[2024-01-24 12:05:50,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:50,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:50,438] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1a42220-95f0-41f4-b39f-0ded70526c18/dqc_reference
[2024-01-24 12:05:52,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:52,741] [INFO] Task started: Prodigal
[2024-01-24 12:05:52,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg33699095-03cb-4515-9377-98a7349225bb/GCF_006539285.1_ASM653928v1_genomic.fna.gz | prodigal -d GCF_006539285.1_ASM653928v1_genomic.fna/cds.fna -a GCF_006539285.1_ASM653928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:59,861] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:59,862] [INFO] Task started: HMMsearch
[2024-01-24 12:05:59,862] [INFO] Running command: hmmsearch --tblout GCF_006539285.1_ASM653928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1a42220-95f0-41f4-b39f-0ded70526c18/dqc_reference/reference_markers.hmm GCF_006539285.1_ASM653928v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:00,073] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:00,074] [INFO] Found 6/6 markers.
[2024-01-24 12:06:00,101] [INFO] Query marker FASTA was written to GCF_006539285.1_ASM653928v1_genomic.fna/markers.fasta
[2024-01-24 12:06:00,101] [INFO] Task started: Blastn
[2024-01-24 12:06:00,101] [INFO] Running command: blastn -query GCF_006539285.1_ASM653928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a42220-95f0-41f4-b39f-0ded70526c18/dqc_reference/reference_markers.fasta -out GCF_006539285.1_ASM653928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:00,682] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:00,686] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:00,687] [INFO] Target genome list was writen to GCF_006539285.1_ASM653928v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:00,865] [INFO] Task started: fastANI
[2024-01-24 12:06:00,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg33699095-03cb-4515-9377-98a7349225bb/GCF_006539285.1_ASM653928v1_genomic.fna.gz --refList GCF_006539285.1_ASM653928v1_genomic.fna/target_genomes.txt --output GCF_006539285.1_ASM653928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:09,977] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:09,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1a42220-95f0-41f4-b39f-0ded70526c18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:09,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1a42220-95f0-41f4-b39f-0ded70526c18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:09,985] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:09,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:09,986] [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
Sporolactobacillus inulinus	strain=NBRC 13595	GCA_006539285.1	2078	2078	type	True	100.0	929	933	95	conclusive
Sporolactobacillus terrae	strain=DSM 11697	GCA_000648615.1	269673	269673	type	True	94.054	789	933	95	below_threshold
Sporolactobacillus putidus	strain=JCM 15325	GCA_014647035.1	492735	492735	type	True	80.4338	124	933	95	below_threshold
Sporolactobacillus laevolacticus	strain=DSM 442	GCA_000497245.1	33018	33018	type	True	78.4449	243	933	95	below_threshold
Sporolactobacillus vineae	strain=SL153	GCA_000246965.2	444463	444463	type	True	77.5973	105	933	95	below_threshold
Sporolactobacillus vineae	strain=DSM 21990	GCA_000377985.1	444463	444463	type	True	77.4761	105	933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:09,987] [INFO] DFAST Taxonomy check result was written to GCF_006539285.1_ASM653928v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:09,988] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:09,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:09,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1a42220-95f0-41f4-b39f-0ded70526c18/dqc_reference/checkm_data
[2024-01-24 12:06:09,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:10,019] [INFO] Task started: CheckM
[2024-01-24 12:06:10,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539285.1_ASM653928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539285.1_ASM653928v1_genomic.fna/checkm_input GCF_006539285.1_ASM653928v1_genomic.fna/checkm_result
[2024-01-24 12:06:37,806] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:37,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:37,841] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:37,841] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:37,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539285.1_ASM653928v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:37,842] [INFO] Task started: Blastn
[2024-01-24 12:06:37,842] [INFO] Running command: blastn -query GCF_006539285.1_ASM653928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a42220-95f0-41f4-b39f-0ded70526c18/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539285.1_ASM653928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:38,659] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:38,663] [INFO] Selected 20 target genomes.
[2024-01-24 12:06:38,663] [INFO] Target genome list was writen to GCF_006539285.1_ASM653928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:38,678] [INFO] Task started: fastANI
[2024-01-24 12:06:38,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg33699095-03cb-4515-9377-98a7349225bb/GCF_006539285.1_ASM653928v1_genomic.fna.gz --refList GCF_006539285.1_ASM653928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539285.1_ASM653928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:51,367] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:51,374] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:51,375] [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_006539285.1	s__Sporolactobacillus inulinus	100.0	929	933	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	99.52	99.06	0.91	0.89	3	conclusive
GCF_000648615.1	s__Sporolactobacillus terrae	94.054	789	933	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	98.89	98.59	0.91	0.87	6	-
GCF_004153165.1	s__Sporolactobacillus sp004153165	82.8746	116	933	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647035.1	s__Sporolactobacillus putidus	80.4338	124	933	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153195.1	s__Sporolactobacillus sp004153195	78.5361	117	933	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497245.1	s__Sporolactobacillus laevolacticus	78.468	241	933	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377985.1	s__Sporolactobacillus vineae	77.4761	105	933	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:51,377] [INFO] GTDB search result was written to GCF_006539285.1_ASM653928v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:51,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:51,381] [INFO] DFAST_QC result json was written to GCF_006539285.1_ASM653928v1_genomic.fna/dqc_result.json
[2024-01-24 12:06:51,381] [INFO] DFAST_QC completed!
[2024-01-24 12:06:51,381] [INFO] Total running time: 0h1m1s