[2024-01-24 11:34:41,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,474] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa1b1319-0019-414b-bbbf-5f28b7dfcc7d/dqc_reference
[2024-01-24 11:34:42,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,854] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f6ea0ae-db22-451c-9943-ca03d2569e57/GCF_001436035.1_ASM143603v1_genomic.fna.gz | prodigal -d GCF_001436035.1_ASM143603v1_genomic.fna/cds.fna -a GCF_001436035.1_ASM143603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:45,177] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:45,178] [INFO] Task started: HMMsearch
[2024-01-24 11:34:45,178] [INFO] Running command: hmmsearch --tblout GCF_001436035.1_ASM143603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa1b1319-0019-414b-bbbf-5f28b7dfcc7d/dqc_reference/reference_markers.hmm GCF_001436035.1_ASM143603v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:45,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:45,384] [INFO] Found 6/6 markers.
[2024-01-24 11:34:45,419] [INFO] Query marker FASTA was written to GCF_001436035.1_ASM143603v1_genomic.fna/markers.fasta
[2024-01-24 11:34:45,420] [INFO] Task started: Blastn
[2024-01-24 11:34:45,420] [INFO] Running command: blastn -query GCF_001436035.1_ASM143603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa1b1319-0019-414b-bbbf-5f28b7dfcc7d/dqc_reference/reference_markers.fasta -out GCF_001436035.1_ASM143603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:46,475] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:46,478] [INFO] Selected 14 target genomes.
[2024-01-24 11:34:46,479] [INFO] Target genome list was writen to GCF_001436035.1_ASM143603v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:46,501] [INFO] Task started: fastANI
[2024-01-24 11:34:46,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f6ea0ae-db22-451c-9943-ca03d2569e57/GCF_001436035.1_ASM143603v1_genomic.fna.gz --refList GCF_001436035.1_ASM143603v1_genomic.fna/target_genomes.txt --output GCF_001436035.1_ASM143603v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:34:50,726] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:50,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa1b1319-0019-414b-bbbf-5f28b7dfcc7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:34:50,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa1b1319-0019-414b-bbbf-5f28b7dfcc7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:34:50,736] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:34:50,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:34:50,736] [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=DSM 20451	GCA_001436035.1	1625	1625	type	True	100.0	376	381	95	conclusive
Fructilactobacillus sanfranciscensis	strain=JCM 5668	GCA_003369815.1	1625	1625	type	True	99.9937	378	381	95	conclusive
Fructilactobacillus sanfranciscensis	strain=TMW 1.53	GCA_002907365.1	1625	1625	type	True	99.9932	379	381	95	conclusive
Fructilactobacillus lindneri	strain=TMW 1.88	GCA_002907375.1	53444	53444	type	True	79.1951	185	381	95	below_threshold
Fructilactobacillus lindneri	strain=DSM 20690	GCA_900167245.1	53444	53444	type	True	79.1224	193	381	95	below_threshold
Apilactobacillus ozensis	strain=JCM 17196	GCA_001311485.1	866801	866801	type	True	77.8178	54	381	95	below_threshold
Apilactobacillus micheneri	strain=Hlig3	GCA_002993975.1	1899430	1899430	type	True	77.7094	67	381	95	below_threshold
Apilactobacillus quenuiae	strain=HV_6	GCA_002994005.1	2008377	2008377	type	True	77.4961	60	381	95	below_threshold
Fructilactobacillus florum	strain=JCM 16035	GCA_001311215.1	640331	640331	type	True	77.2075	61	381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:34:50,738] [INFO] DFAST Taxonomy check result was written to GCF_001436035.1_ASM143603v1_genomic.fna/tc_result.tsv
[2024-01-24 11:34:50,738] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:34:50,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:34:50,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa1b1319-0019-414b-bbbf-5f28b7dfcc7d/dqc_reference/checkm_data
[2024-01-24 11:34:50,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:34:50,756] [INFO] Task started: CheckM
[2024-01-24 11:34:50,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001436035.1_ASM143603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001436035.1_ASM143603v1_genomic.fna/checkm_input GCF_001436035.1_ASM143603v1_genomic.fna/checkm_result
[2024-01-24 11:35:07,484] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:07,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:07,504] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:07,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:07,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001436035.1_ASM143603v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:07,506] [INFO] Task started: Blastn
[2024-01-24 11:35:07,506] [INFO] Running command: blastn -query GCF_001436035.1_ASM143603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa1b1319-0019-414b-bbbf-5f28b7dfcc7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001436035.1_ASM143603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:08,933] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:08,937] [INFO] Selected 21 target genomes.
[2024-01-24 11:35:08,937] [INFO] Target genome list was writen to GCF_001436035.1_ASM143603v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:08,975] [INFO] Task started: fastANI
[2024-01-24 11:35:08,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f6ea0ae-db22-451c-9943-ca03d2569e57/GCF_001436035.1_ASM143603v1_genomic.fna.gz --refList GCF_001436035.1_ASM143603v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001436035.1_ASM143603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:16,938] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:16,944] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:16,944] [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	100.0	376	381	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	79.1951	185	381	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	77.7094	67	381	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	-
GCF_002994005.1	s__Apilactobacillus quenuiae	77.4961	60	381	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993965.1	s__Apilactobacillus timberlakei	77.4518	63	381	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:16,946] [INFO] GTDB search result was written to GCF_001436035.1_ASM143603v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:16,946] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:16,949] [INFO] DFAST_QC result json was written to GCF_001436035.1_ASM143603v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:16,949] [INFO] DFAST_QC completed!
[2024-01-24 11:35:16,949] [INFO] Total running time: 0h0m35s