[2023-06-07 18:18:41,929] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:18:41,931] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:18:41,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf6cfd83-28db-40ad-b417-b56dd7162607/dqc_reference
[2023-06-07 18:18:43,258] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:18:43,259] [INFO] Task started: Prodigal
[2023-06-07 18:18:43,260] [INFO] Running command: gunzip -c /var/lib/cwl/stg24cb90f3-5074-440a-9a33-70316a54162f/GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna.gz | prodigal -d GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/cds.fna -a GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:18:48,694] [INFO] Task succeeded: Prodigal
[2023-06-07 18:18:48,695] [INFO] Task started: HMMsearch
[2023-06-07 18:18:48,695] [INFO] Running command: hmmsearch --tblout GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf6cfd83-28db-40ad-b417-b56dd7162607/dqc_reference/reference_markers.hmm GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:18:48,992] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:18:49,000] [INFO] Found 6/6 markers.
[2023-06-07 18:18:49,039] [INFO] Query marker FASTA was written to GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/markers.fasta
[2023-06-07 18:18:49,039] [INFO] Task started: Blastn
[2023-06-07 18:18:49,039] [INFO] Running command: blastn -query GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf6cfd83-28db-40ad-b417-b56dd7162607/dqc_reference/reference_markers.fasta -out GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:18:49,684] [INFO] Task succeeded: Blastn
[2023-06-07 18:18:49,688] [INFO] Selected 23 target genomes.
[2023-06-07 18:18:49,689] [INFO] Target genome list was writen to GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/target_genomes.txt
[2023-06-07 18:18:49,695] [INFO] Task started: fastANI
[2023-06-07 18:18:49,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg24cb90f3-5074-440a-9a33-70316a54162f/GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna.gz --refList GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/target_genomes.txt --output GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:19:04,498] [INFO] Task succeeded: fastANI
[2023-06-07 18:19:04,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf6cfd83-28db-40ad-b417-b56dd7162607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:19:04,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf6cfd83-28db-40ad-b417-b56dd7162607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:19:04,503] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:19:04,503] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 18:19:04,503] [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
Anaerobiospirillum succiniciproducens	strain=DSM 6400	GCA_000482845.1	13335	13335	type	True	79.2808	248	935	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 18:19:04,506] [INFO] DFAST Taxonomy check result was written to GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/tc_result.tsv
[2023-06-07 18:19:04,506] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:19:04,507] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:19:04,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf6cfd83-28db-40ad-b417-b56dd7162607/dqc_reference/checkm_data
[2023-06-07 18:19:04,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:19:04,551] [INFO] Task started: CheckM
[2023-06-07 18:19:04,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/checkm_input GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/checkm_result
[2023-06-07 18:19:27,445] [INFO] Task succeeded: CheckM
[2023-06-07 18:19:27,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:19:27,475] [INFO] ===== Completeness check finished =====
[2023-06-07 18:19:27,476] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:19:27,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/markers.fasta)
[2023-06-07 18:19:27,477] [INFO] Task started: Blastn
[2023-06-07 18:19:27,477] [INFO] Running command: blastn -query GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf6cfd83-28db-40ad-b417-b56dd7162607/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:19:28,241] [INFO] Task succeeded: Blastn
[2023-06-07 18:19:28,246] [INFO] Selected 18 target genomes.
[2023-06-07 18:19:28,247] [INFO] Target genome list was writen to GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:19:28,261] [INFO] Task started: fastANI
[2023-06-07 18:19:28,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg24cb90f3-5074-440a-9a33-70316a54162f/GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna.gz --refList GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/target_genomes_gtdb.txt --output GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:19:36,493] [INFO] Task succeeded: fastANI
[2023-06-07 18:19:36,512] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 18:19:36,512] [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_900543125.1	s__Anaerobiospirillum sp900543125	99.8791	864	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	99.86	99.86	0.90	0.90	2	conclusive
GCF_000482845.1	s__Anaerobiospirillum succiniciproducens	79.2808	248	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113025.1	s__Anaerobiospirillum stercoravium	78.0962	95	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114785.1	s__Anaerobiospirillum pullistercoris	77.8448	176	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905186145.1	s__Succinivibrio sp905186145	77.2632	75	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018884035.1	s__Anaerobiospirillum pullicola	77.2432	102	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431835.1	s__Succinivibrio sp000431835	77.1434	74	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.12	95.78	0.87	0.82	11	-
GCA_012519775.1	s__Succinivibrio sp012519775	76.88	55	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548485.1	s__Succinivibrio sp900548485	76.8124	53	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.05	99.05	0.77	0.77	2	-
GCA_900316375.1	s__Succinivibrio sp900316375	76.4898	74	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-07 18:19:36,515] [INFO] GTDB search result was written to GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/result_gtdb.tsv
[2023-06-07 18:19:36,515] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:19:36,519] [INFO] DFAST_QC result json was written to GCA_902461495.1_UHGG-TPA_MGYG-HGUT-00338_genomic.fna/dqc_result.json
[2023-06-07 18:19:36,519] [INFO] DFAST_QC completed!
[2023-06-07 18:19:36,519] [INFO] Total running time: 0h0m55s