[2024-01-25 18:03:35,608] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:35,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:35,609] [INFO] DQC Reference Directory: /var/lib/cwl/stga3c6cfbe-1247-4684-ad33-81dac9b15120/dqc_reference
[2024-01-25 18:03:36,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:36,777] [INFO] Task started: Prodigal
[2024-01-25 18:03:36,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fa8d12b-a968-4fcc-bdd7-97a1102d0ced/GCF_000425005.1_ASM42500v1_genomic.fna.gz | prodigal -d GCF_000425005.1_ASM42500v1_genomic.fna/cds.fna -a GCF_000425005.1_ASM42500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:40,724] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:40,724] [INFO] Task started: HMMsearch
[2024-01-25 18:03:40,724] [INFO] Running command: hmmsearch --tblout GCF_000425005.1_ASM42500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3c6cfbe-1247-4684-ad33-81dac9b15120/dqc_reference/reference_markers.hmm GCF_000425005.1_ASM42500v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:40,926] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:40,927] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8fa8d12b-a968-4fcc-bdd7-97a1102d0ced/GCF_000425005.1_ASM42500v1_genomic.fna.gz]
[2024-01-25 18:03:40,953] [INFO] Query marker FASTA was written to GCF_000425005.1_ASM42500v1_genomic.fna/markers.fasta
[2024-01-25 18:03:40,953] [INFO] Task started: Blastn
[2024-01-25 18:03:40,953] [INFO] Running command: blastn -query GCF_000425005.1_ASM42500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3c6cfbe-1247-4684-ad33-81dac9b15120/dqc_reference/reference_markers.fasta -out GCF_000425005.1_ASM42500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:41,502] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:41,506] [INFO] Selected 21 target genomes.
[2024-01-25 18:03:41,506] [INFO] Target genome list was writen to GCF_000425005.1_ASM42500v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:41,514] [INFO] Task started: fastANI
[2024-01-25 18:03:41,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fa8d12b-a968-4fcc-bdd7-97a1102d0ced/GCF_000425005.1_ASM42500v1_genomic.fna.gz --refList GCF_000425005.1_ASM42500v1_genomic.fna/target_genomes.txt --output GCF_000425005.1_ASM42500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:52,000] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:52,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3c6cfbe-1247-4684-ad33-81dac9b15120/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:52,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3c6cfbe-1247-4684-ad33-81dac9b15120/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:52,004] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:52,004] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:52,004] [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
Solobacterium moorei	strain=DSM 22971	GCA_000425005.1	102148	102148	type	True	100.0	685	690	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 18:03:52,005] [INFO] DFAST Taxonomy check result was written to GCF_000425005.1_ASM42500v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:52,006] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:52,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:52,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3c6cfbe-1247-4684-ad33-81dac9b15120/dqc_reference/checkm_data
[2024-01-25 18:03:52,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:52,033] [INFO] Task started: CheckM
[2024-01-25 18:03:52,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425005.1_ASM42500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425005.1_ASM42500v1_genomic.fna/checkm_input GCF_000425005.1_ASM42500v1_genomic.fna/checkm_result
[2024-01-25 18:04:09,970] [INFO] Task succeeded: CheckM
[2024-01-25 18:04:09,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:04:09,986] [INFO] ===== Completeness check finished =====
[2024-01-25 18:04:09,987] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:04:09,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425005.1_ASM42500v1_genomic.fna/markers.fasta)
[2024-01-25 18:04:09,987] [INFO] Task started: Blastn
[2024-01-25 18:04:09,987] [INFO] Running command: blastn -query GCF_000425005.1_ASM42500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3c6cfbe-1247-4684-ad33-81dac9b15120/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425005.1_ASM42500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:10,721] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:10,724] [INFO] Selected 11 target genomes.
[2024-01-25 18:04:10,725] [INFO] Target genome list was writen to GCF_000425005.1_ASM42500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:04:10,733] [INFO] Task started: fastANI
[2024-01-25 18:04:10,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fa8d12b-a968-4fcc-bdd7-97a1102d0ced/GCF_000425005.1_ASM42500v1_genomic.fna.gz --refList GCF_000425005.1_ASM42500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425005.1_ASM42500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:15,246] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:15,251] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:15,251] [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_000425005.1	s__Bulleidia moorei	100.0	685	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.48	97.26	0.79	0.78	5	conclusive
GCA_900554555.1	s__Bulleidia sp900554555	90.9259	222	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015256775.1	s__Bulleidia sp015256775	90.7651	450	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	96.17	95.24	0.85	0.75	15	-
GCA_015256455.1	s__Bulleidia sp015256455	89.1511	405	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.43	97.43	0.79	0.79	2	-
GCA_014610835.1	s__Bulleidia sp900539965	77.0896	64	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.38	98.19	0.87	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:15,600] [INFO] GTDB search result was written to GCF_000425005.1_ASM42500v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:15,601] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:15,603] [INFO] DFAST_QC result json was written to GCF_000425005.1_ASM42500v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:15,603] [INFO] DFAST_QC completed!
[2024-01-25 18:04:15,603] [INFO] Total running time: 0h0m40s