[2024-01-25 19:10:50,667] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:50,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:50,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d88ccd6-7faf-4002-8125-e69c7e8f3116/dqc_reference
[2024-01-25 19:10:51,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:51,805] [INFO] Task started: Prodigal
[2024-01-25 19:10:51,805] [INFO] Running command: gunzip -c /var/lib/cwl/stg61f774e0-0729-431f-8360-f921c9c41aec/GCF_002217945.1_ASM221794v1_genomic.fna.gz | prodigal -d GCF_002217945.1_ASM221794v1_genomic.fna/cds.fna -a GCF_002217945.1_ASM221794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:57,046] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:57,047] [INFO] Task started: HMMsearch
[2024-01-25 19:10:57,047] [INFO] Running command: hmmsearch --tblout GCF_002217945.1_ASM221794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d88ccd6-7faf-4002-8125-e69c7e8f3116/dqc_reference/reference_markers.hmm GCF_002217945.1_ASM221794v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:57,260] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:57,261] [INFO] Found 6/6 markers.
[2024-01-25 19:10:57,285] [INFO] Query marker FASTA was written to GCF_002217945.1_ASM221794v1_genomic.fna/markers.fasta
[2024-01-25 19:10:57,285] [INFO] Task started: Blastn
[2024-01-25 19:10:57,285] [INFO] Running command: blastn -query GCF_002217945.1_ASM221794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d88ccd6-7faf-4002-8125-e69c7e8f3116/dqc_reference/reference_markers.fasta -out GCF_002217945.1_ASM221794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:57,852] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:57,854] [INFO] Selected 15 target genomes.
[2024-01-25 19:10:57,855] [INFO] Target genome list was writen to GCF_002217945.1_ASM221794v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:57,869] [INFO] Task started: fastANI
[2024-01-25 19:10:57,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg61f774e0-0729-431f-8360-f921c9c41aec/GCF_002217945.1_ASM221794v1_genomic.fna.gz --refList GCF_002217945.1_ASM221794v1_genomic.fna/target_genomes.txt --output GCF_002217945.1_ASM221794v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:06,703] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:06,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d88ccd6-7faf-4002-8125-e69c7e8f3116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:06,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d88ccd6-7faf-4002-8125-e69c7e8f3116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:06,712] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:11:06,713] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:06,713] [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 silagei	strain=IWT126	GCA_002217945.1	1293415	1293415	type	True	100.0	870	871	95	conclusive
Secundilactobacillus silagei	strain=DSM 27022	GCA_004354595.1	1293415	1293415	type	True	99.9896	866	871	95	conclusive
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	99.855	851	871	95	conclusive
Secundilactobacillus hailunensis	strain=887-11	GCA_005405185.1	2559923	2559923	type	True	90.8008	706	871	95	below_threshold
Secundilactobacillus yichangensis	strain=F79-211-2	GCA_016861565.1	2799580	2799580	type	True	81.8944	523	871	95	below_threshold
Secundilactobacillus pentosiphilus	strain=IWT25	GCA_002217985.1	1714682	1714682	type	True	81.6724	477	871	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	81.5561	459	871	95	below_threshold
Secundilactobacillus mixtipabuli	strain=IWT30	GCA_002217925.1	1435342	1435342	type	True	81.5106	458	871	95	below_threshold
Secundilactobacillus odoratitofui	strain=JCM 15043	GCA_001313185.1	480930	480930	type	True	78.9243	278	871	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	78.5237	193	871	95	below_threshold
Secundilactobacillus paracollinoides	strain=DSM 15502	GCA_001435115.1	240427	240427	type	True	78.4095	192	871	95	below_threshold
Lactiplantibacillus mudanjiangensis	strain=11050	GCA_005405385.1	1296538	1296538	type	True	77.6477	58	871	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:06,716] [INFO] DFAST Taxonomy check result was written to GCF_002217945.1_ASM221794v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:06,718] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:06,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:06,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d88ccd6-7faf-4002-8125-e69c7e8f3116/dqc_reference/checkm_data
[2024-01-25 19:11:06,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:06,759] [INFO] Task started: CheckM
[2024-01-25 19:11:06,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217945.1_ASM221794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217945.1_ASM221794v1_genomic.fna/checkm_input GCF_002217945.1_ASM221794v1_genomic.fna/checkm_result
[2024-01-25 19:11:27,931] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:27,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:27,952] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:27,952] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:27,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217945.1_ASM221794v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:27,952] [INFO] Task started: Blastn
[2024-01-25 19:11:27,953] [INFO] Running command: blastn -query GCF_002217945.1_ASM221794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d88ccd6-7faf-4002-8125-e69c7e8f3116/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217945.1_ASM221794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:28,752] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:28,755] [INFO] Selected 8 target genomes.
[2024-01-25 19:11:28,755] [INFO] Target genome list was writen to GCF_002217945.1_ASM221794v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:28,762] [INFO] Task started: fastANI
[2024-01-25 19:11:28,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg61f774e0-0729-431f-8360-f921c9c41aec/GCF_002217945.1_ASM221794v1_genomic.fna.gz --refList GCF_002217945.1_ASM221794v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217945.1_ASM221794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:33,329] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:33,335] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:33,335] [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_002217945.1	s__Secundilactobacillus silagei	100.0	870	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.92	99.86	1.00	0.99	3	conclusive
GCF_005405185.1	s__Secundilactobacillus sp005405185	90.8063	705	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861565.1	s__Secundilactobacillus sp016861565	81.8979	523	871	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	81.6763	477	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.11	97.11	0.89	0.89	2	-
GCF_002217925.1	s__Secundilactobacillus mixtipabuli	81.5341	458	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002583405.1	s__Secundilactobacillus silagincola	81.4479	494	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.58	97.58	0.87	0.87	2	-
GCF_001311135.1	s__Secundilactobacillus paracollinoides	78.5113	192	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.57	99.45	0.95	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:33,337] [INFO] GTDB search result was written to GCF_002217945.1_ASM221794v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:33,338] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:33,340] [INFO] DFAST_QC result json was written to GCF_002217945.1_ASM221794v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:33,341] [INFO] DFAST_QC completed!
[2024-01-25 19:11:33,341] [INFO] Total running time: 0h0m43s