[2024-01-25 17:44:50,347] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:50,349] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:50,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bb5df7a-c250-4c20-92f1-e783a37994ad/dqc_reference
[2024-01-25 17:44:51,474] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:51,475] [INFO] Task started: Prodigal
[2024-01-25 17:44:51,475] [INFO] Running command: gunzip -c /var/lib/cwl/stg90e3e519-58f6-4535-848b-975b0117f435/GCF_001436255.1_ASM143625v1_genomic.fna.gz | prodigal -d GCF_001436255.1_ASM143625v1_genomic.fna/cds.fna -a GCF_001436255.1_ASM143625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:57,420] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:57,420] [INFO] Task started: HMMsearch
[2024-01-25 17:44:57,420] [INFO] Running command: hmmsearch --tblout GCF_001436255.1_ASM143625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bb5df7a-c250-4c20-92f1-e783a37994ad/dqc_reference/reference_markers.hmm GCF_001436255.1_ASM143625v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:57,617] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:57,618] [INFO] Found 6/6 markers.
[2024-01-25 17:44:57,641] [INFO] Query marker FASTA was written to GCF_001436255.1_ASM143625v1_genomic.fna/markers.fasta
[2024-01-25 17:44:57,641] [INFO] Task started: Blastn
[2024-01-25 17:44:57,641] [INFO] Running command: blastn -query GCF_001436255.1_ASM143625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb5df7a-c250-4c20-92f1-e783a37994ad/dqc_reference/reference_markers.fasta -out GCF_001436255.1_ASM143625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:58,180] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:58,184] [INFO] Selected 13 target genomes.
[2024-01-25 17:44:58,184] [INFO] Target genome list was writen to GCF_001436255.1_ASM143625v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:58,196] [INFO] Task started: fastANI
[2024-01-25 17:44:58,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e3e519-58f6-4535-848b-975b0117f435/GCF_001436255.1_ASM143625v1_genomic.fna.gz --refList GCF_001436255.1_ASM143625v1_genomic.fna/target_genomes.txt --output GCF_001436255.1_ASM143625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:05,472] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:05,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bb5df7a-c250-4c20-92f1-e783a37994ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:05,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bb5df7a-c250-4c20-92f1-e783a37994ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:05,483] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:45:05,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:05,483] [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
Lentilactobacillus rapi subsp. rapi	strain=DSM 19907	GCA_001436255.1	2944812	481723	type	True	99.9999	912	912	95	conclusive
Lentilactobacillus rapi subsp. rapi	strain=JCM 15042	GCA_001311445.1	2944812	481723	type	True	99.8687	869	912	95	conclusive
Lentilactobacillus kisonensis	strain=JCM 15041	GCA_001311425.1	481722	481722	type	True	80.8858	479	912	95	below_threshold
Lentilactobacillus kisonensis	strain=DSM 19906	GCA_001434135.1	481722	481722	type	True	80.8247	477	912	95	below_threshold
Lentilactobacillus fungorum	strain=YK48G	GCA_016860605.1	2201250	2201250	type	True	79.498	410	912	95	below_threshold
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	79.1985	277	912	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_000415925.1	481720	481720	type	True	79.1325	284	912	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	79.1166	279	912	95	below_threshold
Lentilactobacillus kefiri	strain=NBRC 15888	GCA_007989105.1	33962	33962	type	True	79.1145	255	912	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	77.4976	66	912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:05,486] [INFO] DFAST Taxonomy check result was written to GCF_001436255.1_ASM143625v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:05,488] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:05,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:05,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bb5df7a-c250-4c20-92f1-e783a37994ad/dqc_reference/checkm_data
[2024-01-25 17:45:05,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:05,519] [INFO] Task started: CheckM
[2024-01-25 17:45:05,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001436255.1_ASM143625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001436255.1_ASM143625v1_genomic.fna/checkm_input GCF_001436255.1_ASM143625v1_genomic.fna/checkm_result
[2024-01-25 17:45:28,956] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:28,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:28,981] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:28,981] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:28,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001436255.1_ASM143625v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:28,982] [INFO] Task started: Blastn
[2024-01-25 17:45:28,982] [INFO] Running command: blastn -query GCF_001436255.1_ASM143625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb5df7a-c250-4c20-92f1-e783a37994ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_001436255.1_ASM143625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:29,768] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:29,771] [INFO] Selected 10 target genomes.
[2024-01-25 17:45:29,771] [INFO] Target genome list was writen to GCF_001436255.1_ASM143625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:29,779] [INFO] Task started: fastANI
[2024-01-25 17:45:29,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e3e519-58f6-4535-848b-975b0117f435/GCF_001436255.1_ASM143625v1_genomic.fna.gz --refList GCF_001436255.1_ASM143625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001436255.1_ASM143625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:35,584] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:35,591] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:35,591] [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_001436255.1	s__Lentilactobacillus rapi	99.9999	912	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.94	99.89	1.00	1.00	3	conclusive
GCF_019061365.1	s__Lentilactobacillus sp019061365	93.609	690	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.43	99.43	0.89	0.89	2	-
GCF_001434135.1	s__Lentilactobacillus kisonensis	80.8592	474	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.52	0.95	0.93	3	-
GCF_016860605.1	s__Lentilactobacillus sp016860605	79.5032	410	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434145.1	s__Lentilactobacillus otakiensis	79.2155	276	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.95	99.91	1.00	1.00	3	-
GCF_007989105.1	s__Lentilactobacillus kefiri	79.1145	255	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.76	99.64	0.95	0.93	9	-
GCF_001435575.1	s__Lentilactobacillus sunkii	78.8304	254	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	96.44	96.44	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:35,592] [INFO] GTDB search result was written to GCF_001436255.1_ASM143625v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:35,593] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:35,595] [INFO] DFAST_QC result json was written to GCF_001436255.1_ASM143625v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:35,595] [INFO] DFAST_QC completed!
[2024-01-25 17:45:35,595] [INFO] Total running time: 0h0m45s