[2024-01-24 12:52:25,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:25,289] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:25,290] [INFO] DQC Reference Directory: /var/lib/cwl/stgd972b29c-a064-48f6-ae57-b52c18b2c5cb/dqc_reference
[2024-01-24 12:52:26,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:26,573] [INFO] Task started: Prodigal
[2024-01-24 12:52:26,573] [INFO] Running command: gunzip -c /var/lib/cwl/stg862bda2d-760b-4035-9d75-333e74b2d98e/GCF_019655955.1_ASM1965595v1_genomic.fna.gz | prodigal -d GCF_019655955.1_ASM1965595v1_genomic.fna/cds.fna -a GCF_019655955.1_ASM1965595v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:30,877] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:30,878] [INFO] Task started: HMMsearch
[2024-01-24 12:52:30,878] [INFO] Running command: hmmsearch --tblout GCF_019655955.1_ASM1965595v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd972b29c-a064-48f6-ae57-b52c18b2c5cb/dqc_reference/reference_markers.hmm GCF_019655955.1_ASM1965595v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:31,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:31,123] [INFO] Found 6/6 markers.
[2024-01-24 12:52:31,155] [INFO] Query marker FASTA was written to GCF_019655955.1_ASM1965595v1_genomic.fna/markers.fasta
[2024-01-24 12:52:31,155] [INFO] Task started: Blastn
[2024-01-24 12:52:31,155] [INFO] Running command: blastn -query GCF_019655955.1_ASM1965595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd972b29c-a064-48f6-ae57-b52c18b2c5cb/dqc_reference/reference_markers.fasta -out GCF_019655955.1_ASM1965595v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:31,869] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:31,878] [INFO] Selected 8 target genomes.
[2024-01-24 12:52:31,879] [INFO] Target genome list was writen to GCF_019655955.1_ASM1965595v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:31,884] [INFO] Task started: fastANI
[2024-01-24 12:52:31,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg862bda2d-760b-4035-9d75-333e74b2d98e/GCF_019655955.1_ASM1965595v1_genomic.fna.gz --refList GCF_019655955.1_ASM1965595v1_genomic.fna/target_genomes.txt --output GCF_019655955.1_ASM1965595v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:35,263] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:35,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd972b29c-a064-48f6-ae57-b52c18b2c5cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:35,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd972b29c-a064-48f6-ae57-b52c18b2c5cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:35,270] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:52:35,270] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:35,270] [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 gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	100.0	635	637	95	conclusive
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	99.9994	636	637	95	conclusive
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_019655935.1	1607837	1244	type	True	94.658	558	637	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_020089505.1	1607837	1244	type	True	94.6255	560	637	95	below_threshold
Leuconostoc gelidum subsp. gelidum	strain=KCTC 3527	GCA_000166715.2	1607839	1244	type	True	94.0209	551	637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:35,272] [INFO] DFAST Taxonomy check result was written to GCF_019655955.1_ASM1965595v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:35,273] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:35,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:35,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd972b29c-a064-48f6-ae57-b52c18b2c5cb/dqc_reference/checkm_data
[2024-01-24 12:52:35,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:35,301] [INFO] Task started: CheckM
[2024-01-24 12:52:35,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019655955.1_ASM1965595v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019655955.1_ASM1965595v1_genomic.fna/checkm_input GCF_019655955.1_ASM1965595v1_genomic.fna/checkm_result
[2024-01-24 12:52:56,145] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:56,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:56,167] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:56,167] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:56,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019655955.1_ASM1965595v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:56,168] [INFO] Task started: Blastn
[2024-01-24 12:52:56,168] [INFO] Running command: blastn -query GCF_019655955.1_ASM1965595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd972b29c-a064-48f6-ae57-b52c18b2c5cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_019655955.1_ASM1965595v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:56,953] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:56,959] [INFO] Selected 13 target genomes.
[2024-01-24 12:52:56,959] [INFO] Target genome list was writen to GCF_019655955.1_ASM1965595v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:56,975] [INFO] Task started: fastANI
[2024-01-24 12:52:56,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg862bda2d-760b-4035-9d75-333e74b2d98e/GCF_019655955.1_ASM1965595v1_genomic.fna.gz --refList GCF_019655955.1_ASM1965595v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019655955.1_ASM1965595v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:02,094] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:02,102] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:02,103] [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
GCA_000166735.2	s__Leuconostoc inhae	99.4377	488	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.95	98.13	0.88	0.76	13	conclusive
GCF_000166715.1	s__Leuconostoc gelidum	94.0209	551	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
GCF_016908715.1	s__Leuconostoc rapi	80.0473	333	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207505.1	s__Leuconostoc carnosum	80.0321	268	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	-
GCF_000092505.1	s__Leuconostoc kimchii	80.0111	328	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_004354555.1	s__Leuconostoc citreum	79.2971	224	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.02	98.68	0.92	0.88	33	-
GCF_012396485.1	s__Leuconostoc holzapfelii	79.1646	178	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954625.1	s__Leuconostoc lactis_A	78.7668	190	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.86	96.88	0.92	0.91	7	-
GCF_014634745.1	s__Leuconostoc pseudomesenteroides	78.7306	159	637	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.98	96.85	0.90	0.84	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:02,105] [INFO] GTDB search result was written to GCF_019655955.1_ASM1965595v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:02,105] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:02,109] [INFO] DFAST_QC result json was written to GCF_019655955.1_ASM1965595v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:02,110] [INFO] DFAST_QC completed!
[2024-01-24 12:53:02,110] [INFO] Total running time: 0h0m37s