[2024-01-24 13:40:35,088] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg721b73bb-ddf5-42e0-ae22-bcd164602e51/dqc_reference
[2024-01-24 13:40:36,390] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,391] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,392] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e9fd065-21ad-4eca-8442-c422f014d73d/GCF_004354655.1_ASM435465v1_genomic.fna.gz | prodigal -d GCF_004354655.1_ASM435465v1_genomic.fna/cds.fna -a GCF_004354655.1_ASM435465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:44,150] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:44,150] [INFO] Task started: HMMsearch
[2024-01-24 13:40:44,150] [INFO] Running command: hmmsearch --tblout GCF_004354655.1_ASM435465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg721b73bb-ddf5-42e0-ae22-bcd164602e51/dqc_reference/reference_markers.hmm GCF_004354655.1_ASM435465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:44,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:44,471] [INFO] Found 6/6 markers.
[2024-01-24 13:40:44,501] [INFO] Query marker FASTA was written to GCF_004354655.1_ASM435465v1_genomic.fna/markers.fasta
[2024-01-24 13:40:44,502] [INFO] Task started: Blastn
[2024-01-24 13:40:44,502] [INFO] Running command: blastn -query GCF_004354655.1_ASM435465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg721b73bb-ddf5-42e0-ae22-bcd164602e51/dqc_reference/reference_markers.fasta -out GCF_004354655.1_ASM435465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:45,111] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:45,114] [INFO] Selected 15 target genomes.
[2024-01-24 13:40:45,115] [INFO] Target genome list was writen to GCF_004354655.1_ASM435465v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:45,137] [INFO] Task started: fastANI
[2024-01-24 13:40:45,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e9fd065-21ad-4eca-8442-c422f014d73d/GCF_004354655.1_ASM435465v1_genomic.fna.gz --refList GCF_004354655.1_ASM435465v1_genomic.fna/target_genomes.txt --output GCF_004354655.1_ASM435465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:55,403] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:55,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg721b73bb-ddf5-42e0-ae22-bcd164602e51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:55,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg721b73bb-ddf5-42e0-ae22-bcd164602e51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:55,410] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:40:55,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:55,410] [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
Lacticaseibacillus paracasei subsp. paracasei	strain=ATCC 25302	GCA_004354655.1	47714	1597	type	True	100.0	931	935	95	conclusive
Lacticaseibacillus paracasei subsp. paracasei	strain=JCM 8130	GCA_000829035.1	47714	1597	type	True	99.9931	930	935	95	conclusive
Lacticaseibacillus paracasei subsp. paracasei	strain=DSM 5622	GCA_001436385.1	47714	1597	type	True	99.9298	869	935	95	conclusive
Lacticaseibacillus paracasei subsp. paracasei	strain=NBRC 15889	GCA_007989125.1	47714	1597	type	True	99.9233	870	935	95	conclusive
Lacticaseibacillus paracasei subsp. paracasei	strain=ATCC 25302	GCA_000159495.1	47714	1597	type	True	99.9023	919	935	95	conclusive
Lacticaseibacillus casei	strain=ATCC 393	GCA_000829055.1	1582	1582	suspected-type	True	80.8978	395	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:55,412] [INFO] DFAST Taxonomy check result was written to GCF_004354655.1_ASM435465v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:55,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:55,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:55,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg721b73bb-ddf5-42e0-ae22-bcd164602e51/dqc_reference/checkm_data
[2024-01-24 13:40:55,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:55,450] [INFO] Task started: CheckM
[2024-01-24 13:40:55,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354655.1_ASM435465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354655.1_ASM435465v1_genomic.fna/checkm_input GCF_004354655.1_ASM435465v1_genomic.fna/checkm_result
[2024-01-24 13:41:26,664] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:26,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:26,691] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:26,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:26,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354655.1_ASM435465v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:26,692] [INFO] Task started: Blastn
[2024-01-24 13:41:26,692] [INFO] Running command: blastn -query GCF_004354655.1_ASM435465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg721b73bb-ddf5-42e0-ae22-bcd164602e51/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354655.1_ASM435465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:27,596] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:27,600] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:27,600] [INFO] Target genome list was writen to GCF_004354655.1_ASM435465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:27,625] [INFO] Task started: fastANI
[2024-01-24 13:41:27,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e9fd065-21ad-4eca-8442-c422f014d73d/GCF_004354655.1_ASM435465v1_genomic.fna.gz --refList GCF_004354655.1_ASM435465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354655.1_ASM435465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:37,799] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:37,806] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:37,806] [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_000829035.1	s__Lacticaseibacillus paracasei	99.9931	930	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.30	97.86	0.88	0.73	252	conclusive
GCF_000829055.1	s__Lacticaseibacillus casei	80.8814	397	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.76	95.69	0.93	0.80	19	-
GCF_000260435.1	s__Lacticaseibacillus zeae	80.5904	410	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.07	96.92	0.91	0.87	11	-
GCF_004123795.1	s__Lacticaseibacillus chiayiensis	80.1126	397	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.97	98.62	0.94	0.94	3	-
GCF_900636965.1	s__Lacticaseibacillus rhamnosus	80.0137	435	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.40	96.73	0.93	0.86	237	-
GCF_003946165.1	s__Lacticaseibacillus baoqingensis	79.1197	75	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311785.1	s__Lacticaseibacillus saniviri	78.1267	78	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.88	99.88	0.99	0.99	3	-
GCF_001436115.1	s__Lacticaseibacillus brantae	77.3758	64	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:37,810] [INFO] GTDB search result was written to GCF_004354655.1_ASM435465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:37,811] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:37,819] [INFO] DFAST_QC result json was written to GCF_004354655.1_ASM435465v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:37,819] [INFO] DFAST_QC completed!
[2024-01-24 13:41:37,819] [INFO] Total running time: 0h1m3s