[2024-01-25 20:03:35,564] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:35,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:35,565] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa3808d8-d37d-4f94-8017-0e0ca6d41f8c/dqc_reference
[2024-01-25 20:03:36,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:36,709] [INFO] Task started: Prodigal
[2024-01-25 20:03:36,709] [INFO] Running command: gunzip -c /var/lib/cwl/stge4f72e30-73bd-4342-92c7-4e328ad20d5a/GCF_024345205.1_ASM2434520v1_genomic.fna.gz | prodigal -d GCF_024345205.1_ASM2434520v1_genomic.fna/cds.fna -a GCF_024345205.1_ASM2434520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:42,090] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:42,090] [INFO] Task started: HMMsearch
[2024-01-25 20:03:42,090] [INFO] Running command: hmmsearch --tblout GCF_024345205.1_ASM2434520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa3808d8-d37d-4f94-8017-0e0ca6d41f8c/dqc_reference/reference_markers.hmm GCF_024345205.1_ASM2434520v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:42,304] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:42,305] [INFO] Found 6/6 markers.
[2024-01-25 20:03:42,326] [INFO] Query marker FASTA was written to GCF_024345205.1_ASM2434520v1_genomic.fna/markers.fasta
[2024-01-25 20:03:42,327] [INFO] Task started: Blastn
[2024-01-25 20:03:42,327] [INFO] Running command: blastn -query GCF_024345205.1_ASM2434520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa3808d8-d37d-4f94-8017-0e0ca6d41f8c/dqc_reference/reference_markers.fasta -out GCF_024345205.1_ASM2434520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:42,874] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:42,876] [INFO] Selected 25 target genomes.
[2024-01-25 20:03:42,876] [INFO] Target genome list was writen to GCF_024345205.1_ASM2434520v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:42,911] [INFO] Task started: fastANI
[2024-01-25 20:03:42,911] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f72e30-73bd-4342-92c7-4e328ad20d5a/GCF_024345205.1_ASM2434520v1_genomic.fna.gz --refList GCF_024345205.1_ASM2434520v1_genomic.fna/target_genomes.txt --output GCF_024345205.1_ASM2434520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:54,924] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:54,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa3808d8-d37d-4f94-8017-0e0ca6d41f8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:54,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa3808d8-d37d-4f94-8017-0e0ca6d41f8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:54,929] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:03:54,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:03:54,929] [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
Lapidilactobacillus achengensis	strain=247-4	GCA_003946655.1	2486000	2486000	type	True	87.2188	510	823	95	below_threshold
Lapidilactobacillus gannanensis	strain=143-1	GCA_003946675.1	2486002	2486002	type	True	81.0381	147	823	95	below_threshold
Lapidilactobacillus bayanensis	strain=54-5	GCA_003946695.1	2485998	2485998	type	True	78.0474	77	823	95	below_threshold
Lapidilactobacillus mulanensis	strain=143-6	GCA_003946215.1	2485999	2485999	type	True	78.0452	91	823	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:54,931] [INFO] DFAST Taxonomy check result was written to GCF_024345205.1_ASM2434520v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:54,931] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:54,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:54,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa3808d8-d37d-4f94-8017-0e0ca6d41f8c/dqc_reference/checkm_data
[2024-01-25 20:03:54,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:54,960] [INFO] Task started: CheckM
[2024-01-25 20:03:54,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024345205.1_ASM2434520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024345205.1_ASM2434520v1_genomic.fna/checkm_input GCF_024345205.1_ASM2434520v1_genomic.fna/checkm_result
[2024-01-25 20:04:16,316] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:16,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:16,332] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:16,332] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:16,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024345205.1_ASM2434520v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:16,332] [INFO] Task started: Blastn
[2024-01-25 20:04:16,332] [INFO] Running command: blastn -query GCF_024345205.1_ASM2434520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa3808d8-d37d-4f94-8017-0e0ca6d41f8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024345205.1_ASM2434520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:17,084] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:17,089] [INFO] Selected 25 target genomes.
[2024-01-25 20:04:17,089] [INFO] Target genome list was writen to GCF_024345205.1_ASM2434520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:17,118] [INFO] Task started: fastANI
[2024-01-25 20:04:17,118] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f72e30-73bd-4342-92c7-4e328ad20d5a/GCF_024345205.1_ASM2434520v1_genomic.fna.gz --refList GCF_024345205.1_ASM2434520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024345205.1_ASM2434520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:30,131] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:30,134] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:04:30,135] [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_003946655.1	s__Lapidilactobacillus achengensis	87.2228	512	823	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946675.1	s__Lapidilactobacillus gannanensis	81.0381	147	823	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946695.1	s__Lapidilactobacillus bayanensis	78.0474	77	823	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946215.1	s__Lapidilactobacillus mulanensis	78.0452	91	823	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lapidilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:30,136] [INFO] GTDB search result was written to GCF_024345205.1_ASM2434520v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:30,136] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:30,138] [INFO] DFAST_QC result json was written to GCF_024345205.1_ASM2434520v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:30,138] [INFO] DFAST_QC completed!
[2024-01-25 20:04:30,139] [INFO] Total running time: 0h0m55s