[2024-01-24 10:57:38,591] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg74dbd1cb-a7c9-49a8-b078-91e739176035/dqc_reference
[2024-01-24 10:57:40,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,014] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,015] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ae01231-209d-4fa7-aacf-18b076aace0e/GCF_013133775.1_ASM1313377v1_genomic.fna.gz | prodigal -d GCF_013133775.1_ASM1313377v1_genomic.fna/cds.fna -a GCF_013133775.1_ASM1313377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:45,688] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:45,689] [INFO] Task started: HMMsearch
[2024-01-24 10:57:45,689] [INFO] Running command: hmmsearch --tblout GCF_013133775.1_ASM1313377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74dbd1cb-a7c9-49a8-b078-91e739176035/dqc_reference/reference_markers.hmm GCF_013133775.1_ASM1313377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:45,938] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:45,940] [INFO] Found 6/6 markers.
[2024-01-24 10:57:45,965] [INFO] Query marker FASTA was written to GCF_013133775.1_ASM1313377v1_genomic.fna/markers.fasta
[2024-01-24 10:57:45,966] [INFO] Task started: Blastn
[2024-01-24 10:57:45,966] [INFO] Running command: blastn -query GCF_013133775.1_ASM1313377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74dbd1cb-a7c9-49a8-b078-91e739176035/dqc_reference/reference_markers.fasta -out GCF_013133775.1_ASM1313377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:46,631] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:46,635] [INFO] Selected 19 target genomes.
[2024-01-24 10:57:46,636] [INFO] Target genome list was writen to GCF_013133775.1_ASM1313377v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:46,738] [INFO] Task started: fastANI
[2024-01-24 10:57:46,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae01231-209d-4fa7-aacf-18b076aace0e/GCF_013133775.1_ASM1313377v1_genomic.fna.gz --refList GCF_013133775.1_ASM1313377v1_genomic.fna/target_genomes.txt --output GCF_013133775.1_ASM1313377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:57,974] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:57,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74dbd1cb-a7c9-49a8-b078-91e739176035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:57,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74dbd1cb-a7c9-49a8-b078-91e739176035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:57,981] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:57,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:57,981] [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
Pelistega europaea	strain=LMG10982	GCA_013133775.1	106147	106147	type	True	100.0	799	800	95	conclusive
Pelistega suis	strain=3340-03	GCA_013133795.1	1631957	1631957	type	True	78.4286	234	800	95	below_threshold
Pelistega indica	strain=HM-7	GCA_000506865.1	1414851	1414851	type	True	77.8954	172	800	95	below_threshold
Pelistega ratti	strain=NLN63	GCA_009833965.1	2652177	2652177	type	True	77.8473	170	800	95	below_threshold
Taylorella equigenitalis	strain=ATCC 35865	GCA_000276685.1	29575	29575	type	True	76.4262	52	800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:57,984] [INFO] DFAST Taxonomy check result was written to GCF_013133775.1_ASM1313377v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:57,984] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:57,984] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:57,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74dbd1cb-a7c9-49a8-b078-91e739176035/dqc_reference/checkm_data
[2024-01-24 10:57:57,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:58,015] [INFO] Task started: CheckM
[2024-01-24 10:57:58,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013133775.1_ASM1313377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013133775.1_ASM1313377v1_genomic.fna/checkm_input GCF_013133775.1_ASM1313377v1_genomic.fna/checkm_result
[2024-01-24 10:58:21,764] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:21,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:21,791] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:21,791] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:21,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013133775.1_ASM1313377v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:21,792] [INFO] Task started: Blastn
[2024-01-24 10:58:21,792] [INFO] Running command: blastn -query GCF_013133775.1_ASM1313377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74dbd1cb-a7c9-49a8-b078-91e739176035/dqc_reference/reference_markers_gtdb.fasta -out GCF_013133775.1_ASM1313377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:22,884] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:22,889] [INFO] Selected 20 target genomes.
[2024-01-24 10:58:22,889] [INFO] Target genome list was writen to GCF_013133775.1_ASM1313377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:22,919] [INFO] Task started: fastANI
[2024-01-24 10:58:22,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae01231-209d-4fa7-aacf-18b076aace0e/GCF_013133775.1_ASM1313377v1_genomic.fna.gz --refList GCF_013133775.1_ASM1313377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013133775.1_ASM1313377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:31,456] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:31,467] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:31,467] [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
GCF_013133775.1	s__Pelistega europaea	100.0	799	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013133795.1	s__Pelistega suis	78.4287	234	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000506865.1	s__Pelistega indica	77.8948	172	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	99.45	98.91	0.95	0.92	3	-
GCF_009833965.1	s__Pelistega ratti	77.8473	170	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	97.82	97.82	0.91	0.91	2	-
GCF_000276685.1	s__Taylorella equigenitalis	76.4262	52	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Taylorella	95.0	99.66	99.39	0.98	0.96	12	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:31,469] [INFO] GTDB search result was written to GCF_013133775.1_ASM1313377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:31,469] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:31,472] [INFO] DFAST_QC result json was written to GCF_013133775.1_ASM1313377v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:31,472] [INFO] DFAST_QC completed!
[2024-01-24 10:58:31,472] [INFO] Total running time: 0h0m53s