[2024-01-24 13:57:42,902] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,904] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg2051819a-a505-4a3f-bede-688499d95709/dqc_reference
[2024-01-24 13:57:44,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,259] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,260] [INFO] Running command: gunzip -c /var/lib/cwl/stga48b7d0a-496c-4ad4-ac93-59a63420e5f5/GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna.gz | prodigal -d GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/cds.fna -a GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:52,172] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:52,173] [INFO] Task started: HMMsearch
[2024-01-24 13:57:52,173] [INFO] Running command: hmmsearch --tblout GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2051819a-a505-4a3f-bede-688499d95709/dqc_reference/reference_markers.hmm GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:52,447] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:52,448] [INFO] Found 6/6 markers.
[2024-01-24 13:57:52,485] [INFO] Query marker FASTA was written to GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/markers.fasta
[2024-01-24 13:57:52,485] [INFO] Task started: Blastn
[2024-01-24 13:57:52,485] [INFO] Running command: blastn -query GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2051819a-a505-4a3f-bede-688499d95709/dqc_reference/reference_markers.fasta -out GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:53,242] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:53,252] [INFO] Selected 26 target genomes.
[2024-01-24 13:57:53,253] [INFO] Target genome list was writen to GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:57:53,263] [INFO] Task started: fastANI
[2024-01-24 13:57:53,264] [INFO] Running command: fastANI --query /var/lib/cwl/stga48b7d0a-496c-4ad4-ac93-59a63420e5f5/GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna.gz --refList GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/target_genomes.txt --output GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:09,568] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2051819a-a505-4a3f-bede-688499d95709/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:09,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2051819a-a505-4a3f-bede-688499d95709/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:09,572] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:09,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:09,573] [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
Ferrovum myxofaciens	strain=P3G	GCA_000735045.1	416213	416213	type	True	100.0	754	758	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,579] [INFO] DFAST Taxonomy check result was written to GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:58:09,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:09,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:09,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2051819a-a505-4a3f-bede-688499d95709/dqc_reference/checkm_data
[2024-01-24 13:58:09,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:09,611] [INFO] Task started: CheckM
[2024-01-24 13:58:09,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/checkm_input GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/checkm_result
[2024-01-24 13:58:39,438] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:39,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:39,459] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:39,460] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:39,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:58:39,460] [INFO] Task started: Blastn
[2024-01-24 13:58:39,460] [INFO] Running command: blastn -query GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2051819a-a505-4a3f-bede-688499d95709/dqc_reference/reference_markers_gtdb.fasta -out GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:40,659] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:40,663] [INFO] Selected 27 target genomes.
[2024-01-24 13:58:40,664] [INFO] Target genome list was writen to GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:40,723] [INFO] Task started: fastANI
[2024-01-24 13:58:40,724] [INFO] Running command: fastANI --query /var/lib/cwl/stga48b7d0a-496c-4ad4-ac93-59a63420e5f5/GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna.gz --refList GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:54,554] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:54,557] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:54,558] [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_000735045.1	s__Ferrovum myxofaciens	100.0	754	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ferrovaceae;g__Ferrovum	95.0	98.82	98.23	0.87	0.85	7	conclusive
GCA_010435995.1	s__Ferrovum sp010435995	78.3606	155	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ferrovaceae;g__Ferrovum	95.0	99.83	99.83	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:54,560] [INFO] GTDB search result was written to GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:54,560] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:54,563] [INFO] DFAST_QC result json was written to GCF_000735045.1_Fv_myxofaciens_P3G_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:58:54,563] [INFO] DFAST_QC completed!
[2024-01-24 13:58:54,563] [INFO] Total running time: 0h1m12s