[2024-01-24 14:23:17,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:17,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:17,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5a8479a-455a-4506-9f67-38dc01c96584/dqc_reference
[2024-01-24 14:23:18,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:18,764] [INFO] Task started: Prodigal
[2024-01-24 14:23:18,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg35fa652c-c4a3-407e-959e-4d854b0dcab4/GCF_003217555.1_ASM321755v1_genomic.fna.gz | prodigal -d GCF_003217555.1_ASM321755v1_genomic.fna/cds.fna -a GCF_003217555.1_ASM321755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:29,451] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:29,451] [INFO] Task started: HMMsearch
[2024-01-24 14:23:29,451] [INFO] Running command: hmmsearch --tblout GCF_003217555.1_ASM321755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5a8479a-455a-4506-9f67-38dc01c96584/dqc_reference/reference_markers.hmm GCF_003217555.1_ASM321755v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:29,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:29,888] [INFO] Found 6/6 markers.
[2024-01-24 14:23:29,941] [INFO] Query marker FASTA was written to GCF_003217555.1_ASM321755v1_genomic.fna/markers.fasta
[2024-01-24 14:23:29,942] [INFO] Task started: Blastn
[2024-01-24 14:23:29,942] [INFO] Running command: blastn -query GCF_003217555.1_ASM321755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5a8479a-455a-4506-9f67-38dc01c96584/dqc_reference/reference_markers.fasta -out GCF_003217555.1_ASM321755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:30,639] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:30,658] [INFO] Selected 19 target genomes.
[2024-01-24 14:23:30,659] [INFO] Target genome list was writen to GCF_003217555.1_ASM321755v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:30,676] [INFO] Task started: fastANI
[2024-01-24 14:23:30,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg35fa652c-c4a3-407e-959e-4d854b0dcab4/GCF_003217555.1_ASM321755v1_genomic.fna.gz --refList GCF_003217555.1_ASM321755v1_genomic.fna/target_genomes.txt --output GCF_003217555.1_ASM321755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:50,261] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:50,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5a8479a-455a-4506-9f67-38dc01c96584/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:50,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5a8479a-455a-4506-9f67-38dc01c96584/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:50,269] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:50,269] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:50,269] [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
Aneurinibacillus soli	strain=CECT 8566	GCA_003217555.1	1500254	1500254	type	True	100.0	1313	1319	95	conclusive
Aneurinibacillus soli	strain=CB4	GCA_002355375.1	1500254	1500254	type	True	99.996	1319	1319	95	conclusive
Aneurinibacillus migulanus	strain=NCTC 7096	GCA_000878905.1	47500	47500	type	True	78.1167	199	1319	95	below_threshold
Aneurinibacillus migulanus	strain=NBRC 15520	GCA_006539965.1	47500	47500	type	True	77.8931	189	1319	95	below_threshold
Aneurinibacillus thermoaerophilus	strain=L 420-91	GCA_900099925.1	143495	143495	type	True	77.3278	168	1319	95	below_threshold
Brevibacillus brevis	strain=NRRL NRS-604	GCA_003012835.1	1393	1393	suspected-type	True	76.5733	50	1319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:50,270] [INFO] DFAST Taxonomy check result was written to GCF_003217555.1_ASM321755v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:50,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:50,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:50,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5a8479a-455a-4506-9f67-38dc01c96584/dqc_reference/checkm_data
[2024-01-24 14:23:50,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:50,316] [INFO] Task started: CheckM
[2024-01-24 14:23:50,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217555.1_ASM321755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217555.1_ASM321755v1_genomic.fna/checkm_input GCF_003217555.1_ASM321755v1_genomic.fna/checkm_result
[2024-01-24 14:24:27,817] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:27,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:27,839] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:27,840] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:27,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217555.1_ASM321755v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:27,841] [INFO] Task started: Blastn
[2024-01-24 14:24:27,841] [INFO] Running command: blastn -query GCF_003217555.1_ASM321755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5a8479a-455a-4506-9f67-38dc01c96584/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217555.1_ASM321755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:28,576] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:28,579] [INFO] Selected 24 target genomes.
[2024-01-24 14:24:28,579] [INFO] Target genome list was writen to GCF_003217555.1_ASM321755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:28,596] [INFO] Task started: fastANI
[2024-01-24 14:24:28,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg35fa652c-c4a3-407e-959e-4d854b0dcab4/GCF_003217555.1_ASM321755v1_genomic.fna.gz --refList GCF_003217555.1_ASM321755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217555.1_ASM321755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:51,129] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:51,140] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:51,140] [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_002355375.1	s__Aneurinibacillus soli	99.996	1319	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001274715.1	s__Aneurinibacillus migulanus	78.0542	198	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.46	98.76	0.96	0.91	8	-
GCF_007991215.1	s__Aneurinibacillus danicus	77.4932	188	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.16	99.16	0.84	0.84	2	-
GCF_900099925.1	s__Aneurinibacillus thermoaerophilus	77.3278	168	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.68	99.68	0.95	0.95	2	-
GCF_900637055.1	s__Brevibacillus brevis	76.8693	50	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:51,142] [INFO] GTDB search result was written to GCF_003217555.1_ASM321755v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:51,143] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:51,145] [INFO] DFAST_QC result json was written to GCF_003217555.1_ASM321755v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:51,145] [INFO] DFAST_QC completed!
[2024-01-24 14:24:51,146] [INFO] Total running time: 0h1m34s