[2024-01-24 13:49:13,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:13,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:13,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ee8c360-54bf-4a44-94a2-1be7fc936594/dqc_reference
[2024-01-24 13:49:14,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:14,842] [INFO] Task started: Prodigal
[2024-01-24 13:49:14,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e230fc8-1bdf-4b51-84d8-12070e7b4b57/GCF_030814225.1_ASM3081422v1_genomic.fna.gz | prodigal -d GCF_030814225.1_ASM3081422v1_genomic.fna/cds.fna -a GCF_030814225.1_ASM3081422v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:23,280] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:23,280] [INFO] Task started: HMMsearch
[2024-01-24 13:49:23,280] [INFO] Running command: hmmsearch --tblout GCF_030814225.1_ASM3081422v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ee8c360-54bf-4a44-94a2-1be7fc936594/dqc_reference/reference_markers.hmm GCF_030814225.1_ASM3081422v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:23,608] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:23,610] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3e230fc8-1bdf-4b51-84d8-12070e7b4b57/GCF_030814225.1_ASM3081422v1_genomic.fna.gz]
[2024-01-24 13:49:23,661] [INFO] Query marker FASTA was written to GCF_030814225.1_ASM3081422v1_genomic.fna/markers.fasta
[2024-01-24 13:49:23,661] [INFO] Task started: Blastn
[2024-01-24 13:49:23,662] [INFO] Running command: blastn -query GCF_030814225.1_ASM3081422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ee8c360-54bf-4a44-94a2-1be7fc936594/dqc_reference/reference_markers.fasta -out GCF_030814225.1_ASM3081422v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:24,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:24,291] [INFO] Selected 27 target genomes.
[2024-01-24 13:49:24,292] [INFO] Target genome list was writen to GCF_030814225.1_ASM3081422v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:24,386] [INFO] Task started: fastANI
[2024-01-24 13:49:24,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e230fc8-1bdf-4b51-84d8-12070e7b4b57/GCF_030814225.1_ASM3081422v1_genomic.fna.gz --refList GCF_030814225.1_ASM3081422v1_genomic.fna/target_genomes.txt --output GCF_030814225.1_ASM3081422v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:35,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:35,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ee8c360-54bf-4a44-94a2-1be7fc936594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:35,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ee8c360-54bf-4a44-94a2-1be7fc936594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:35,797] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:35,797] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:35,798] [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	78.1271	187	1423	95	below_threshold
Amedibacterium intestinale	strain=9CBEGH2	GCA_010537335.1	2583452	2583452	type	True	76.9566	52	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:35,799] [INFO] DFAST Taxonomy check result was written to GCF_030814225.1_ASM3081422v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:35,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:35,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:35,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ee8c360-54bf-4a44-94a2-1be7fc936594/dqc_reference/checkm_data
[2024-01-24 13:49:35,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:35,842] [INFO] Task started: CheckM
[2024-01-24 13:49:35,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814225.1_ASM3081422v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814225.1_ASM3081422v1_genomic.fna/checkm_input GCF_030814225.1_ASM3081422v1_genomic.fna/checkm_result
[2024-01-24 13:50:08,070] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:08,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,100] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:08,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:08,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814225.1_ASM3081422v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:08,101] [INFO] Task started: Blastn
[2024-01-24 13:50:08,101] [INFO] Running command: blastn -query GCF_030814225.1_ASM3081422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ee8c360-54bf-4a44-94a2-1be7fc936594/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814225.1_ASM3081422v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:09,012] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:09,017] [INFO] Selected 26 target genomes.
[2024-01-24 13:50:09,017] [INFO] Target genome list was writen to GCF_030814225.1_ASM3081422v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:09,043] [INFO] Task started: fastANI
[2024-01-24 13:50:09,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e230fc8-1bdf-4b51-84d8-12070e7b4b57/GCF_030814225.1_ASM3081422v1_genomic.fna.gz --refList GCF_030814225.1_ASM3081422v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814225.1_ASM3081422v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:17,969] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:17,976] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:17,977] [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	78.1271	187	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Breznakia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001695645.1	s__Breznakia sp001695645	77.9067	158	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Breznakia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010537335.1	s__Amedibacterium intestinale	76.9566	52	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	98.96	98.46	0.86	0.72	14	-
GCA_904395785.1	s__Amedibacterium sp904395785	76.584	53	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455285.1	s__Stoquefichus massiliensis	75.6246	66	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_000508865.1	s__Erysipelatoclostridium sp000508865	74.9978	53	1423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,978] [INFO] GTDB search result was written to GCF_030814225.1_ASM3081422v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:17,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:17,982] [INFO] DFAST_QC result json was written to GCF_030814225.1_ASM3081422v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:17,982] [INFO] DFAST_QC completed!
[2024-01-24 13:50:17,982] [INFO] Total running time: 0h1m5s