[2024-01-24 12:53:41,736] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:41,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:41,739] [INFO] DQC Reference Directory: /var/lib/cwl/stgafc71cb7-771e-42d9-ad27-e48f8c88ca88/dqc_reference
[2024-01-24 12:53:43,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:43,248] [INFO] Task started: Prodigal
[2024-01-24 12:53:43,248] [INFO] Running command: gunzip -c /var/lib/cwl/stgbad9badb-86d1-4287-ae27-2675ae797ca5/GCF_002907365.1_ASM290736v1_genomic.fna.gz | prodigal -d GCF_002907365.1_ASM290736v1_genomic.fna/cds.fna -a GCF_002907365.1_ASM290736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:45,819] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:45,820] [INFO] Task started: HMMsearch
[2024-01-24 12:53:45,820] [INFO] Running command: hmmsearch --tblout GCF_002907365.1_ASM290736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafc71cb7-771e-42d9-ad27-e48f8c88ca88/dqc_reference/reference_markers.hmm GCF_002907365.1_ASM290736v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:46,149] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:46,151] [INFO] Found 6/6 markers.
[2024-01-24 12:53:46,174] [INFO] Query marker FASTA was written to GCF_002907365.1_ASM290736v1_genomic.fna/markers.fasta
[2024-01-24 12:53:46,174] [INFO] Task started: Blastn
[2024-01-24 12:53:46,175] [INFO] Running command: blastn -query GCF_002907365.1_ASM290736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafc71cb7-771e-42d9-ad27-e48f8c88ca88/dqc_reference/reference_markers.fasta -out GCF_002907365.1_ASM290736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:47,929] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:47,932] [INFO] Selected 14 target genomes.
[2024-01-24 12:53:47,932] [INFO] Target genome list was writen to GCF_002907365.1_ASM290736v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:47,944] [INFO] Task started: fastANI
[2024-01-24 12:53:47,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad9badb-86d1-4287-ae27-2675ae797ca5/GCF_002907365.1_ASM290736v1_genomic.fna.gz --refList GCF_002907365.1_ASM290736v1_genomic.fna/target_genomes.txt --output GCF_002907365.1_ASM290736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:52,531] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:52,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafc71cb7-771e-42d9-ad27-e48f8c88ca88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:52,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafc71cb7-771e-42d9-ad27-e48f8c88ca88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:52,543] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:53:52,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:52,544] [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
Fructilactobacillus sanfranciscensis	strain=TMW 1.53	GCA_002907365.1	1625	1625	type	True	100.0	406	409	95	conclusive
Fructilactobacillus sanfranciscensis	strain=JCM 5668	GCA_003369815.1	1625	1625	type	True	99.9526	389	409	95	conclusive
Fructilactobacillus sanfranciscensis	strain=DSM 20451	GCA_001436035.1	1625	1625	type	True	99.8767	374	409	95	conclusive
Fructilactobacillus lindneri	strain=TMW 1.88	GCA_002907375.1	53444	53444	type	True	79.5871	199	409	95	below_threshold
Fructilactobacillus lindneri	strain=DSM 20690	GCA_900167245.1	53444	53444	type	True	79.3338	202	409	95	below_threshold
Apilactobacillus ozensis	strain=JCM 17196	GCA_001311485.1	866801	866801	type	True	78.362	53	409	95	below_threshold
Apilactobacillus micheneri	strain=Hlig3	GCA_002993975.1	1899430	1899430	type	True	78.2488	63	409	95	below_threshold
Fructilactobacillus florum	strain=JCM 16035	GCA_001311215.1	640331	640331	type	True	77.853	63	409	95	below_threshold
Apilactobacillus quenuiae	strain=HV_6	GCA_002994005.1	2008377	2008377	type	True	77.7	63	409	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:52,546] [INFO] DFAST Taxonomy check result was written to GCF_002907365.1_ASM290736v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:52,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:52,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:52,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafc71cb7-771e-42d9-ad27-e48f8c88ca88/dqc_reference/checkm_data
[2024-01-24 12:53:52,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:52,565] [INFO] Task started: CheckM
[2024-01-24 12:53:52,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002907365.1_ASM290736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002907365.1_ASM290736v1_genomic.fna/checkm_input GCF_002907365.1_ASM290736v1_genomic.fna/checkm_result
[2024-01-24 12:54:11,492] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:11,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:11,525] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:11,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:11,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002907365.1_ASM290736v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:11,527] [INFO] Task started: Blastn
[2024-01-24 12:54:11,527] [INFO] Running command: blastn -query GCF_002907365.1_ASM290736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafc71cb7-771e-42d9-ad27-e48f8c88ca88/dqc_reference/reference_markers_gtdb.fasta -out GCF_002907365.1_ASM290736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:12,358] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:12,363] [INFO] Selected 21 target genomes.
[2024-01-24 12:54:12,363] [INFO] Target genome list was writen to GCF_002907365.1_ASM290736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:12,378] [INFO] Task started: fastANI
[2024-01-24 12:54:12,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad9badb-86d1-4287-ae27-2675ae797ca5/GCF_002907365.1_ASM290736v1_genomic.fna.gz --refList GCF_002907365.1_ASM290736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002907365.1_ASM290736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:19,071] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:19,080] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:19,081] [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_001436035.1	s__Fructilactobacillus sanfranciscensis	99.8767	374	409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.31	98.98	0.96	0.90	32	conclusive
GCF_002907375.1	s__Fructilactobacillus lindneri	79.5895	198	409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.90	99.78	0.98	0.96	12	-
GCF_002993975.1	s__Apilactobacillus micheneri	78.2488	63	409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	-
GCF_002993965.1	s__Apilactobacillus timberlakei	78.0499	64	409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	-
GCF_002994005.1	s__Apilactobacillus quenuiae	77.6831	64	409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:19,082] [INFO] GTDB search result was written to GCF_002907365.1_ASM290736v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:19,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:19,085] [INFO] DFAST_QC result json was written to GCF_002907365.1_ASM290736v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:19,085] [INFO] DFAST_QC completed!
[2024-01-24 12:54:19,085] [INFO] Total running time: 0h0m37s