[2024-01-25 20:13:05,560] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:05,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:05,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg88dcfa69-e902-42ac-a68c-230159e67480/dqc_reference
[2024-01-25 20:13:06,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:06,682] [INFO] Task started: Prodigal
[2024-01-25 20:13:06,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg64f72322-9876-4147-8fc8-c911be15af25/GCF_022836475.1_ASM2283647v1_genomic.fna.gz | prodigal -d GCF_022836475.1_ASM2283647v1_genomic.fna/cds.fna -a GCF_022836475.1_ASM2283647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:11,041] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:11,041] [INFO] Task started: HMMsearch
[2024-01-25 20:13:11,042] [INFO] Running command: hmmsearch --tblout GCF_022836475.1_ASM2283647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88dcfa69-e902-42ac-a68c-230159e67480/dqc_reference/reference_markers.hmm GCF_022836475.1_ASM2283647v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:11,226] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:11,227] [INFO] Found 6/6 markers.
[2024-01-25 20:13:11,249] [INFO] Query marker FASTA was written to GCF_022836475.1_ASM2283647v1_genomic.fna/markers.fasta
[2024-01-25 20:13:11,249] [INFO] Task started: Blastn
[2024-01-25 20:13:11,249] [INFO] Running command: blastn -query GCF_022836475.1_ASM2283647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88dcfa69-e902-42ac-a68c-230159e67480/dqc_reference/reference_markers.fasta -out GCF_022836475.1_ASM2283647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:11,808] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:11,813] [INFO] Selected 30 target genomes.
[2024-01-25 20:13:11,813] [INFO] Target genome list was writen to GCF_022836475.1_ASM2283647v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:11,831] [INFO] Task started: fastANI
[2024-01-25 20:13:11,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg64f72322-9876-4147-8fc8-c911be15af25/GCF_022836475.1_ASM2283647v1_genomic.fna.gz --refList GCF_022836475.1_ASM2283647v1_genomic.fna/target_genomes.txt --output GCF_022836475.1_ASM2283647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:21,226] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:21,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88dcfa69-e902-42ac-a68c-230159e67480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:21,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88dcfa69-e902-42ac-a68c-230159e67480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:21,237] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:13:21,237] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:13:21,237] [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
Ligilactobacillus pobuzihii	strain=NBRC 103219	GCA_007991295.1	449659	449659	type	True	79.4203	259	755	95	below_threshold
Ligilactobacillus pobuzihii	strain=NBRC 103219	GCA_001438865.1	449659	449659	type	True	79.4138	258	755	95	below_threshold
Ligilactobacillus pobuzihii	strain=E100301	GCA_000349725.1	449659	449659	type	True	79.3733	260	755	95	below_threshold
Ligilactobacillus pobuzihii	strain=KCTC 13174	GCA_001433815.1	449659	449659	type	True	79.3686	254	755	95	below_threshold
Ligilactobacillus acidipiscis	strain=DSM 15836	GCA_001435755.1	89059	89059	type	True	79.2458	217	755	95	below_threshold
Ligilactobacillus salitolerans	strain=YK43	GCA_003864415.1	1808352	1808352	type	True	79.0988	195	755	95	below_threshold
Ligilactobacillus apodemi	strain=DSM 16634	GCA_001434405.1	307126	307126	type	True	78.0007	74	755	95	below_threshold
Ligilactobacillus apodemi	strain=JCM 16172	GCA_000615885.1	307126	307126	type	True	77.9062	72	755	95	below_threshold
Ligilactobacillus animalis	strain=DSM 20602	GCA_001434535.1	1605	1605	type	True	77.4811	71	755	95	below_threshold
Ligilactobacillus animalis	strain=KCTC 3501	GCA_000183825.1	1605	1605	type	True	77.4465	72	755	95	below_threshold
Ligilactobacillus ceti	strain=DSM 22408	GCA_001438785.1	395085	395085	type	True	77.2973	59	755	95	below_threshold
Lactiplantibacillus mudanjiangensis	strain=11050	GCA_005405385.1	1296538	1296538	type	True	77.1478	58	755	95	below_threshold
Ligilactobacillus ceti	strain=DSM 22408	GCA_000423245.1	395085	395085	type	True	77.0759	59	755	95	below_threshold
Liquorilactobacillus capillatus	strain=DSM 19910	GCA_001434915.1	480931	480931	type	True	76.8523	50	755	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:21,239] [INFO] DFAST Taxonomy check result was written to GCF_022836475.1_ASM2283647v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:21,240] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:21,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:21,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88dcfa69-e902-42ac-a68c-230159e67480/dqc_reference/checkm_data
[2024-01-25 20:13:21,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:21,271] [INFO] Task started: CheckM
[2024-01-25 20:13:21,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022836475.1_ASM2283647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022836475.1_ASM2283647v1_genomic.fna/checkm_input GCF_022836475.1_ASM2283647v1_genomic.fna/checkm_result
[2024-01-25 20:13:40,740] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:40,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:40,769] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:40,769] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:40,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022836475.1_ASM2283647v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:40,770] [INFO] Task started: Blastn
[2024-01-25 20:13:40,770] [INFO] Running command: blastn -query GCF_022836475.1_ASM2283647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88dcfa69-e902-42ac-a68c-230159e67480/dqc_reference/reference_markers_gtdb.fasta -out GCF_022836475.1_ASM2283647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:41,534] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:41,543] [INFO] Selected 22 target genomes.
[2024-01-25 20:13:41,543] [INFO] Target genome list was writen to GCF_022836475.1_ASM2283647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:41,561] [INFO] Task started: fastANI
[2024-01-25 20:13:41,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg64f72322-9876-4147-8fc8-c911be15af25/GCF_022836475.1_ASM2283647v1_genomic.fna.gz --refList GCF_022836475.1_ASM2283647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022836475.1_ASM2283647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:50,130] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:50,138] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:50,138] [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
GCA_019114105.1	s__Ligilactobacillus excrementipullorum	96.7261	503	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000349725.1	s__Ligilactobacillus pobuzihii	79.3759	258	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.99	99.98	1.00	0.99	4	-
GCA_019116985.1	s__Ligilactobacillus excrementavium	79.3124	242	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.12	97.12	0.91	0.91	2	-
GCF_001435755.1	s__Ligilactobacillus acidipiscis	79.2465	217	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.45	97.83	0.82	0.76	9	-
GCF_003864415.1	s__Ligilactobacillus salitolerans	79.1098	194	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434405.1	s__Ligilactobacillus apodemi	78.0007	74	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001434535.1	s__Ligilactobacillus animalis	77.4811	71	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.99	95.79	0.93	0.90	12	-
GCA_910587695.1	s__Ligilactobacillus sp910587695	77.4447	65	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423245.1	s__Ligilactobacillus ceti	76.9893	59	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001434915.1	s__Liquorilactobacillus capillatus	76.8523	50	755	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:50,139] [INFO] GTDB search result was written to GCF_022836475.1_ASM2283647v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:50,140] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:50,146] [INFO] DFAST_QC result json was written to GCF_022836475.1_ASM2283647v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:50,146] [INFO] DFAST_QC completed!
[2024-01-25 20:13:50,146] [INFO] Total running time: 0h0m45s