[2024-01-24 14:05:53,823] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg72c9bf79-04fc-4b7b-b975-d8259a7ffb66/dqc_reference
[2024-01-24 14:05:55,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,223] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,224] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd2c1464-876a-471a-9370-33cc061d2bda/GCF_002583405.1_ASM258340v1_genomic.fna.gz | prodigal -d GCF_002583405.1_ASM258340v1_genomic.fna/cds.fna -a GCF_002583405.1_ASM258340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:01,401] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:01,401] [INFO] Task started: HMMsearch
[2024-01-24 14:06:01,401] [INFO] Running command: hmmsearch --tblout GCF_002583405.1_ASM258340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72c9bf79-04fc-4b7b-b975-d8259a7ffb66/dqc_reference/reference_markers.hmm GCF_002583405.1_ASM258340v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:01,670] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:01,672] [INFO] Found 6/6 markers.
[2024-01-24 14:06:01,700] [INFO] Query marker FASTA was written to GCF_002583405.1_ASM258340v1_genomic.fna/markers.fasta
[2024-01-24 14:06:01,701] [INFO] Task started: Blastn
[2024-01-24 14:06:01,701] [INFO] Running command: blastn -query GCF_002583405.1_ASM258340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72c9bf79-04fc-4b7b-b975-d8259a7ffb66/dqc_reference/reference_markers.fasta -out GCF_002583405.1_ASM258340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:02,335] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:02,344] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:02,345] [INFO] Target genome list was writen to GCF_002583405.1_ASM258340v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:02,352] [INFO] Task started: fastANI
[2024-01-24 14:06:02,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd2c1464-876a-471a-9370-33cc061d2bda/GCF_002583405.1_ASM258340v1_genomic.fna.gz --refList GCF_002583405.1_ASM258340v1_genomic.fna/target_genomes.txt --output GCF_002583405.1_ASM258340v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:10,673] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:10,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72c9bf79-04fc-4b7b-b975-d8259a7ffb66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:10,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72c9bf79-04fc-4b7b-b975-d8259a7ffb66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:10,686] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:10,686] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:10,686] [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
Secundilactobacillus silagincola	strain=IWT5	GCA_002583405.1	1714681	1714681	type	True	100.0	853	854	95	conclusive
Secundilactobacillus yichangensis	strain=F79-211-2	GCA_016861565.1	2799580	2799580	type	True	83.0512	567	854	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	82.9545	513	854	95	below_threshold
Secundilactobacillus mixtipabuli	strain=IWT30	GCA_002217925.1	1435342	1435342	type	True	82.6834	529	854	95	below_threshold
Secundilactobacillus pentosiphilus	strain=IWT25	GCA_002217985.1	1714682	1714682	type	True	82.1188	506	854	95	below_threshold
Secundilactobacillus silagei	strain=IWT126	GCA_002217945.1	1293415	1293415	type	True	81.6007	487	854	95	below_threshold
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	81.5864	475	854	95	below_threshold
Secundilactobacillus silagei	strain=DSM 27022	GCA_004354595.1	1293415	1293415	type	True	81.4725	489	854	95	below_threshold
Secundilactobacillus hailunensis	strain=887-11	GCA_005405185.1	2559923	2559923	type	True	81.2559	491	854	95	below_threshold
Secundilactobacillus folii	strain=CRM56-3	GCA_009720675.1	2678357	2678357	type	True	79.2043	286	854	95	below_threshold
Paucilactobacillus hokkaidonensis	strain=JCM 18461	GCA_001311505.1	1193095	1193095	type	True	79.0485	53	854	95	below_threshold
Lentilactobacillus senioris	strain=JCM 17472	GCA_001312065.1	931534	931534	type	True	77.344	52	854	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	77.2342	71	854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:10,688] [INFO] DFAST Taxonomy check result was written to GCF_002583405.1_ASM258340v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:10,689] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:10,689] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:10,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72c9bf79-04fc-4b7b-b975-d8259a7ffb66/dqc_reference/checkm_data
[2024-01-24 14:06:10,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:10,721] [INFO] Task started: CheckM
[2024-01-24 14:06:10,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002583405.1_ASM258340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002583405.1_ASM258340v1_genomic.fna/checkm_input GCF_002583405.1_ASM258340v1_genomic.fna/checkm_result
[2024-01-24 14:06:36,923] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:36,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:36,946] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:36,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:36,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002583405.1_ASM258340v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:36,947] [INFO] Task started: Blastn
[2024-01-24 14:06:36,947] [INFO] Running command: blastn -query GCF_002583405.1_ASM258340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72c9bf79-04fc-4b7b-b975-d8259a7ffb66/dqc_reference/reference_markers_gtdb.fasta -out GCF_002583405.1_ASM258340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:37,761] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:37,764] [INFO] Selected 9 target genomes.
[2024-01-24 14:06:37,764] [INFO] Target genome list was writen to GCF_002583405.1_ASM258340v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:37,772] [INFO] Task started: fastANI
[2024-01-24 14:06:37,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd2c1464-876a-471a-9370-33cc061d2bda/GCF_002583405.1_ASM258340v1_genomic.fna.gz --refList GCF_002583405.1_ASM258340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002583405.1_ASM258340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:43,641] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:43,650] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:43,650] [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_002583405.1	s__Secundilactobacillus silagincola	100.0	853	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.58	97.58	0.87	0.87	2	conclusive
GCF_016861565.1	s__Secundilactobacillus sp016861565	83.0435	567	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641075.1	s__Secundilactobacillus sp012641075	82.9622	512	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217925.1	s__Secundilactobacillus mixtipabuli	82.6642	530	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217985.1	s__Secundilactobacillus pentosiphilus	82.1265	505	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.11	97.11	0.89	0.89	2	-
GCF_002217945.1	s__Secundilactobacillus silagei	81.5712	489	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.92	99.86	1.00	0.99	3	-
GCF_005405185.1	s__Secundilactobacillus sp005405185	81.2571	491	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720675.1	s__Secundilactobacillus folii	79.2213	285	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311075.1	s__Secundilactobacillus similis	79.0043	228	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.93	99.93	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:43,653] [INFO] GTDB search result was written to GCF_002583405.1_ASM258340v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:43,653] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:43,657] [INFO] DFAST_QC result json was written to GCF_002583405.1_ASM258340v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:43,657] [INFO] DFAST_QC completed!
[2024-01-24 14:06:43,657] [INFO] Total running time: 0h0m50s