[2023-06-13 14:06:26,366] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:06:26,368] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:06:26,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fb2d701-0d60-4e46-85bd-60a72eb97bf5/dqc_reference
[2023-06-13 14:06:27,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:06:27,767] [INFO] Task started: Prodigal
[2023-06-13 14:06:27,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg8614b757-5d22-4c99-9bf1-f174f33179ed/GCA_022709645.1_ASM2270964v1_genomic.fna.gz | prodigal -d GCA_022709645.1_ASM2270964v1_genomic.fna/cds.fna -a GCA_022709645.1_ASM2270964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:06:46,529] [INFO] Task succeeded: Prodigal
[2023-06-13 14:06:46,529] [INFO] Task started: HMMsearch
[2023-06-13 14:06:46,529] [INFO] Running command: hmmsearch --tblout GCA_022709645.1_ASM2270964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fb2d701-0d60-4e46-85bd-60a72eb97bf5/dqc_reference/reference_markers.hmm GCA_022709645.1_ASM2270964v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:06:46,815] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:06:46,816] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8614b757-5d22-4c99-9bf1-f174f33179ed/GCA_022709645.1_ASM2270964v1_genomic.fna.gz]
[2023-06-13 14:06:46,859] [INFO] Query marker FASTA was written to GCA_022709645.1_ASM2270964v1_genomic.fna/markers.fasta
[2023-06-13 14:06:46,859] [INFO] Task started: Blastn
[2023-06-13 14:06:46,859] [INFO] Running command: blastn -query GCA_022709645.1_ASM2270964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fb2d701-0d60-4e46-85bd-60a72eb97bf5/dqc_reference/reference_markers.fasta -out GCA_022709645.1_ASM2270964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:06:47,519] [INFO] Task succeeded: Blastn
[2023-06-13 14:06:47,523] [INFO] Selected 15 target genomes.
[2023-06-13 14:06:47,523] [INFO] Target genome list was writen to GCA_022709645.1_ASM2270964v1_genomic.fna/target_genomes.txt
[2023-06-13 14:06:47,529] [INFO] Task started: fastANI
[2023-06-13 14:06:47,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg8614b757-5d22-4c99-9bf1-f174f33179ed/GCA_022709645.1_ASM2270964v1_genomic.fna.gz --refList GCA_022709645.1_ASM2270964v1_genomic.fna/target_genomes.txt --output GCA_022709645.1_ASM2270964v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:06:58,747] [INFO] Task succeeded: fastANI
[2023-06-13 14:06:58,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fb2d701-0d60-4e46-85bd-60a72eb97bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:06:58,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fb2d701-0d60-4e46-85bd-60a72eb97bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:06:58,750] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:06:58,750] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 14:06:58,750] [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
--------------------------------------------------------------------------------
[2023-06-13 14:06:58,753] [INFO] DFAST Taxonomy check result was written to GCA_022709645.1_ASM2270964v1_genomic.fna/tc_result.tsv
[2023-06-13 14:06:58,753] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:06:58,753] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:06:58,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fb2d701-0d60-4e46-85bd-60a72eb97bf5/dqc_reference/checkm_data
[2023-06-13 14:06:58,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:06:58,791] [INFO] Task started: CheckM
[2023-06-13 14:06:58,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022709645.1_ASM2270964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022709645.1_ASM2270964v1_genomic.fna/checkm_input GCA_022709645.1_ASM2270964v1_genomic.fna/checkm_result
[2023-06-13 14:07:51,267] [INFO] Task succeeded: CheckM
[2023-06-13 14:07:51,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:07:51,290] [INFO] ===== Completeness check finished =====
[2023-06-13 14:07:51,290] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:07:51,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022709645.1_ASM2270964v1_genomic.fna/markers.fasta)
[2023-06-13 14:07:51,291] [INFO] Task started: Blastn
[2023-06-13 14:07:51,291] [INFO] Running command: blastn -query GCA_022709645.1_ASM2270964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fb2d701-0d60-4e46-85bd-60a72eb97bf5/dqc_reference/reference_markers_gtdb.fasta -out GCA_022709645.1_ASM2270964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:07:52,096] [INFO] Task succeeded: Blastn
[2023-06-13 14:07:52,101] [INFO] Selected 13 target genomes.
[2023-06-13 14:07:52,101] [INFO] Target genome list was writen to GCA_022709645.1_ASM2270964v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:07:52,111] [INFO] Task started: fastANI
[2023-06-13 14:07:52,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg8614b757-5d22-4c99-9bf1-f174f33179ed/GCA_022709645.1_ASM2270964v1_genomic.fna.gz --refList GCA_022709645.1_ASM2270964v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022709645.1_ASM2270964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:08:02,551] [INFO] Task succeeded: fastANI
[2023-06-13 14:08:02,568] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:08:02,568] [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_903912925.1	s__PALSA-1440 sp903912925	77.9113	245	892	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PALSA-1440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517205.1	s__UBA8199 sp003527065	77.8654	217	892	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__UBA8199	95.0	99.50	99.40	0.92	0.86	6	-
GCA_003152225.1	s__PALSA-1440 sp003152225	77.8148	279	892	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PALSA-1440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873945.1	s__CAIQQM01 sp903873945	76.6451	69	892	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__CAIQQM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003159675.1	s__BOG-1460 sp003159675	76.4157	66	892	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA3939;g__BOG-1460	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003218515.1	s__AV2 sp003218515	76.1358	56	892	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__AV2;g__AV2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385705.1	s__UBA3939 sp002385705	76.0037	65	892	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA3939;g__UBA3939	95.0	99.95	99.95	0.96	0.96	2	-
GCA_016871715.1	s__VHCO01 sp016871715	75.9593	55	892	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__VHCO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:08:02,570] [INFO] GTDB search result was written to GCA_022709645.1_ASM2270964v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:08:02,571] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:08:02,575] [INFO] DFAST_QC result json was written to GCA_022709645.1_ASM2270964v1_genomic.fna/dqc_result.json
[2023-06-13 14:08:02,576] [INFO] DFAST_QC completed!
[2023-06-13 14:08:02,576] [INFO] Total running time: 0h1m36s