[2023-06-19 12:58:50,987] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:58:50,989] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:58:50,989] [INFO] DQC Reference Directory: /var/lib/cwl/stgd19e2946-b27c-44d7-a143-4c3adcf771bb/dqc_reference
[2023-06-19 12:58:52,322] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:58:52,323] [INFO] Task started: Prodigal
[2023-06-19 12:58:52,324] [INFO] Running command: gunzip -c /var/lib/cwl/stgd22bfdf9-7f67-455d-92b2-53457b983e2f/GCA_018384035.1_ASM1838403v1_genomic.fna.gz | prodigal -d GCA_018384035.1_ASM1838403v1_genomic.fna/cds.fna -a GCA_018384035.1_ASM1838403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:59:02,341] [INFO] Task succeeded: Prodigal
[2023-06-19 12:59:02,341] [INFO] Task started: HMMsearch
[2023-06-19 12:59:02,342] [INFO] Running command: hmmsearch --tblout GCA_018384035.1_ASM1838403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd19e2946-b27c-44d7-a143-4c3adcf771bb/dqc_reference/reference_markers.hmm GCA_018384035.1_ASM1838403v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:59:02,594] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:59:02,595] [INFO] Found 6/6 markers.
[2023-06-19 12:59:02,626] [INFO] Query marker FASTA was written to GCA_018384035.1_ASM1838403v1_genomic.fna/markers.fasta
[2023-06-19 12:59:02,627] [INFO] Task started: Blastn
[2023-06-19 12:59:02,627] [INFO] Running command: blastn -query GCA_018384035.1_ASM1838403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd19e2946-b27c-44d7-a143-4c3adcf771bb/dqc_reference/reference_markers.fasta -out GCA_018384035.1_ASM1838403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:59:03,218] [INFO] Task succeeded: Blastn
[2023-06-19 12:59:03,222] [INFO] Selected 28 target genomes.
[2023-06-19 12:59:03,223] [INFO] Target genome list was writen to GCA_018384035.1_ASM1838403v1_genomic.fna/target_genomes.txt
[2023-06-19 12:59:03,229] [INFO] Task started: fastANI
[2023-06-19 12:59:03,229] [INFO] Running command: fastANI --query /var/lib/cwl/stgd22bfdf9-7f67-455d-92b2-53457b983e2f/GCA_018384035.1_ASM1838403v1_genomic.fna.gz --refList GCA_018384035.1_ASM1838403v1_genomic.fna/target_genomes.txt --output GCA_018384035.1_ASM1838403v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:59:20,576] [INFO] Task succeeded: fastANI
[2023-06-19 12:59:20,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd19e2946-b27c-44d7-a143-4c3adcf771bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:59:20,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd19e2946-b27c-44d7-a143-4c3adcf771bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:59:20,579] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:59:20,580] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 12:59:20,580] [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
--------------------------------------------------------------------------------
[2023-06-19 12:59:20,582] [INFO] DFAST Taxonomy check result was written to GCA_018384035.1_ASM1838403v1_genomic.fna/tc_result.tsv
[2023-06-19 12:59:20,583] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:59:20,583] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:59:20,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd19e2946-b27c-44d7-a143-4c3adcf771bb/dqc_reference/checkm_data
[2023-06-19 12:59:20,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:59:20,613] [INFO] Task started: CheckM
[2023-06-19 12:59:20,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018384035.1_ASM1838403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018384035.1_ASM1838403v1_genomic.fna/checkm_input GCA_018384035.1_ASM1838403v1_genomic.fna/checkm_result
[2023-06-19 12:59:55,678] [INFO] Task succeeded: CheckM
[2023-06-19 12:59:55,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 12.50%
Strain heterogeneity: 30.77%
--------------------------------------------------------------------------------
[2023-06-19 12:59:55,705] [INFO] ===== Completeness check finished =====
[2023-06-19 12:59:55,706] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:59:55,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018384035.1_ASM1838403v1_genomic.fna/markers.fasta)
[2023-06-19 12:59:55,706] [INFO] Task started: Blastn
[2023-06-19 12:59:55,707] [INFO] Running command: blastn -query GCA_018384035.1_ASM1838403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd19e2946-b27c-44d7-a143-4c3adcf771bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_018384035.1_ASM1838403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:59:56,476] [INFO] Task succeeded: Blastn
[2023-06-19 12:59:56,480] [INFO] Selected 19 target genomes.
[2023-06-19 12:59:56,480] [INFO] Target genome list was writen to GCA_018384035.1_ASM1838403v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:59:56,492] [INFO] Task started: fastANI
[2023-06-19 12:59:56,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgd22bfdf9-7f67-455d-92b2-53457b983e2f/GCA_018384035.1_ASM1838403v1_genomic.fna.gz --refList GCA_018384035.1_ASM1838403v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018384035.1_ASM1838403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:00:03,149] [INFO] Task succeeded: fastANI
[2023-06-19 13:00:03,159] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:00:03,160] [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_018384035.1	s__Cryptobacteroides sp018384035	100.0	592	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900767375.1	s__Cryptobacteroides sp900767375	77.8716	71	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785785.1	s__Cryptobacteroides sp900321245	77.3034	76	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.82	95.44	0.88	0.77	10	-
GCA_017620335.1	s__Cryptobacteroides sp017620335	76.9769	71	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002314885.1	s__Cryptobacteroides sp002314885	76.5144	59	600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:00:03,162] [INFO] GTDB search result was written to GCA_018384035.1_ASM1838403v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:00:03,163] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:00:03,166] [INFO] DFAST_QC result json was written to GCA_018384035.1_ASM1838403v1_genomic.fna/dqc_result.json
[2023-06-19 13:00:03,167] [INFO] DFAST_QC completed!
[2023-06-19 13:00:03,167] [INFO] Total running time: 0h1m12s