[2023-06-18 21:21:17,077] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:21:17,079] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:21:17,079] [INFO] DQC Reference Directory: /var/lib/cwl/stge2d6554d-04e1-43ab-99ca-6e3d7a469750/dqc_reference
[2023-06-18 21:21:18,364] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:21:18,365] [INFO] Task started: Prodigal
[2023-06-18 21:21:18,366] [INFO] Running command: gunzip -c /var/lib/cwl/stgcad3ca3a-34bc-4438-95fc-49e10650795f/GCA_018969745.1_ASM1896974v1_genomic.fna.gz | prodigal -d GCA_018969745.1_ASM1896974v1_genomic.fna/cds.fna -a GCA_018969745.1_ASM1896974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:21:29,606] [INFO] Task succeeded: Prodigal
[2023-06-18 21:21:29,607] [INFO] Task started: HMMsearch
[2023-06-18 21:21:29,607] [INFO] Running command: hmmsearch --tblout GCA_018969745.1_ASM1896974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2d6554d-04e1-43ab-99ca-6e3d7a469750/dqc_reference/reference_markers.hmm GCA_018969745.1_ASM1896974v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:21:29,890] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:21:29,891] [INFO] Found 6/6 markers.
[2023-06-18 21:21:29,923] [INFO] Query marker FASTA was written to GCA_018969745.1_ASM1896974v1_genomic.fna/markers.fasta
[2023-06-18 21:21:29,924] [INFO] Task started: Blastn
[2023-06-18 21:21:29,924] [INFO] Running command: blastn -query GCA_018969745.1_ASM1896974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d6554d-04e1-43ab-99ca-6e3d7a469750/dqc_reference/reference_markers.fasta -out GCA_018969745.1_ASM1896974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:21:30,545] [INFO] Task succeeded: Blastn
[2023-06-18 21:21:30,550] [INFO] Selected 25 target genomes.
[2023-06-18 21:21:30,550] [INFO] Target genome list was writen to GCA_018969745.1_ASM1896974v1_genomic.fna/target_genomes.txt
[2023-06-18 21:21:30,555] [INFO] Task started: fastANI
[2023-06-18 21:21:30,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad3ca3a-34bc-4438-95fc-49e10650795f/GCA_018969745.1_ASM1896974v1_genomic.fna.gz --refList GCA_018969745.1_ASM1896974v1_genomic.fna/target_genomes.txt --output GCA_018969745.1_ASM1896974v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:21:46,885] [INFO] Task succeeded: fastANI
[2023-06-18 21:21:46,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2d6554d-04e1-43ab-99ca-6e3d7a469750/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:21:46,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2d6554d-04e1-43ab-99ca-6e3d7a469750/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:21:46,888] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:21:46,888] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 21:21:46,889] [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
--------------------------------------------------------------------------------
[2023-06-18 21:21:46,895] [INFO] DFAST Taxonomy check result was written to GCA_018969745.1_ASM1896974v1_genomic.fna/tc_result.tsv
[2023-06-18 21:21:46,896] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:21:46,896] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:21:46,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2d6554d-04e1-43ab-99ca-6e3d7a469750/dqc_reference/checkm_data
[2023-06-18 21:21:46,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:21:46,950] [INFO] Task started: CheckM
[2023-06-18 21:21:46,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018969745.1_ASM1896974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018969745.1_ASM1896974v1_genomic.fna/checkm_input GCA_018969745.1_ASM1896974v1_genomic.fna/checkm_result
[2023-06-18 21:22:25,120] [INFO] Task succeeded: CheckM
[2023-06-18 21:22:25,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 21:22:25,154] [INFO] ===== Completeness check finished =====
[2023-06-18 21:22:25,154] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:22:25,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018969745.1_ASM1896974v1_genomic.fna/markers.fasta)
[2023-06-18 21:22:25,155] [INFO] Task started: Blastn
[2023-06-18 21:22:25,155] [INFO] Running command: blastn -query GCA_018969745.1_ASM1896974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d6554d-04e1-43ab-99ca-6e3d7a469750/dqc_reference/reference_markers_gtdb.fasta -out GCA_018969745.1_ASM1896974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:22:25,950] [INFO] Task succeeded: Blastn
[2023-06-18 21:22:25,955] [INFO] Selected 27 target genomes.
[2023-06-18 21:22:25,955] [INFO] Target genome list was writen to GCA_018969745.1_ASM1896974v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:22:25,980] [INFO] Task started: fastANI
[2023-06-18 21:22:25,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad3ca3a-34bc-4438-95fc-49e10650795f/GCA_018969745.1_ASM1896974v1_genomic.fna.gz --refList GCA_018969745.1_ASM1896974v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018969745.1_ASM1896974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:22:44,893] [INFO] Task succeeded: fastANI
[2023-06-18 21:22:44,899] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 21:22:44,900] [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_014190515.1	s__BJGN01 sp014190515	83.548	476	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__BJGN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858735.1	s__BJGN01 sp017858735	82.3323	527	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__BJGN01	95.0	99.65	99.65	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-18 21:22:44,902] [INFO] GTDB search result was written to GCA_018969745.1_ASM1896974v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:22:44,902] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:22:44,904] [INFO] DFAST_QC result json was written to GCA_018969745.1_ASM1896974v1_genomic.fna/dqc_result.json
[2023-06-18 21:22:44,904] [INFO] DFAST_QC completed!
[2023-06-18 21:22:44,905] [INFO] Total running time: 0h1m28s