[2024-01-24 11:26:12,692] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg22e3ef35-a1f6-4595-8bf8-093570f0872f/dqc_reference
[2024-01-24 11:26:14,168] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,169] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,169] [INFO] Running command: gunzip -c /var/lib/cwl/stgb04c49a2-cbc4-457c-8ba4-99b2910628fc/GCF_001437255.1_ASM143725v1_genomic.fna.gz | prodigal -d GCF_001437255.1_ASM143725v1_genomic.fna/cds.fna -a GCF_001437255.1_ASM143725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:18,543] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:18,543] [INFO] Task started: HMMsearch
[2024-01-24 11:26:18,543] [INFO] Running command: hmmsearch --tblout GCF_001437255.1_ASM143725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22e3ef35-a1f6-4595-8bf8-093570f0872f/dqc_reference/reference_markers.hmm GCF_001437255.1_ASM143725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:18,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:18,842] [INFO] Found 6/6 markers.
[2024-01-24 11:26:18,865] [INFO] Query marker FASTA was written to GCF_001437255.1_ASM143725v1_genomic.fna/markers.fasta
[2024-01-24 11:26:18,866] [INFO] Task started: Blastn
[2024-01-24 11:26:18,866] [INFO] Running command: blastn -query GCF_001437255.1_ASM143725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22e3ef35-a1f6-4595-8bf8-093570f0872f/dqc_reference/reference_markers.fasta -out GCF_001437255.1_ASM143725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:19,497] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:19,500] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:19,501] [INFO] Target genome list was writen to GCF_001437255.1_ASM143725v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:19,511] [INFO] Task started: fastANI
[2024-01-24 11:26:19,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04c49a2-cbc4-457c-8ba4-99b2910628fc/GCF_001437255.1_ASM143725v1_genomic.fna.gz --refList GCF_001437255.1_ASM143725v1_genomic.fna/target_genomes.txt --output GCF_001437255.1_ASM143725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:25,502] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:25,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22e3ef35-a1f6-4595-8bf8-093570f0872f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:25,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22e3ef35-a1f6-4595-8bf8-093570f0872f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:25,511] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:25,512] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:25,512] [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
Pediococcus damnosus	strain=DSM 20331	GCA_001437255.1	51663	51663	type	True	100.0	646	648	95	conclusive
Pediococcus inopinatus	strain=DSM 20285	GCA_002982135.1	114090	114090	type	True	82.7933	456	648	95	below_threshold
Pediococcus inopinatus	strain=DSM 20285	GCA_001438725.1	114090	114090	type	True	82.6289	440	648	95	below_threshold
Pediococcus parvulus	strain=JCM 5889	GCA_014651215.1	54062	54062	type	True	79.9352	284	648	95	below_threshold
Pediococcus parvulus	strain=NBRC 100673	GCA_007990205.1	54062	54062	type	True	79.8678	276	648	95	below_threshold
Pediococcus ethanolidurans	strain=DSM 22301	GCA_001437405.1	319653	319653	type	True	79.8138	311	648	95	below_threshold
Pediococcus ethanolidurans	strain=CGMCC 1.3889	GCA_900111205.1	319653	319653	type	True	79.7783	321	648	95	below_threshold
Paucilactobacillus hokkaidonensis	strain=JCM 18461	GCA_001311505.1	1193095	1193095	type	True	79.3284	69	648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:25,514] [INFO] DFAST Taxonomy check result was written to GCF_001437255.1_ASM143725v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:25,514] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:25,515] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:25,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22e3ef35-a1f6-4595-8bf8-093570f0872f/dqc_reference/checkm_data
[2024-01-24 11:26:25,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:25,553] [INFO] Task started: CheckM
[2024-01-24 11:26:25,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001437255.1_ASM143725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001437255.1_ASM143725v1_genomic.fna/checkm_input GCF_001437255.1_ASM143725v1_genomic.fna/checkm_result
[2024-01-24 11:26:46,640] [INFO] Task succeeded: CheckM
[2024-01-24 11:26:46,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:26:46,668] [INFO] ===== Completeness check finished =====
[2024-01-24 11:26:46,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:26:46,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001437255.1_ASM143725v1_genomic.fna/markers.fasta)
[2024-01-24 11:26:46,669] [INFO] Task started: Blastn
[2024-01-24 11:26:46,669] [INFO] Running command: blastn -query GCF_001437255.1_ASM143725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22e3ef35-a1f6-4595-8bf8-093570f0872f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001437255.1_ASM143725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:47,568] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:47,572] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:47,572] [INFO] Target genome list was writen to GCF_001437255.1_ASM143725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:26:47,588] [INFO] Task started: fastANI
[2024-01-24 11:26:47,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04c49a2-cbc4-457c-8ba4-99b2910628fc/GCF_001437255.1_ASM143725v1_genomic.fna.gz --refList GCF_001437255.1_ASM143725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001437255.1_ASM143725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:26:55,115] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:55,124] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:26:55,124] [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_001437255.1	s__Pediococcus damnosus	100.0	646	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.57	99.19	0.93	0.88	12	conclusive
GCF_002982135.1	s__Pediococcus inopinatus	82.7933	456	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.47	98.95	0.96	0.92	3	-
GCF_007990205.1	s__Pediococcus parvulus	79.85	277	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.29	98.77	0.93	0.88	4	-
GCF_001437405.1	s__Pediococcus ethanolidurans	79.8448	310	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.63	97.25	0.91	0.81	5	-
GCF_003946385.1	s__Loigolactobacillus zhaoyuanensis	79.6133	50	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001438655.1	s__Pediococcus cellicola	79.5914	242	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001437605.1	s__Pediococcus argentinicus	78.6717	75	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.99	99.98	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:26:55,127] [INFO] GTDB search result was written to GCF_001437255.1_ASM143725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:26:55,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:26:55,131] [INFO] DFAST_QC result json was written to GCF_001437255.1_ASM143725v1_genomic.fna/dqc_result.json
[2024-01-24 11:26:55,132] [INFO] DFAST_QC completed!
[2024-01-24 11:26:55,132] [INFO] Total running time: 0h0m42s