[2024-01-24 13:18:33,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,234] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,234] [INFO] DQC Reference Directory: /var/lib/cwl/stgb46bff3a-1881-4fd5-8c18-f6083f0c3cfd/dqc_reference
[2024-01-24 13:18:34,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,605] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b583197-b31d-4564-91d0-24827d7cf888/GCF_000428925.1_ASM42892v1_genomic.fna.gz | prodigal -d GCF_000428925.1_ASM42892v1_genomic.fna/cds.fna -a GCF_000428925.1_ASM42892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:41,646] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:41,646] [INFO] Task started: HMMsearch
[2024-01-24 13:18:41,646] [INFO] Running command: hmmsearch --tblout GCF_000428925.1_ASM42892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb46bff3a-1881-4fd5-8c18-f6083f0c3cfd/dqc_reference/reference_markers.hmm GCF_000428925.1_ASM42892v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:41,930] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:41,931] [INFO] Found 6/6 markers.
[2024-01-24 13:18:41,963] [INFO] Query marker FASTA was written to GCF_000428925.1_ASM42892v1_genomic.fna/markers.fasta
[2024-01-24 13:18:41,964] [INFO] Task started: Blastn
[2024-01-24 13:18:41,964] [INFO] Running command: blastn -query GCF_000428925.1_ASM42892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb46bff3a-1881-4fd5-8c18-f6083f0c3cfd/dqc_reference/reference_markers.fasta -out GCF_000428925.1_ASM42892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:42,599] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:42,602] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:42,602] [INFO] Target genome list was writen to GCF_000428925.1_ASM42892v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:42,609] [INFO] Task started: fastANI
[2024-01-24 13:18:42,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b583197-b31d-4564-91d0-24827d7cf888/GCF_000428925.1_ASM42892v1_genomic.fna.gz --refList GCF_000428925.1_ASM42892v1_genomic.fna/target_genomes.txt --output GCF_000428925.1_ASM42892v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:48,767] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:48,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb46bff3a-1881-4fd5-8c18-f6083f0c3cfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:48,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb46bff3a-1881-4fd5-8c18-f6083f0c3cfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:48,775] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:48,775] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:48,776] [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
Furfurilactobacillus rossiae	strain=DSM 15814	GCA_000428925.1	231049	231049	type	True	100.0	933	938	95	conclusive
Furfurilactobacillus rossiae	strain=DSM 15814	GCA_000277855.1	231049	231049	type	True	99.9838	918	938	95	conclusive
Furfurilactobacillus rossiae	strain=DSM 15814	GCA_001435135.1	231049	231049	type	True	99.9653	912	938	95	conclusive
Furfurilactobacillus milii	strain=FUA3430	GCA_021654115.1	2888272	2888272	type	True	93.0307	767	938	95	below_threshold
Furfurilactobacillus siliginis	strain=DSM 22696	GCA_001437435.1	348151	348151	type	True	79.4461	183	938	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	77.3506	50	938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:48,777] [INFO] DFAST Taxonomy check result was written to GCF_000428925.1_ASM42892v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:48,778] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:48,778] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:48,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb46bff3a-1881-4fd5-8c18-f6083f0c3cfd/dqc_reference/checkm_data
[2024-01-24 13:18:48,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:48,809] [INFO] Task started: CheckM
[2024-01-24 13:18:48,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428925.1_ASM42892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428925.1_ASM42892v1_genomic.fna/checkm_input GCF_000428925.1_ASM42892v1_genomic.fna/checkm_result
[2024-01-24 13:19:17,105] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:17,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:17,127] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:17,127] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:17,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428925.1_ASM42892v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:17,128] [INFO] Task started: Blastn
[2024-01-24 13:19:17,128] [INFO] Running command: blastn -query GCF_000428925.1_ASM42892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb46bff3a-1881-4fd5-8c18-f6083f0c3cfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428925.1_ASM42892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:17,954] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:17,957] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:17,957] [INFO] Target genome list was writen to GCF_000428925.1_ASM42892v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:17,972] [INFO] Task started: fastANI
[2024-01-24 13:19:17,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b583197-b31d-4564-91d0-24827d7cf888/GCF_000428925.1_ASM42892v1_genomic.fna.gz --refList GCF_000428925.1_ASM42892v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428925.1_ASM42892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:25,146] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:25,160] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:25,161] [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_000428925.1	s__Furfurilactobacillus rossiae	100.0	933	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	99.59	97.96	0.97	0.87	6	conclusive
GCF_009864005.1	s__Furfurilactobacillus rossiae_B	92.9308	766	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394045.1	s__Furfurilactobacillus rossiae_A	92.8622	741	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	97.68	95.37	0.95	0.90	3	-
GCA_003482405.1	s__Furfurilactobacillus sp003482405	81.2631	320	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	99.38	99.38	0.79	0.79	2	-
GCF_001437435.1	s__Furfurilactobacillus siliginis	79.4461	183	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	77.3506	50	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,162] [INFO] GTDB search result was written to GCF_000428925.1_ASM42892v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:25,163] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:25,167] [INFO] DFAST_QC result json was written to GCF_000428925.1_ASM42892v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:25,168] [INFO] DFAST_QC completed!
[2024-01-24 13:19:25,168] [INFO] Total running time: 0h0m52s