[2023-06-05 01:18:29,278] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:18:29,295] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:18:29,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg8aa7d8d4-7cc9-448b-95aa-94ae6deaf9af/dqc_reference
[2023-06-05 01:18:30,741] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:18:30,741] [INFO] Task started: Prodigal
[2023-06-05 01:18:30,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a935cba-ec52-4336-8759-e3aa795aacfb/GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna.gz | prodigal -d GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/cds.fna -a GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:18:34,534] [INFO] Task succeeded: Prodigal
[2023-06-05 01:18:34,534] [INFO] Task started: HMMsearch
[2023-06-05 01:18:34,534] [INFO] Running command: hmmsearch --tblout GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8aa7d8d4-7cc9-448b-95aa-94ae6deaf9af/dqc_reference/reference_markers.hmm GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:18:34,801] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:18:34,802] [INFO] Found 6/6 markers.
[2023-06-05 01:18:34,823] [INFO] Query marker FASTA was written to GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/markers.fasta
[2023-06-05 01:18:34,824] [INFO] Task started: Blastn
[2023-06-05 01:18:34,824] [INFO] Running command: blastn -query GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aa7d8d4-7cc9-448b-95aa-94ae6deaf9af/dqc_reference/reference_markers.fasta -out GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:35,454] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:35,476] [INFO] Selected 16 target genomes.
[2023-06-05 01:18:35,477] [INFO] Target genome list was writen to GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/target_genomes.txt
[2023-06-05 01:18:35,504] [INFO] Task started: fastANI
[2023-06-05 01:18:35,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a935cba-ec52-4336-8759-e3aa795aacfb/GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna.gz --refList GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/target_genomes.txt --output GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:18:45,329] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:45,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8aa7d8d4-7cc9-448b-95aa-94ae6deaf9af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:18:45,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8aa7d8d4-7cc9-448b-95aa-94ae6deaf9af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:18:45,332] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:18:45,332] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 01:18:45,332] [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
--------------------------------------------------------------------------------
[2023-06-05 01:18:45,334] [INFO] DFAST Taxonomy check result was written to GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/tc_result.tsv
[2023-06-05 01:18:45,334] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:18:45,335] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:18:45,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8aa7d8d4-7cc9-448b-95aa-94ae6deaf9af/dqc_reference/checkm_data
[2023-06-05 01:18:45,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:18:45,359] [INFO] Task started: CheckM
[2023-06-05 01:18:45,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/checkm_input GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/checkm_result
[2023-06-05 01:19:04,253] [INFO] Task succeeded: CheckM
[2023-06-05 01:19:04,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:19:04,273] [INFO] ===== Completeness check finished =====
[2023-06-05 01:19:04,273] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:19:04,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/markers.fasta)
[2023-06-05 01:19:04,274] [INFO] Task started: Blastn
[2023-06-05 01:19:04,274] [INFO] Running command: blastn -query GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aa7d8d4-7cc9-448b-95aa-94ae6deaf9af/dqc_reference/reference_markers_gtdb.fasta -out GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:19:05,250] [INFO] Task succeeded: Blastn
[2023-06-05 01:19:05,255] [INFO] Selected 19 target genomes.
[2023-06-05 01:19:05,256] [INFO] Target genome list was writen to GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:19:05,283] [INFO] Task started: fastANI
[2023-06-05 01:19:05,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a935cba-ec52-4336-8759-e3aa795aacfb/GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna.gz --refList GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/target_genomes_gtdb.txt --output GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:19:11,549] [INFO] Task succeeded: fastANI
[2023-06-05 01:19:11,556] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:19:11,557] [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_900552285.1	s__UMGS1484 sp900552285	99.5058	354	449	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1484	95.0	99.13	98.75	0.83	0.79	4	conclusive
GCA_905193225.1	s__UMGS1484 sp905193225	81.5104	273	449	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1484	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902388225.1	s__UMGS1484 sp902388225	81.1704	220	449	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1484	95.0	99.69	99.69	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-05 01:19:11,559] [INFO] GTDB search result was written to GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/result_gtdb.tsv
[2023-06-05 01:19:11,559] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:19:11,562] [INFO] DFAST_QC result json was written to GCA_902406245.1_UHGG_MGYG-HGUT-04279_genomic.fna/dqc_result.json
[2023-06-05 01:19:11,562] [INFO] DFAST_QC completed!
[2023-06-05 01:19:11,562] [INFO] Total running time: 0h0m42s