[2023-06-29 04:17:38,711] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:17:38,715] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:17:38,715] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9b516cf-c379-4772-8b6f-8bf04cfa1d57/dqc_reference
[2023-06-29 04:17:40,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:17:40,617] [INFO] Task started: Prodigal
[2023-06-29 04:17:40,617] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5d03e8b-302f-4ccc-8077-e78471ef6d26/GCA_020437665.1_ASM2043766v1_genomic.fna.gz | prodigal -d GCA_020437665.1_ASM2043766v1_genomic.fna/cds.fna -a GCA_020437665.1_ASM2043766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:17:46,760] [INFO] Task succeeded: Prodigal
[2023-06-29 04:17:46,761] [INFO] Task started: HMMsearch
[2023-06-29 04:17:46,761] [INFO] Running command: hmmsearch --tblout GCA_020437665.1_ASM2043766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9b516cf-c379-4772-8b6f-8bf04cfa1d57/dqc_reference/reference_markers.hmm GCA_020437665.1_ASM2043766v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:17:47,057] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:17:47,058] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd5d03e8b-302f-4ccc-8077-e78471ef6d26/GCA_020437665.1_ASM2043766v1_genomic.fna.gz]
[2023-06-29 04:17:47,101] [INFO] Query marker FASTA was written to GCA_020437665.1_ASM2043766v1_genomic.fna/markers.fasta
[2023-06-29 04:17:47,101] [INFO] Task started: Blastn
[2023-06-29 04:17:47,102] [INFO] Running command: blastn -query GCA_020437665.1_ASM2043766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9b516cf-c379-4772-8b6f-8bf04cfa1d57/dqc_reference/reference_markers.fasta -out GCA_020437665.1_ASM2043766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:17:47,701] [INFO] Task succeeded: Blastn
[2023-06-29 04:17:47,705] [INFO] Selected 16 target genomes.
[2023-06-29 04:17:47,705] [INFO] Target genome list was writen to GCA_020437665.1_ASM2043766v1_genomic.fna/target_genomes.txt
[2023-06-29 04:17:47,708] [INFO] Task started: fastANI
[2023-06-29 04:17:47,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5d03e8b-302f-4ccc-8077-e78471ef6d26/GCA_020437665.1_ASM2043766v1_genomic.fna.gz --refList GCA_020437665.1_ASM2043766v1_genomic.fna/target_genomes.txt --output GCA_020437665.1_ASM2043766v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:17:55,985] [INFO] Task succeeded: fastANI
[2023-06-29 04:17:55,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9b516cf-c379-4772-8b6f-8bf04cfa1d57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:17:55,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9b516cf-c379-4772-8b6f-8bf04cfa1d57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:17:55,987] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:17:55,988] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 04:17:55,988] [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
--------------------------------------------------------------------------------
[2023-06-29 04:17:55,993] [INFO] DFAST Taxonomy check result was written to GCA_020437665.1_ASM2043766v1_genomic.fna/tc_result.tsv
[2023-06-29 04:17:55,994] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:17:55,994] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:17:55,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9b516cf-c379-4772-8b6f-8bf04cfa1d57/dqc_reference/checkm_data
[2023-06-29 04:17:55,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:17:56,043] [INFO] Task started: CheckM
[2023-06-29 04:17:56,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020437665.1_ASM2043766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020437665.1_ASM2043766v1_genomic.fna/checkm_input GCA_020437665.1_ASM2043766v1_genomic.fna/checkm_result
[2023-06-29 04:18:21,686] [INFO] Task succeeded: CheckM
[2023-06-29 04:18:21,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 8.33%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 04:18:21,715] [INFO] ===== Completeness check finished =====
[2023-06-29 04:18:21,715] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:18:21,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020437665.1_ASM2043766v1_genomic.fna/markers.fasta)
[2023-06-29 04:18:21,716] [INFO] Task started: Blastn
[2023-06-29 04:18:21,716] [INFO] Running command: blastn -query GCA_020437665.1_ASM2043766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9b516cf-c379-4772-8b6f-8bf04cfa1d57/dqc_reference/reference_markers_gtdb.fasta -out GCA_020437665.1_ASM2043766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:18:22,428] [INFO] Task succeeded: Blastn
[2023-06-29 04:18:22,433] [INFO] Selected 17 target genomes.
[2023-06-29 04:18:22,433] [INFO] Target genome list was writen to GCA_020437665.1_ASM2043766v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:18:22,452] [INFO] Task started: fastANI
[2023-06-29 04:18:22,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5d03e8b-302f-4ccc-8077-e78471ef6d26/GCA_020437665.1_ASM2043766v1_genomic.fna.gz --refList GCA_020437665.1_ASM2043766v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020437665.1_ASM2043766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:18:30,500] [INFO] Task succeeded: fastANI
[2023-06-29 04:18:30,510] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:18:30,510] [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_016708125.1	s__GCA-2746605 sp016708125	77.7384	188	675	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716225.1	s__GCA-2746605 sp016716225	77.497	174	675	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713565.1	s__GCA-2746605 sp016713565	76.5817	125	675	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	99.17	99.17	0.95	0.95	2	-
GCA_002746605.1	s__GCA-2746605 sp002746605	75.5055	50	675	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:18:30,512] [INFO] GTDB search result was written to GCA_020437665.1_ASM2043766v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:18:30,513] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:18:30,516] [INFO] DFAST_QC result json was written to GCA_020437665.1_ASM2043766v1_genomic.fna/dqc_result.json
[2023-06-29 04:18:30,516] [INFO] DFAST_QC completed!
[2023-06-29 04:18:30,516] [INFO] Total running time: 0h0m52s