[2023-06-08 10:56:38,609] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:56:38,621] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:56:38,621] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0b62524-76b1-4d84-9811-172361611564/dqc_reference
[2023-06-08 10:56:39,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:56:39,832] [INFO] Task started: Prodigal
[2023-06-08 10:56:39,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg6090da43-12ff-48de-9ecf-7b5931fb6460/GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna.gz | prodigal -d GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/cds.fna -a GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:56:46,674] [INFO] Task succeeded: Prodigal
[2023-06-08 10:56:46,675] [INFO] Task started: HMMsearch
[2023-06-08 10:56:46,675] [INFO] Running command: hmmsearch --tblout GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0b62524-76b1-4d84-9811-172361611564/dqc_reference/reference_markers.hmm GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:56:46,885] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:56:46,887] [INFO] Found 6/6 markers.
[2023-06-08 10:56:46,911] [INFO] Query marker FASTA was written to GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/markers.fasta
[2023-06-08 10:56:46,912] [INFO] Task started: Blastn
[2023-06-08 10:56:46,912] [INFO] Running command: blastn -query GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0b62524-76b1-4d84-9811-172361611564/dqc_reference/reference_markers.fasta -out GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:56:47,552] [INFO] Task succeeded: Blastn
[2023-06-08 10:56:47,556] [INFO] Selected 25 target genomes.
[2023-06-08 10:56:47,556] [INFO] Target genome list was writen to GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/target_genomes.txt
[2023-06-08 10:56:47,560] [INFO] Task started: fastANI
[2023-06-08 10:56:47,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg6090da43-12ff-48de-9ecf-7b5931fb6460/GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna.gz --refList GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/target_genomes.txt --output GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:57:00,337] [INFO] Task succeeded: fastANI
[2023-06-08 10:57:00,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0b62524-76b1-4d84-9811-172361611564/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:57:00,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0b62524-76b1-4d84-9811-172361611564/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:57:00,345] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:57:00,345] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 10:57:00,345] [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
--------------------------------------------------------------------------------
[2023-06-08 10:57:00,351] [INFO] DFAST Taxonomy check result was written to GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/tc_result.tsv
[2023-06-08 10:57:00,352] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:57:00,352] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:57:00,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0b62524-76b1-4d84-9811-172361611564/dqc_reference/checkm_data
[2023-06-08 10:57:00,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:57:00,378] [INFO] Task started: CheckM
[2023-06-08 10:57:00,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/checkm_input GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/checkm_result
[2023-06-08 10:57:26,334] [INFO] Task succeeded: CheckM
[2023-06-08 10:57:26,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:57:26,359] [INFO] ===== Completeness check finished =====
[2023-06-08 10:57:26,359] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:57:26,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/markers.fasta)
[2023-06-08 10:57:26,360] [INFO] Task started: Blastn
[2023-06-08 10:57:26,360] [INFO] Running command: blastn -query GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0b62524-76b1-4d84-9811-172361611564/dqc_reference/reference_markers_gtdb.fasta -out GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:57:27,370] [INFO] Task succeeded: Blastn
[2023-06-08 10:57:27,374] [INFO] Selected 28 target genomes.
[2023-06-08 10:57:27,374] [INFO] Target genome list was writen to GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:57:27,385] [INFO] Task started: fastANI
[2023-06-08 10:57:27,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg6090da43-12ff-48de-9ecf-7b5931fb6460/GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna.gz --refList GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/target_genomes_gtdb.txt --output GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:57:36,686] [INFO] Task succeeded: fastANI
[2023-06-08 10:57:36,696] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:57:36,697] [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_902795785.1	s__Cryptobacteroides sp902795785	98.2321	294	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.23	98.23	0.84	0.84	2	conclusive
GCA_018066125.1	s__Cryptobacteroides sp018066125	77.4385	61	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900167925.1	s__Cryptobacteroides sp900167925	76.935	64	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.91	97.12	0.93	0.91	9	-
GCA_000431015.1	s__Cryptobacteroides sp000431015	76.1769	51	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.39	98.13	0.87	0.74	9	-
GCA_017618815.1	s__Cryptobacteroides sp017618815	76.0283	55	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 10:57:36,703] [INFO] GTDB search result was written to GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/result_gtdb.tsv
[2023-06-08 10:57:36,704] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:57:36,707] [INFO] DFAST_QC result json was written to GCA_902766165.1_Rumen_uncultured_genome_RUG11134_genomic.fna/dqc_result.json
[2023-06-08 10:57:36,707] [INFO] DFAST_QC completed!
[2023-06-08 10:57:36,707] [INFO] Total running time: 0h0m58s