[2023-06-28 12:17:49,234] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:17:49,237] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:17:49,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg89409961-61c3-4016-901b-b8673d673d10/dqc_reference
[2023-06-28 12:17:50,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:17:50,522] [INFO] Task started: Prodigal
[2023-06-28 12:17:50,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b50ffdd-afd5-46ba-bde1-df887db130c9/GCA_017389985.1_ASM1738998v1_genomic.fna.gz | prodigal -d GCA_017389985.1_ASM1738998v1_genomic.fna/cds.fna -a GCA_017389985.1_ASM1738998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:18:01,780] [INFO] Task succeeded: Prodigal
[2023-06-28 12:18:01,781] [INFO] Task started: HMMsearch
[2023-06-28 12:18:01,781] [INFO] Running command: hmmsearch --tblout GCA_017389985.1_ASM1738998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89409961-61c3-4016-901b-b8673d673d10/dqc_reference/reference_markers.hmm GCA_017389985.1_ASM1738998v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:18:02,012] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:18:02,014] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9b50ffdd-afd5-46ba-bde1-df887db130c9/GCA_017389985.1_ASM1738998v1_genomic.fna.gz]
[2023-06-28 12:18:02,042] [INFO] Query marker FASTA was written to GCA_017389985.1_ASM1738998v1_genomic.fna/markers.fasta
[2023-06-28 12:18:02,042] [INFO] Task started: Blastn
[2023-06-28 12:18:02,042] [INFO] Running command: blastn -query GCA_017389985.1_ASM1738998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89409961-61c3-4016-901b-b8673d673d10/dqc_reference/reference_markers.fasta -out GCA_017389985.1_ASM1738998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:18:02,547] [INFO] Task succeeded: Blastn
[2023-06-28 12:18:02,553] [INFO] Selected 22 target genomes.
[2023-06-28 12:18:02,553] [INFO] Target genome list was writen to GCA_017389985.1_ASM1738998v1_genomic.fna/target_genomes.txt
[2023-06-28 12:18:02,555] [INFO] Task started: fastANI
[2023-06-28 12:18:02,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b50ffdd-afd5-46ba-bde1-df887db130c9/GCA_017389985.1_ASM1738998v1_genomic.fna.gz --refList GCA_017389985.1_ASM1738998v1_genomic.fna/target_genomes.txt --output GCA_017389985.1_ASM1738998v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:18:13,244] [INFO] Task succeeded: fastANI
[2023-06-28 12:18:13,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89409961-61c3-4016-901b-b8673d673d10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:18:13,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89409961-61c3-4016-901b-b8673d673d10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:18:13,248] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:18:13,248] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:18:13,248] [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
--------------------------------------------------------------------------------
[2023-06-28 12:18:13,251] [INFO] DFAST Taxonomy check result was written to GCA_017389985.1_ASM1738998v1_genomic.fna/tc_result.tsv
[2023-06-28 12:18:13,252] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:18:13,253] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:18:13,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89409961-61c3-4016-901b-b8673d673d10/dqc_reference/checkm_data
[2023-06-28 12:18:13,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:18:13,287] [INFO] Task started: CheckM
[2023-06-28 12:18:13,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017389985.1_ASM1738998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017389985.1_ASM1738998v1_genomic.fna/checkm_input GCA_017389985.1_ASM1738998v1_genomic.fna/checkm_result
[2023-06-28 12:18:50,709] [INFO] Task succeeded: CheckM
[2023-06-28 12:18:50,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.20%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:18:50,733] [INFO] ===== Completeness check finished =====
[2023-06-28 12:18:50,733] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:18:50,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017389985.1_ASM1738998v1_genomic.fna/markers.fasta)
[2023-06-28 12:18:50,734] [INFO] Task started: Blastn
[2023-06-28 12:18:50,734] [INFO] Running command: blastn -query GCA_017389985.1_ASM1738998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89409961-61c3-4016-901b-b8673d673d10/dqc_reference/reference_markers_gtdb.fasta -out GCA_017389985.1_ASM1738998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:18:51,284] [INFO] Task succeeded: Blastn
[2023-06-28 12:18:51,289] [INFO] Selected 11 target genomes.
[2023-06-28 12:18:51,289] [INFO] Target genome list was writen to GCA_017389985.1_ASM1738998v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:18:51,295] [INFO] Task started: fastANI
[2023-06-28 12:18:51,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b50ffdd-afd5-46ba-bde1-df887db130c9/GCA_017389985.1_ASM1738998v1_genomic.fna.gz --refList GCA_017389985.1_ASM1738998v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017389985.1_ASM1738998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:18:57,964] [INFO] Task succeeded: fastANI
[2023-06-28 12:18:57,972] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:18:57,972] [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_900313845.1	s__UBA3839 sp900313845	96.0896	175	231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.94	95.74	0.85	0.70	7	conclusive
GCA_902798705.1	s__UBA3839 sp902798705	84.6569	159	231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.86	96.85	0.82	0.82	3	-
GCA_002393575.1	s__UBA3839 sp002393575	83.0394	156	231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA3839	95.0	96.72	96.72	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-28 12:18:57,975] [INFO] GTDB search result was written to GCA_017389985.1_ASM1738998v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:18:57,976] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:18:57,978] [INFO] DFAST_QC result json was written to GCA_017389985.1_ASM1738998v1_genomic.fna/dqc_result.json
[2023-06-28 12:18:57,978] [INFO] DFAST_QC completed!
[2023-06-28 12:18:57,979] [INFO] Total running time: 0h1m9s