[2023-06-28 14:06:00,038] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:06:00,040] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:06:00,041] [INFO] DQC Reference Directory: /var/lib/cwl/stgc970fd8d-2a03-4fde-b0df-cbca36e74321/dqc_reference
[2023-06-28 14:06:01,346] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:06:01,347] [INFO] Task started: Prodigal
[2023-06-28 14:06:01,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d9cb866-b435-40ce-b9a4-2412292145f6/GCA_020059645.1_ASM2005964v1_genomic.fna.gz | prodigal -d GCA_020059645.1_ASM2005964v1_genomic.fna/cds.fna -a GCA_020059645.1_ASM2005964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:06:06,829] [INFO] Task succeeded: Prodigal
[2023-06-28 14:06:06,830] [INFO] Task started: HMMsearch
[2023-06-28 14:06:06,830] [INFO] Running command: hmmsearch --tblout GCA_020059645.1_ASM2005964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc970fd8d-2a03-4fde-b0df-cbca36e74321/dqc_reference/reference_markers.hmm GCA_020059645.1_ASM2005964v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:06:07,089] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:06:07,090] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6d9cb866-b435-40ce-b9a4-2412292145f6/GCA_020059645.1_ASM2005964v1_genomic.fna.gz]
[2023-06-28 14:06:07,114] [INFO] Query marker FASTA was written to GCA_020059645.1_ASM2005964v1_genomic.fna/markers.fasta
[2023-06-28 14:06:07,114] [INFO] Task started: Blastn
[2023-06-28 14:06:07,114] [INFO] Running command: blastn -query GCA_020059645.1_ASM2005964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc970fd8d-2a03-4fde-b0df-cbca36e74321/dqc_reference/reference_markers.fasta -out GCA_020059645.1_ASM2005964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:06:07,670] [INFO] Task succeeded: Blastn
[2023-06-28 14:06:07,675] [INFO] Selected 3 target genomes.
[2023-06-28 14:06:07,675] [INFO] Target genome list was writen to GCA_020059645.1_ASM2005964v1_genomic.fna/target_genomes.txt
[2023-06-28 14:06:07,678] [INFO] Task started: fastANI
[2023-06-28 14:06:07,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d9cb866-b435-40ce-b9a4-2412292145f6/GCA_020059645.1_ASM2005964v1_genomic.fna.gz --refList GCA_020059645.1_ASM2005964v1_genomic.fna/target_genomes.txt --output GCA_020059645.1_ASM2005964v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:06:08,969] [INFO] Task succeeded: fastANI
[2023-06-28 14:06:08,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc970fd8d-2a03-4fde-b0df-cbca36e74321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:06:08,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc970fd8d-2a03-4fde-b0df-cbca36e74321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:06:08,971] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:06:08,972] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 14:06:08,972] [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 14:06:08,974] [INFO] DFAST Taxonomy check result was written to GCA_020059645.1_ASM2005964v1_genomic.fna/tc_result.tsv
[2023-06-28 14:06:08,975] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:06:08,975] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:06:08,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc970fd8d-2a03-4fde-b0df-cbca36e74321/dqc_reference/checkm_data
[2023-06-28 14:06:08,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:06:09,007] [INFO] Task started: CheckM
[2023-06-28 14:06:09,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020059645.1_ASM2005964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020059645.1_ASM2005964v1_genomic.fna/checkm_input GCA_020059645.1_ASM2005964v1_genomic.fna/checkm_result
[2023-06-28 14:06:33,336] [INFO] Task succeeded: CheckM
[2023-06-28 14:06:33,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 9.26%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:06:33,360] [INFO] ===== Completeness check finished =====
[2023-06-28 14:06:33,361] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:06:33,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020059645.1_ASM2005964v1_genomic.fna/markers.fasta)
[2023-06-28 14:06:33,362] [INFO] Task started: Blastn
[2023-06-28 14:06:33,362] [INFO] Running command: blastn -query GCA_020059645.1_ASM2005964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc970fd8d-2a03-4fde-b0df-cbca36e74321/dqc_reference/reference_markers_gtdb.fasta -out GCA_020059645.1_ASM2005964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:06:34,105] [INFO] Task succeeded: Blastn
[2023-06-28 14:06:34,110] [INFO] Selected 20 target genomes.
[2023-06-28 14:06:34,110] [INFO] Target genome list was writen to GCA_020059645.1_ASM2005964v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:06:34,129] [INFO] Task started: fastANI
[2023-06-28 14:06:34,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d9cb866-b435-40ce-b9a4-2412292145f6/GCA_020059645.1_ASM2005964v1_genomic.fna.gz --refList GCA_020059645.1_ASM2005964v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020059645.1_ASM2005964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:06:45,048] [INFO] Task succeeded: fastANI
[2023-06-28 14:06:45,061] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 14:06:45,061] [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_002840735.1	s__UBA6170 sp002840735	93.2027	121	655	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA6170	95.0	99.19	99.09	0.96	0.94	5	-
GCA_002842045.1	s__UBA6170 sp002842045	86.0912	117	655	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA6170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860845.1	s__UBA6170 sp014860845	83.9981	94	655	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA6170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403105.1	s__UBA4781 sp002403105	79.6219	239	655	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA4781	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012797975.1	s__UBA4781 sp012797975	77.8011	163	655	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA4781	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446605.1	s__UBA4781 sp003446605	77.377	95	655	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA4781	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798455.1	s__UBA4781 sp012798455	77.2291	103	655	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA4781	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012797815.1	s__UBA4781 sp012797815	76.9439	118	655	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA4781	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:06:45,063] [INFO] GTDB search result was written to GCA_020059645.1_ASM2005964v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:06:45,063] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:06:45,067] [INFO] DFAST_QC result json was written to GCA_020059645.1_ASM2005964v1_genomic.fna/dqc_result.json
[2023-06-28 14:06:45,067] [INFO] DFAST_QC completed!
[2023-06-28 14:06:45,068] [INFO] Total running time: 0h0m45s