[2024-01-25 19:07:05,806] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:05,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:05,811] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb0fc6ec-c99d-40a8-8456-bb370b2b67f5/dqc_reference
[2024-01-25 19:07:06,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:06,968] [INFO] Task started: Prodigal
[2024-01-25 19:07:06,968] [INFO] Running command: gunzip -c /var/lib/cwl/stge19307a1-b9a1-4ed2-b9cd-bce1fbedc2f3/GCF_018437265.1_ASM1843726v1_genomic.fna.gz | prodigal -d GCF_018437265.1_ASM1843726v1_genomic.fna/cds.fna -a GCF_018437265.1_ASM1843726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:09,885] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:09,886] [INFO] Task started: HMMsearch
[2024-01-25 19:07:09,886] [INFO] Running command: hmmsearch --tblout GCF_018437265.1_ASM1843726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb0fc6ec-c99d-40a8-8456-bb370b2b67f5/dqc_reference/reference_markers.hmm GCF_018437265.1_ASM1843726v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:10,090] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:10,091] [INFO] Found 6/6 markers.
[2024-01-25 19:07:10,104] [INFO] Query marker FASTA was written to GCF_018437265.1_ASM1843726v1_genomic.fna/markers.fasta
[2024-01-25 19:07:10,105] [INFO] Task started: Blastn
[2024-01-25 19:07:10,105] [INFO] Running command: blastn -query GCF_018437265.1_ASM1843726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb0fc6ec-c99d-40a8-8456-bb370b2b67f5/dqc_reference/reference_markers.fasta -out GCF_018437265.1_ASM1843726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:10,652] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:10,655] [INFO] Selected 13 target genomes.
[2024-01-25 19:07:10,655] [INFO] Target genome list was writen to GCF_018437265.1_ASM1843726v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:10,660] [INFO] Task started: fastANI
[2024-01-25 19:07:10,660] [INFO] Running command: fastANI --query /var/lib/cwl/stge19307a1-b9a1-4ed2-b9cd-bce1fbedc2f3/GCF_018437265.1_ASM1843726v1_genomic.fna.gz --refList GCF_018437265.1_ASM1843726v1_genomic.fna/target_genomes.txt --output GCF_018437265.1_ASM1843726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:14,733] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:14,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb0fc6ec-c99d-40a8-8456-bb370b2b67f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:14,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb0fc6ec-c99d-40a8-8456-bb370b2b67f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:14,741] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:07:14,741] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:14,741] [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
Fructobacillus parabroussonetiae	strain=S1-1	GCA_018437265.1	2713174	2713174	type	True	100.0	397	397	95	conclusive
Fructobacillus papyrifericola	strain=M1-21	GCA_018437235.1	2713172	2713172	type	True	84.1454	298	397	95	below_threshold
Fructobacillus fructosus	strain=NRIC 1058	GCA_001047095.2	1631	1631	type	True	82.1321	210	397	95	below_threshold
Fructobacillus fructosus	strain=KCTC 3544	GCA_000185045.2	1631	1631	type	True	82.0677	206	397	95	below_threshold
Fructobacillus fructosus	strain=DSM 20349	GCA_001438695.1	1631	1631	type	True	81.9297	212	397	95	below_threshold
Fructobacillus durionis	strain=DSM 19113	GCA_900112405.1	283737	283737	type	True	81.41	215	397	95	below_threshold
Fructobacillus papyriferae	strain=M1-10	GCA_018437225.1	2713171	2713171	type	True	81.3427	234	397	95	below_threshold
Fructobacillus broussonetiae	strain=M2-14	GCA_018437275.1	2713173	2713173	type	True	80.6642	189	397	95	below_threshold
Fructobacillus pseudoficulneus	strain=DSM 15468	GCA_900108455.1	220714	220714	type	True	79.4349	131	397	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:14,743] [INFO] DFAST Taxonomy check result was written to GCF_018437265.1_ASM1843726v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:14,743] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:14,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:14,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb0fc6ec-c99d-40a8-8456-bb370b2b67f5/dqc_reference/checkm_data
[2024-01-25 19:07:14,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:14,758] [INFO] Task started: CheckM
[2024-01-25 19:07:14,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018437265.1_ASM1843726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018437265.1_ASM1843726v1_genomic.fna/checkm_input GCF_018437265.1_ASM1843726v1_genomic.fna/checkm_result
[2024-01-25 19:07:29,896] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:29,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:29,910] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:29,911] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:29,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018437265.1_ASM1843726v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:29,911] [INFO] Task started: Blastn
[2024-01-25 19:07:29,911] [INFO] Running command: blastn -query GCF_018437265.1_ASM1843726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb0fc6ec-c99d-40a8-8456-bb370b2b67f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_018437265.1_ASM1843726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:30,651] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:30,653] [INFO] Selected 13 target genomes.
[2024-01-25 19:07:30,653] [INFO] Target genome list was writen to GCF_018437265.1_ASM1843726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:30,662] [INFO] Task started: fastANI
[2024-01-25 19:07:30,662] [INFO] Running command: fastANI --query /var/lib/cwl/stge19307a1-b9a1-4ed2-b9cd-bce1fbedc2f3/GCF_018437265.1_ASM1843726v1_genomic.fna.gz --refList GCF_018437265.1_ASM1843726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018437265.1_ASM1843726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:36,340] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:36,346] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:36,346] [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_018437265.1	s__Fructobacillus sp018437265	100.0	397	397	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018437235.1	s__Fructobacillus sp018437235	84.1454	298	397	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001438695.1	s__Fructobacillus fructosus	81.9297	212	397	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.37	98.18	0.96	0.91	4	-
GCF_900112405.1	s__Fructobacillus durionis	81.41	215	397	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018437225.1	s__Fructobacillus sp018437225	81.3427	234	397	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018437275.1	s__Fructobacillus sp018437275	80.6657	190	397	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001047075.2	s__Fructobacillus ficulneus	79.5135	120	397	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108455.1	s__Fructobacillus pseudoficulneus	79.415	132	397	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:36,348] [INFO] GTDB search result was written to GCF_018437265.1_ASM1843726v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:36,349] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:36,351] [INFO] DFAST_QC result json was written to GCF_018437265.1_ASM1843726v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:36,351] [INFO] DFAST_QC completed!
[2024-01-25 19:07:36,352] [INFO] Total running time: 0h0m31s