[2023-06-27 06:49:44,515] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:49:44,541] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:49:44,541] [INFO] DQC Reference Directory: /var/lib/cwl/stga34e07a5-caa7-4a54-b87b-16012e635581/dqc_reference
[2023-06-27 06:49:46,881] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:49:46,882] [INFO] Task started: Prodigal
[2023-06-27 06:49:46,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg23769c6d-66b0-4d0c-9ba8-f5f6b9d8a676/GCA_026397285.1_ASM2639728v1_genomic.fna.gz | prodigal -d GCA_026397285.1_ASM2639728v1_genomic.fna/cds.fna -a GCA_026397285.1_ASM2639728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:49:49,400] [INFO] Task succeeded: Prodigal
[2023-06-27 06:49:49,400] [INFO] Task started: HMMsearch
[2023-06-27 06:49:49,401] [INFO] Running command: hmmsearch --tblout GCA_026397285.1_ASM2639728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga34e07a5-caa7-4a54-b87b-16012e635581/dqc_reference/reference_markers.hmm GCA_026397285.1_ASM2639728v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:49:49,600] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:49:49,602] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg23769c6d-66b0-4d0c-9ba8-f5f6b9d8a676/GCA_026397285.1_ASM2639728v1_genomic.fna.gz]
[2023-06-27 06:49:49,614] [INFO] Query marker FASTA was written to GCA_026397285.1_ASM2639728v1_genomic.fna/markers.fasta
[2023-06-27 06:49:49,614] [INFO] Task started: Blastn
[2023-06-27 06:49:49,614] [INFO] Running command: blastn -query GCA_026397285.1_ASM2639728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga34e07a5-caa7-4a54-b87b-16012e635581/dqc_reference/reference_markers.fasta -out GCA_026397285.1_ASM2639728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:49:50,938] [INFO] Task succeeded: Blastn
[2023-06-27 06:49:50,968] [INFO] Selected 8 target genomes.
[2023-06-27 06:49:50,968] [INFO] Target genome list was writen to GCA_026397285.1_ASM2639728v1_genomic.fna/target_genomes.txt
[2023-06-27 06:49:50,972] [INFO] Task started: fastANI
[2023-06-27 06:49:50,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg23769c6d-66b0-4d0c-9ba8-f5f6b9d8a676/GCA_026397285.1_ASM2639728v1_genomic.fna.gz --refList GCA_026397285.1_ASM2639728v1_genomic.fna/target_genomes.txt --output GCA_026397285.1_ASM2639728v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:49:54,130] [INFO] Task succeeded: fastANI
[2023-06-27 06:49:54,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga34e07a5-caa7-4a54-b87b-16012e635581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:49:54,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga34e07a5-caa7-4a54-b87b-16012e635581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:49:54,133] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:49:54,133] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:49:54,133] [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
--------------------------------------------------------------------------------
[2023-06-27 06:49:54,150] [INFO] DFAST Taxonomy check result was written to GCA_026397285.1_ASM2639728v1_genomic.fna/tc_result.tsv
[2023-06-27 06:49:54,151] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:49:54,151] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:49:54,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga34e07a5-caa7-4a54-b87b-16012e635581/dqc_reference/checkm_data
[2023-06-27 06:49:54,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:49:54,173] [INFO] Task started: CheckM
[2023-06-27 06:49:54,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026397285.1_ASM2639728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026397285.1_ASM2639728v1_genomic.fna/checkm_input GCA_026397285.1_ASM2639728v1_genomic.fna/checkm_result
[2023-06-27 06:50:09,853] [INFO] Task succeeded: CheckM
[2023-06-27 06:50:09,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.07%
Contamintation: 10.42%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-27 06:50:09,877] [INFO] ===== Completeness check finished =====
[2023-06-27 06:50:09,877] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:50:09,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026397285.1_ASM2639728v1_genomic.fna/markers.fasta)
[2023-06-27 06:50:09,878] [INFO] Task started: Blastn
[2023-06-27 06:50:09,878] [INFO] Running command: blastn -query GCA_026397285.1_ASM2639728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga34e07a5-caa7-4a54-b87b-16012e635581/dqc_reference/reference_markers_gtdb.fasta -out GCA_026397285.1_ASM2639728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:50:10,594] [INFO] Task succeeded: Blastn
[2023-06-27 06:50:10,674] [INFO] Selected 18 target genomes.
[2023-06-27 06:50:10,674] [INFO] Target genome list was writen to GCA_026397285.1_ASM2639728v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:50:10,688] [INFO] Task started: fastANI
[2023-06-27 06:50:10,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg23769c6d-66b0-4d0c-9ba8-f5f6b9d8a676/GCA_026397285.1_ASM2639728v1_genomic.fna.gz --refList GCA_026397285.1_ASM2639728v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026397285.1_ASM2639728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:50:13,684] [INFO] Task succeeded: fastANI
[2023-06-27 06:50:13,691] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:50:13,692] [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_016213445.1	s__UBA10092 sp016213445	77.6005	52	191	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA10092;f__UBA10092;g__UBA10092	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826255.1	s__UBA10092 sp018826255	77.5536	56	191	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA10092;f__UBA10092;g__UBA10092	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:50:13,694] [INFO] GTDB search result was written to GCA_026397285.1_ASM2639728v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:50:13,695] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:50:13,698] [INFO] DFAST_QC result json was written to GCA_026397285.1_ASM2639728v1_genomic.fna/dqc_result.json
[2023-06-27 06:50:13,698] [INFO] DFAST_QC completed!
[2023-06-27 06:50:13,698] [INFO] Total running time: 0h0m29s