[2024-01-24 11:02:49,220] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:02:49,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:02:49,222] [INFO] DQC Reference Directory: /var/lib/cwl/stgf678370f-1742-4a25-9274-59466637985e/dqc_reference
[2024-01-24 11:02:50,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:02:50,438] [INFO] Task started: Prodigal
[2024-01-24 11:02:50,439] [INFO] Running command: gunzip -c /var/lib/cwl/stg59a17c97-542b-44b8-9645-8dcf53c32ffb/GCF_014207505.1_ASM1420750v1_genomic.fna.gz | prodigal -d GCF_014207505.1_ASM1420750v1_genomic.fna/cds.fna -a GCF_014207505.1_ASM1420750v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:02:54,310] [INFO] Task succeeded: Prodigal
[2024-01-24 11:02:54,310] [INFO] Task started: HMMsearch
[2024-01-24 11:02:54,310] [INFO] Running command: hmmsearch --tblout GCF_014207505.1_ASM1420750v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf678370f-1742-4a25-9274-59466637985e/dqc_reference/reference_markers.hmm GCF_014207505.1_ASM1420750v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:02:54,516] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:02:54,518] [INFO] Found 6/6 markers.
[2024-01-24 11:02:54,538] [INFO] Query marker FASTA was written to GCF_014207505.1_ASM1420750v1_genomic.fna/markers.fasta
[2024-01-24 11:02:54,538] [INFO] Task started: Blastn
[2024-01-24 11:02:54,538] [INFO] Running command: blastn -query GCF_014207505.1_ASM1420750v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf678370f-1742-4a25-9274-59466637985e/dqc_reference/reference_markers.fasta -out GCF_014207505.1_ASM1420750v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:02:55,133] [INFO] Task succeeded: Blastn
[2024-01-24 11:02:55,137] [INFO] Selected 22 target genomes.
[2024-01-24 11:02:55,138] [INFO] Target genome list was writen to GCF_014207505.1_ASM1420750v1_genomic.fna/target_genomes.txt
[2024-01-24 11:02:55,152] [INFO] Task started: fastANI
[2024-01-24 11:02:55,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a17c97-542b-44b8-9645-8dcf53c32ffb/GCF_014207505.1_ASM1420750v1_genomic.fna.gz --refList GCF_014207505.1_ASM1420750v1_genomic.fna/target_genomes.txt --output GCF_014207505.1_ASM1420750v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:03:02,963] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:02,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf678370f-1742-4a25-9274-59466637985e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:03:02,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf678370f-1742-4a25-9274-59466637985e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:03:02,979] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:03:02,979] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:03:02,979] [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
Leuconostoc carnosum	strain=DSM 5576	GCA_014207505.1	1252	1252	type	True	100.0	598	598	95	conclusive
Leuconostoc carnosum	strain=JCM 9695	GCA_019655915.1	1252	1252	type	True	99.9595	560	598	95	conclusive
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	80.0777	258	598	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_019655935.1	1607837	1244	type	True	79.9928	261	598	95	below_threshold
Leuconostoc inhae	strain=DSM 15101	GCA_019656015.1	178001	178001	suspected-type	True	79.9706	249	598	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	79.9512	272	598	95	below_threshold
Leuconostoc rapi	strain=DSM 27776	GCA_019656095.1	1406906	1406906	type	True	79.9102	236	598	95	below_threshold
Leuconostoc lactis	strain=JCM 6123	GCA_014651235.1	1246	1246	type	True	79.8893	166	598	95	below_threshold
Leuconostoc gelidum subsp. gelidum	strain=KCTC 3527	GCA_000166715.2	1607839	1244	type	True	79.8567	266	598	95	below_threshold
Leuconostoc rapi	strain=DSM 27776	GCA_016908715.1	1406906	1406906	type	True	79.7712	238	598	95	below_threshold
Leuconostoc miyukkimchii	strain=JCM 17445	GCA_019656055.1	910540	910540	type	True	79.6204	262	598	95	below_threshold
Leuconostoc holzapfelii	strain=CCUG 54536	GCA_012396485.1	434464	434464	type	True	79.3456	176	598	95	below_threshold
Leuconostoc holzapfelii	strain=JCM 16942	GCA_019655995.1	434464	434464	type	True	79.314	175	598	95	below_threshold
Leuconostoc palmae	strain=JCM 16944	GCA_019656075.1	501487	501487	type	True	79.1743	178	598	95	below_threshold
Weissella sagaensis	strain=X0750	GCA_005405285.1	2559928	2559928	type	True	78.833	55	598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:03:02,981] [INFO] DFAST Taxonomy check result was written to GCF_014207505.1_ASM1420750v1_genomic.fna/tc_result.tsv
[2024-01-24 11:03:02,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:03:02,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:03:02,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf678370f-1742-4a25-9274-59466637985e/dqc_reference/checkm_data
[2024-01-24 11:03:02,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:03:03,006] [INFO] Task started: CheckM
[2024-01-24 11:03:03,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207505.1_ASM1420750v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207505.1_ASM1420750v1_genomic.fna/checkm_input GCF_014207505.1_ASM1420750v1_genomic.fna/checkm_result
[2024-01-24 11:03:22,030] [INFO] Task succeeded: CheckM
[2024-01-24 11:03:22,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:03:22,055] [INFO] ===== Completeness check finished =====
[2024-01-24 11:03:22,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:03:22,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207505.1_ASM1420750v1_genomic.fna/markers.fasta)
[2024-01-24 11:03:22,057] [INFO] Task started: Blastn
[2024-01-24 11:03:22,057] [INFO] Running command: blastn -query GCF_014207505.1_ASM1420750v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf678370f-1742-4a25-9274-59466637985e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207505.1_ASM1420750v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:22,867] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:22,872] [INFO] Selected 17 target genomes.
[2024-01-24 11:03:22,872] [INFO] Target genome list was writen to GCF_014207505.1_ASM1420750v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:03:22,908] [INFO] Task started: fastANI
[2024-01-24 11:03:22,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a17c97-542b-44b8-9645-8dcf53c32ffb/GCF_014207505.1_ASM1420750v1_genomic.fna.gz --refList GCF_014207505.1_ASM1420750v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207505.1_ASM1420750v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:03:29,121] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:29,134] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:03:29,135] [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_014207505.1	s__Leuconostoc carnosum	100.0	598	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	conclusive
GCF_000092505.1	s__Leuconostoc kimchii	80.0103	250	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCA_000166735.2	s__Leuconostoc inhae	79.9922	228	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.95	98.13	0.88	0.76	13	-
GCF_014651235.1	s__Leuconostoc lactis	79.954	164	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.49	96.95	0.90	0.86	22	-
GCF_000166715.1	s__Leuconostoc gelidum	79.862	265	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
GCF_000014445.1	s__Leuconostoc mesenteroides	79.8483	183	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.82	97.34	0.92	0.82	89	-
GCF_016908715.1	s__Leuconostoc rapi	79.7594	239	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001891125.1	s__Leuconostoc suionicum	79.7418	175	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.16	97.05	0.94	0.91	7	-
GCF_007954625.1	s__Leuconostoc lactis_A	79.6626	177	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.86	96.88	0.92	0.91	7	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	79.5609	180	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012396485.1	s__Leuconostoc holzapfelii	79.3456	176	598	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:03:29,136] [INFO] GTDB search result was written to GCF_014207505.1_ASM1420750v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:03:29,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:03:29,140] [INFO] DFAST_QC result json was written to GCF_014207505.1_ASM1420750v1_genomic.fna/dqc_result.json
[2024-01-24 11:03:29,140] [INFO] DFAST_QC completed!
[2024-01-24 11:03:29,140] [INFO] Total running time: 0h0m40s