[2024-01-24 13:32:15,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:15,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:15,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fe9cff6-3501-4086-bbfd-d41a4026c290/dqc_reference
[2024-01-24 13:32:16,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:16,817] [INFO] Task started: Prodigal
[2024-01-24 13:32:16,817] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f0303ef-97de-4679-bf8b-bff2b33eebe9/GCF_004365815.1_ASM436581v1_genomic.fna.gz | prodigal -d GCF_004365815.1_ASM436581v1_genomic.fna/cds.fna -a GCF_004365815.1_ASM436581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:22,117] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:22,118] [INFO] Task started: HMMsearch
[2024-01-24 13:32:22,118] [INFO] Running command: hmmsearch --tblout GCF_004365815.1_ASM436581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fe9cff6-3501-4086-bbfd-d41a4026c290/dqc_reference/reference_markers.hmm GCF_004365815.1_ASM436581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:22,345] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:22,346] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f0303ef-97de-4679-bf8b-bff2b33eebe9/GCF_004365815.1_ASM436581v1_genomic.fna.gz]
[2024-01-24 13:32:22,374] [INFO] Query marker FASTA was written to GCF_004365815.1_ASM436581v1_genomic.fna/markers.fasta
[2024-01-24 13:32:22,374] [INFO] Task started: Blastn
[2024-01-24 13:32:22,375] [INFO] Running command: blastn -query GCF_004365815.1_ASM436581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fe9cff6-3501-4086-bbfd-d41a4026c290/dqc_reference/reference_markers.fasta -out GCF_004365815.1_ASM436581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:23,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:23,007] [INFO] Selected 26 target genomes.
[2024-01-24 13:32:23,008] [INFO] Target genome list was writen to GCF_004365815.1_ASM436581v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:23,039] [INFO] Task started: fastANI
[2024-01-24 13:32:23,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f0303ef-97de-4679-bf8b-bff2b33eebe9/GCF_004365815.1_ASM436581v1_genomic.fna.gz --refList GCF_004365815.1_ASM436581v1_genomic.fna/target_genomes.txt --output GCF_004365815.1_ASM436581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:33,825] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:33,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fe9cff6-3501-4086-bbfd-d41a4026c290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:33,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fe9cff6-3501-4086-bbfd-d41a4026c290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:33,832] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:33,832] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:33,832] [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
Breznakia blatticola	strain=DSM 28867	GCA_004365815.1	1754012	1754012	type	True	100.0	769	772	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:32:33,834] [INFO] DFAST Taxonomy check result was written to GCF_004365815.1_ASM436581v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:33,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:33,836] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:33,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fe9cff6-3501-4086-bbfd-d41a4026c290/dqc_reference/checkm_data
[2024-01-24 13:32:33,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:33,868] [INFO] Task started: CheckM
[2024-01-24 13:32:33,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365815.1_ASM436581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365815.1_ASM436581v1_genomic.fna/checkm_input GCF_004365815.1_ASM436581v1_genomic.fna/checkm_result
[2024-01-24 13:32:57,640] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:57,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:57,667] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:57,667] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:57,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365815.1_ASM436581v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:57,668] [INFO] Task started: Blastn
[2024-01-24 13:32:57,668] [INFO] Running command: blastn -query GCF_004365815.1_ASM436581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fe9cff6-3501-4086-bbfd-d41a4026c290/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365815.1_ASM436581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:58,556] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:58,560] [INFO] Selected 21 target genomes.
[2024-01-24 13:32:58,560] [INFO] Target genome list was writen to GCF_004365815.1_ASM436581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:58,593] [INFO] Task started: fastANI
[2024-01-24 13:32:58,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f0303ef-97de-4679-bf8b-bff2b33eebe9/GCF_004365815.1_ASM436581v1_genomic.fna.gz --refList GCF_004365815.1_ASM436581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365815.1_ASM436581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:06,880] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:06,884] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:06,884] [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_004365815.1	s__Breznakia blatticola	100.0	769	772	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Breznakia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001695645.1	s__Breznakia sp001695645	83.3953	437	772	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Breznakia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395785.1	s__Amedibacterium sp904395785	76.84	54	772	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:06,886] [INFO] GTDB search result was written to GCF_004365815.1_ASM436581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:06,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:06,888] [INFO] DFAST_QC result json was written to GCF_004365815.1_ASM436581v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:06,888] [INFO] DFAST_QC completed!
[2024-01-24 13:33:06,888] [INFO] Total running time: 0h0m51s