[2024-01-24 14:13:01,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf8596f7-3c77-4f8f-859f-b5ae099d6118/dqc_reference
[2024-01-24 14:13:03,054] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:03,055] [INFO] Task started: Prodigal
[2024-01-24 14:13:03,055] [INFO] Running command: gunzip -c /var/lib/cwl/stgfec1891d-6afb-4aae-bee0-076c28112b32/GCF_019656055.1_ASM1965605v1_genomic.fna.gz | prodigal -d GCF_019656055.1_ASM1965605v1_genomic.fna/cds.fna -a GCF_019656055.1_ASM1965605v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:07,173] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:07,174] [INFO] Task started: HMMsearch
[2024-01-24 14:13:07,174] [INFO] Running command: hmmsearch --tblout GCF_019656055.1_ASM1965605v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf8596f7-3c77-4f8f-859f-b5ae099d6118/dqc_reference/reference_markers.hmm GCF_019656055.1_ASM1965605v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:07,437] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:07,439] [INFO] Found 6/6 markers.
[2024-01-24 14:13:07,461] [INFO] Query marker FASTA was written to GCF_019656055.1_ASM1965605v1_genomic.fna/markers.fasta
[2024-01-24 14:13:07,462] [INFO] Task started: Blastn
[2024-01-24 14:13:07,462] [INFO] Running command: blastn -query GCF_019656055.1_ASM1965605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8596f7-3c77-4f8f-859f-b5ae099d6118/dqc_reference/reference_markers.fasta -out GCF_019656055.1_ASM1965605v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:08,049] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:08,054] [INFO] Selected 17 target genomes.
[2024-01-24 14:13:08,054] [INFO] Target genome list was writen to GCF_019656055.1_ASM1965605v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:08,113] [INFO] Task started: fastANI
[2024-01-24 14:13:08,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgfec1891d-6afb-4aae-bee0-076c28112b32/GCF_019656055.1_ASM1965605v1_genomic.fna.gz --refList GCF_019656055.1_ASM1965605v1_genomic.fna/target_genomes.txt --output GCF_019656055.1_ASM1965605v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:13,931] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:13,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf8596f7-3c77-4f8f-859f-b5ae099d6118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:13,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf8596f7-3c77-4f8f-859f-b5ae099d6118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:13,943] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:13,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:13,943] [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 miyukkimchii	strain=JCM 17445	GCA_019656055.1	910540	910540	type	True	100.0	631	631	95	conclusive
Leuconostoc inhae	strain=DSM 15101	GCA_019656015.1	178001	178001	suspected-type	True	80.5314	359	631	95	below_threshold
Leuconostoc rapi	strain=DSM 27776	GCA_019656095.1	1406906	1406906	type	True	80.4214	292	631	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	80.3626	328	631	95	below_threshold
Leuconostoc rapi	strain=DSM 27776	GCA_016908715.1	1406906	1406906	type	True	80.2925	300	631	95	below_threshold
Leuconostoc gelidum subsp. gelidum	strain=KCTC 3527	GCA_000166715.2	1607839	1244	type	True	80.2029	333	631	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	80.1684	343	631	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_020089505.1	1607837	1244	type	True	79.9402	352	631	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_019655935.1	1607837	1244	type	True	79.9226	346	631	95	below_threshold
Leuconostoc carnosum	strain=DSM 5576	GCA_014207505.1	1252	1252	type	True	79.5324	249	631	95	below_threshold
Leuconostoc holzapfelii	strain=CCUG 54536	GCA_012396485.1	434464	434464	type	True	79.5201	172	631	95	below_threshold
Leuconostoc carnosum	strain=JCM 9695	GCA_019655915.1	1252	1252	type	True	79.1465	243	631	95	below_threshold
Leuconostoc suionicum	strain=DSM 20241	GCA_001891125.1	1511761	1511761	type	True	78.9219	182	631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:13,945] [INFO] DFAST Taxonomy check result was written to GCF_019656055.1_ASM1965605v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:13,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:13,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:13,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf8596f7-3c77-4f8f-859f-b5ae099d6118/dqc_reference/checkm_data
[2024-01-24 14:13:13,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:13,967] [INFO] Task started: CheckM
[2024-01-24 14:13:13,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019656055.1_ASM1965605v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019656055.1_ASM1965605v1_genomic.fna/checkm_input GCF_019656055.1_ASM1965605v1_genomic.fna/checkm_result
[2024-01-24 14:13:34,902] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:34,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:34,922] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:34,923] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:34,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019656055.1_ASM1965605v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:34,923] [INFO] Task started: Blastn
[2024-01-24 14:13:34,923] [INFO] Running command: blastn -query GCF_019656055.1_ASM1965605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8596f7-3c77-4f8f-859f-b5ae099d6118/dqc_reference/reference_markers_gtdb.fasta -out GCF_019656055.1_ASM1965605v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:35,703] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:35,707] [INFO] Selected 15 target genomes.
[2024-01-24 14:13:35,707] [INFO] Target genome list was writen to GCF_019656055.1_ASM1965605v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:35,736] [INFO] Task started: fastANI
[2024-01-24 14:13:35,736] [INFO] Running command: fastANI --query /var/lib/cwl/stgfec1891d-6afb-4aae-bee0-076c28112b32/GCF_019656055.1_ASM1965605v1_genomic.fna.gz --refList GCF_019656055.1_ASM1965605v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019656055.1_ASM1965605v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:40,787] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:40,798] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:13:40,798] [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_000092505.1	s__Leuconostoc kimchii	80.874	313	631	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	80.4427	271	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.95	98.13	0.88	0.76	13	-
GCF_016908715.1	s__Leuconostoc rapi	80.3119	299	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166715.1	s__Leuconostoc gelidum	80.2029	333	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
GCF_007954625.1	s__Leuconostoc lactis_A	79.8482	195	631	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	79.7025	170	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004354555.1	s__Leuconostoc citreum	79.5415	210	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.02	98.68	0.92	0.88	33	-
GCF_014207505.1	s__Leuconostoc carnosum	79.5124	250	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	-
GCF_012396485.1	s__Leuconostoc holzapfelii	79.5065	174	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651235.1	s__Leuconostoc lactis	79.2768	173	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.49	96.95	0.90	0.86	22	-
GCF_001891125.1	s__Leuconostoc suionicum	78.898	183	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.16	97.05	0.94	0.91	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:40,800] [INFO] GTDB search result was written to GCF_019656055.1_ASM1965605v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:40,800] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:40,805] [INFO] DFAST_QC result json was written to GCF_019656055.1_ASM1965605v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:40,806] [INFO] DFAST_QC completed!
[2024-01-24 14:13:40,806] [INFO] Total running time: 0h0m39s