[2024-01-24 14:06:17,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:17,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:17,925] [INFO] DQC Reference Directory: /var/lib/cwl/stgbeac0f3a-f67e-4798-a5a0-9d5ff49bd013/dqc_reference
[2024-01-24 14:06:19,304] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:19,305] [INFO] Task started: Prodigal
[2024-01-24 14:06:19,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dc31c54-08f0-4336-929f-5ffdd6a8335d/GCF_002844535.1_ASM284453v1_genomic.fna.gz | prodigal -d GCF_002844535.1_ASM284453v1_genomic.fna/cds.fna -a GCF_002844535.1_ASM284453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:25,977] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:25,978] [INFO] Task started: HMMsearch
[2024-01-24 14:06:25,978] [INFO] Running command: hmmsearch --tblout GCF_002844535.1_ASM284453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbeac0f3a-f67e-4798-a5a0-9d5ff49bd013/dqc_reference/reference_markers.hmm GCF_002844535.1_ASM284453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:26,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:26,282] [INFO] Found 6/6 markers.
[2024-01-24 14:06:26,310] [INFO] Query marker FASTA was written to GCF_002844535.1_ASM284453v1_genomic.fna/markers.fasta
[2024-01-24 14:06:26,310] [INFO] Task started: Blastn
[2024-01-24 14:06:26,310] [INFO] Running command: blastn -query GCF_002844535.1_ASM284453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeac0f3a-f67e-4798-a5a0-9d5ff49bd013/dqc_reference/reference_markers.fasta -out GCF_002844535.1_ASM284453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:26,951] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:26,954] [INFO] Selected 27 target genomes.
[2024-01-24 14:06:26,955] [INFO] Target genome list was writen to GCF_002844535.1_ASM284453v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:27,096] [INFO] Task started: fastANI
[2024-01-24 14:06:27,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc31c54-08f0-4336-929f-5ffdd6a8335d/GCF_002844535.1_ASM284453v1_genomic.fna.gz --refList GCF_002844535.1_ASM284453v1_genomic.fna/target_genomes.txt --output GCF_002844535.1_ASM284453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:45,407] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:45,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbeac0f3a-f67e-4798-a5a0-9d5ff49bd013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:45,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbeac0f3a-f67e-4798-a5a0-9d5ff49bd013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:45,413] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:45,414] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:45,414] [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
Halalkalibacillus sediminis	strain=B3227	GCA_002844535.1	2018042	2018042	type	True	100.0	949	950	95	conclusive
Alkalibacillus haloalkaliphilus	strain=NBRC 103110	GCA_007991275.1	94136	94136	type	True	77.4038	110	950	95	below_threshold
Alkalibacillus almallahensis	strain=CECT 8373	GCA_011761495.1	1379154	1379154	type	True	77.0783	84	950	95	below_threshold
Piscibacillus halophilus	strain=DSM 21633	GCA_900110685.1	571933	571933	type	True	76.9657	113	950	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:45,415] [INFO] DFAST Taxonomy check result was written to GCF_002844535.1_ASM284453v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:45,416] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:45,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:45,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbeac0f3a-f67e-4798-a5a0-9d5ff49bd013/dqc_reference/checkm_data
[2024-01-24 14:06:45,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:45,453] [INFO] Task started: CheckM
[2024-01-24 14:06:45,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002844535.1_ASM284453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002844535.1_ASM284453v1_genomic.fna/checkm_input GCF_002844535.1_ASM284453v1_genomic.fna/checkm_result
[2024-01-24 14:07:12,390] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:12,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:12,413] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:12,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:12,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002844535.1_ASM284453v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:12,414] [INFO] Task started: Blastn
[2024-01-24 14:07:12,414] [INFO] Running command: blastn -query GCF_002844535.1_ASM284453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeac0f3a-f67e-4798-a5a0-9d5ff49bd013/dqc_reference/reference_markers_gtdb.fasta -out GCF_002844535.1_ASM284453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:13,170] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:13,175] [INFO] Selected 22 target genomes.
[2024-01-24 14:07:13,176] [INFO] Target genome list was writen to GCF_002844535.1_ASM284453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:13,202] [INFO] Task started: fastANI
[2024-01-24 14:07:13,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc31c54-08f0-4336-929f-5ffdd6a8335d/GCF_002844535.1_ASM284453v1_genomic.fna.gz --refList GCF_002844535.1_ASM284453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002844535.1_ASM284453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:26,681] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:26,692] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:26,692] [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_002844535.1	s__Halalkalibacillus_A sediminis	100.0	949	950	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Halalkalibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007991275.1	s__Alkalibacillus haloalkaliphilus	77.4038	110	950	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	77.3351	93	950	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_011761495.1	s__Alkalibacillus almallahensis	77.0783	84	950	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	76.982	114	950	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_900103915.1	s__Tenuibacillus multivorans	76.8348	96	950	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Tenuibacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:26,694] [INFO] GTDB search result was written to GCF_002844535.1_ASM284453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:26,695] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:26,697] [INFO] DFAST_QC result json was written to GCF_002844535.1_ASM284453v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:26,698] [INFO] DFAST_QC completed!
[2024-01-24 14:07:26,698] [INFO] Total running time: 0h1m9s