[2024-01-24 13:40:30,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,172] [INFO] DQC Reference Directory: /var/lib/cwl/stg153f5f66-bb2c-4a2f-bb65-03a81477dfba/dqc_reference
[2024-01-24 13:40:31,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,620] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f6b11b6-aeb2-42fa-a66e-bff1ca999715/GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/cds.fna -a GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:40,417] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:40,418] [INFO] Task started: HMMsearch
[2024-01-24 13:40:40,418] [INFO] Running command: hmmsearch --tblout GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg153f5f66-bb2c-4a2f-bb65-03a81477dfba/dqc_reference/reference_markers.hmm GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:40,730] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:40,731] [INFO] Found 6/6 markers.
[2024-01-24 13:40:40,773] [INFO] Query marker FASTA was written to GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:40,774] [INFO] Task started: Blastn
[2024-01-24 13:40:40,774] [INFO] Running command: blastn -query GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg153f5f66-bb2c-4a2f-bb65-03a81477dfba/dqc_reference/reference_markers.fasta -out GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:41,407] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:41,410] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:41,411] [INFO] Target genome list was writen to GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:41,425] [INFO] Task started: fastANI
[2024-01-24 13:40:41,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f6b11b6-aeb2-42fa-a66e-bff1ca999715/GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna.gz --refList GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:53,071] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:53,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg153f5f66-bb2c-4a2f-bb65-03a81477dfba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:53,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg153f5f66-bb2c-4a2f-bb65-03a81477dfba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:53,080] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:53,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:53,081] [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 nakayamae	strain=ATCC 700379	GCA_900113325.1	269670	269670	type	True	100.0	1151	1157	95	conclusive
Sporolactobacillus shoreicorticis	strain=LMG 29111	GCA_024125445.1	1923877	1923877	type	True	80.6602	630	1157	95	below_threshold
Sporolactobacillus putidus	strain=JCM 15325	GCA_014647035.1	492735	492735	type	True	80.1657	131	1157	95	below_threshold
Sporolactobacillus terrae	strain=DSM 11697	GCA_000648615.1	269673	269673	type	True	80.0114	365	1157	95	below_threshold
Sporolactobacillus pectinivorans	strain=GD201205	GCA_002802965.1	1591408	1591408	type	True	79.3756	159	1157	95	below_threshold
Sporolactobacillus laevolacticus	strain=DSM 442	GCA_000497245.1	33018	33018	type	True	79.0278	399	1157	95	below_threshold
Sporolactobacillus vineae	strain=DSM 21990	GCA_000377985.1	444463	444463	type	True	77.4827	120	1157	95	below_threshold
Sporolactobacillus vineae	strain=SL153	GCA_000246965.2	444463	444463	type	True	77.4706	123	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:53,087] [INFO] DFAST Taxonomy check result was written to GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:40:53,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:53,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:53,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg153f5f66-bb2c-4a2f-bb65-03a81477dfba/dqc_reference/checkm_data
[2024-01-24 13:40:53,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:53,128] [INFO] Task started: CheckM
[2024-01-24 13:40:53,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/checkm_input GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:41:25,796] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:25,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:25,827] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:25,827] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:25,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:41:25,828] [INFO] Task started: Blastn
[2024-01-24 13:41:25,828] [INFO] Running command: blastn -query GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg153f5f66-bb2c-4a2f-bb65-03a81477dfba/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:26,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:26,724] [INFO] Selected 25 target genomes.
[2024-01-24 13:41:26,724] [INFO] Target genome list was writen to GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:26,745] [INFO] Task started: fastANI
[2024-01-24 13:41:26,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f6b11b6-aeb2-42fa-a66e-bff1ca999715/GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna.gz --refList GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:43,697] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:43,709] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:43,710] [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_900113325.1	s__Sporolactobacillus nakayamae	100.0	1151	1157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009718825.1	s__Terrilactibacillus tamarindi	83.5648	55	1157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Terrilactibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647035.1	s__Sporolactobacillus putidus	80.1655	131	1157	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_000648615.1	s__Sporolactobacillus terrae	80.0544	363	1157	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_002802965.1	s__Sporolactobacillus pectinivorans	79.3756	159	1157	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	79.007	401	1157	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	77.4827	120	1157	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 13:41:43,712] [INFO] GTDB search result was written to GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:43,712] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:43,716] [INFO] DFAST_QC result json was written to GCF_900113325.1_IMG-taxon_2597490367_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:41:43,716] [INFO] DFAST_QC completed!
[2024-01-24 13:41:43,716] [INFO] Total running time: 0h1m14s