:45,366] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 08:30:45,366] [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_016719645.1	s__PNOJ01 sp016719645	78.6218	354	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__PNOJ01	95.0	96.99	95.77	0.87	0.87	3	-
GCA_018814885.1	s__JAHIYU01 sp018814885	78.5453	318	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__JAHIYU01	95.0	99.82	99.76	0.96	0.95	3	-
GCA_013824755.1	s__PNOJ01 sp013824755	78.4257	280	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__PNOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859985.1	s__LZORAL124-64-63 sp014859985	77.9615	223	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__LZORAL124-64-63	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829565.1	s__LZORAL124-64-63 sp018829565	77.4051	201	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__LZORAL124-64-63	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903859215.1	s__CAINDZ01 sp903859215	77.1412	168	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	99.58	99.58	0.89	0.89	2	-
GCA_903847545.1	s__CAINDZ01 sp903847545	77.1005	132	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	98.70	98.54	0.79	0.77	4	-
GCA_016712675.1	s__CAINDZ01 sp016712675	76.9498	173	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014730255.1	s__Glo-17 sp014730255	76.938	157	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__Glo-17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873405.1	s__CAINDZ01 sp016873405	76.8631	99	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003353795.1	s__Glo-17 sp003353795	76.6892	180	949	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__Glo-17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 08:30:45,368] [INFO] GTDB search result was written to GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-08 08:30:45,369] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:30:45,371] [INFO] DFAST_QC result json was written to GCA_902751385.1_P1994_106_bin124_mag_fasta_genomic.fna/dqc_result.json
[2023-06-08 08:30:45,372] [INFO] DFAST_QC completed!
[2023-06-08 08:30:45,372] [INFO] Total running time: 0h1m10s