[2024-01-24 15:02:03,504] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:03,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:03,507] [INFO] DQC Reference Directory: /var/lib/cwl/stgc24c1f63-b9ce-4391-9d9a-30c832609233/dqc_reference
[2024-01-24 15:02:06,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:06,127] [INFO] Task started: Prodigal
[2024-01-24 15:02:06,128] [INFO] Running command: gunzip -c /var/lib/cwl/stg81f6884e-89eb-4673-b2b9-fe8af12bbe99/GCF_018138385.1_ASM1813838v1_genomic.fna.gz | prodigal -d GCF_018138385.1_ASM1813838v1_genomic.fna/cds.fna -a GCF_018138385.1_ASM1813838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:11,609] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:11,610] [INFO] Task started: HMMsearch
[2024-01-24 15:02:11,610] [INFO] Running command: hmmsearch --tblout GCF_018138385.1_ASM1813838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc24c1f63-b9ce-4391-9d9a-30c832609233/dqc_reference/reference_markers.hmm GCF_018138385.1_ASM1813838v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:11,978] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:11,980] [INFO] Found 6/6 markers.
[2024-01-24 15:02:12,010] [INFO] Query marker FASTA was written to GCF_018138385.1_ASM1813838v1_genomic.fna/markers.fasta
[2024-01-24 15:02:12,011] [INFO] Task started: Blastn
[2024-01-24 15:02:12,012] [INFO] Running command: blastn -query GCF_018138385.1_ASM1813838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc24c1f63-b9ce-4391-9d9a-30c832609233/dqc_reference/reference_markers.fasta -out GCF_018138385.1_ASM1813838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:15,460] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:15,467] [INFO] Selected 18 target genomes.
[2024-01-24 15:02:15,468] [INFO] Target genome list was writen to GCF_018138385.1_ASM1813838v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:15,518] [INFO] Task started: fastANI
[2024-01-24 15:02:15,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg81f6884e-89eb-4673-b2b9-fe8af12bbe99/GCF_018138385.1_ASM1813838v1_genomic.fna.gz --refList GCF_018138385.1_ASM1813838v1_genomic.fna/target_genomes.txt --output GCF_018138385.1_ASM1813838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:26,689] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:26,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc24c1f63-b9ce-4391-9d9a-30c832609233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:26,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc24c1f63-b9ce-4391-9d9a-30c832609233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:26,706] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:26,706] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:26,706] [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
Allobacillus saliphilus	strain=SKP8-2	GCA_018138385.1	2912308	2912308	type	True	100.0	806	816	95	conclusive
Allobacillus salarius	strain=SKP4-8	GCA_007559425.1	1955272	1955272	type	True	94.3143	706	816	95	below_threshold
Allobacillus halotolerans	strain=LMG 24826	GCA_018967645.1	570278	570278	type	True	87.7541	704	816	95	below_threshold
Alkalibacillus aidingensis	strain=YIM 98829	GCA_014595945.1	2747607	2747607	type	True	77.1263	83	816	95	below_threshold
Piscibacillus halophilus	strain=DSM 21633	GCA_900110685.1	571933	571933	type	True	76.8422	85	816	95	below_threshold
Alkalibacillus haloalkaliphilus	strain=NBRC 103110	GCA_007991275.1	94136	94136	type	True	76.6873	87	816	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:26,708] [INFO] DFAST Taxonomy check result was written to GCF_018138385.1_ASM1813838v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:26,709] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:26,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:26,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc24c1f63-b9ce-4391-9d9a-30c832609233/dqc_reference/checkm_data
[2024-01-24 15:02:26,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:26,741] [INFO] Task started: CheckM
[2024-01-24 15:02:26,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018138385.1_ASM1813838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018138385.1_ASM1813838v1_genomic.fna/checkm_input GCF_018138385.1_ASM1813838v1_genomic.fna/checkm_result
[2024-01-24 15:02:51,950] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:51,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:51,974] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:51,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:51,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018138385.1_ASM1813838v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:51,976] [INFO] Task started: Blastn
[2024-01-24 15:02:51,977] [INFO] Running command: blastn -query GCF_018138385.1_ASM1813838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc24c1f63-b9ce-4391-9d9a-30c832609233/dqc_reference/reference_markers_gtdb.fasta -out GCF_018138385.1_ASM1813838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:53,262] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:53,266] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:53,267] [INFO] Target genome list was writen to GCF_018138385.1_ASM1813838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:53,285] [INFO] Task started: fastANI
[2024-01-24 15:02:53,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg81f6884e-89eb-4673-b2b9-fe8af12bbe99/GCF_018138385.1_ASM1813838v1_genomic.fna.gz --refList GCF_018138385.1_ASM1813838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018138385.1_ASM1813838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:04,784] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:04,795] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:04,795] [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_018138385.1	s__Allobacillus sp018138385	100.0	803	816	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007559425.1	s__Allobacillus sp007559425	94.3143	706	816	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018967645.1	s__Allobacillus halotolerans	87.7448	705	816	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	97.75	97.75	0.93	0.93	2	-
GCF_014595945.1	s__Alkalibacillus sp014595945	77.1263	83	816	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110685.1	s__Piscibacillus halophilus	76.8422	85	816	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Piscibacillus	95.0	99.37	99.37	0.93	0.93	2	-
GCF_007991275.1	s__Alkalibacillus haloalkaliphilus	76.6873	87	816	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000269905.1	s__Alkalibacillus haloalkaliphilus_A	76.4199	79	816	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:04,796] [INFO] GTDB search result was written to GCF_018138385.1_ASM1813838v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:04,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:04,799] [INFO] DFAST_QC result json was written to GCF_018138385.1_ASM1813838v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:04,800] [INFO] DFAST_QC completed!
[2024-01-24 15:03:04,800] [INFO] Total running time: 0h1m1s