[2024-01-24 13:26:26,045] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:26,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:26,047] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdcba67a-69b5-4c52-a00c-fd0afe0a3ad7/dqc_reference
[2024-01-24 13:26:27,261] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:27,262] [INFO] Task started: Prodigal
[2024-01-24 13:26:27,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dfdac09-d9ec-4960-8c65-b7024446c226/GCF_007989665.1_ASM798966v1_genomic.fna.gz | prodigal -d GCF_007989665.1_ASM798966v1_genomic.fna/cds.fna -a GCF_007989665.1_ASM798966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:30,951] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:30,951] [INFO] Task started: HMMsearch
[2024-01-24 13:26:30,952] [INFO] Running command: hmmsearch --tblout GCF_007989665.1_ASM798966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdcba67a-69b5-4c52-a00c-fd0afe0a3ad7/dqc_reference/reference_markers.hmm GCF_007989665.1_ASM798966v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:31,198] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:31,200] [INFO] Found 6/6 markers.
[2024-01-24 13:26:31,220] [INFO] Query marker FASTA was written to GCF_007989665.1_ASM798966v1_genomic.fna/markers.fasta
[2024-01-24 13:26:31,221] [INFO] Task started: Blastn
[2024-01-24 13:26:31,221] [INFO] Running command: blastn -query GCF_007989665.1_ASM798966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdcba67a-69b5-4c52-a00c-fd0afe0a3ad7/dqc_reference/reference_markers.fasta -out GCF_007989665.1_ASM798966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:31,820] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:31,825] [INFO] Selected 20 target genomes.
[2024-01-24 13:26:31,825] [INFO] Target genome list was writen to GCF_007989665.1_ASM798966v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:32,071] [INFO] Task started: fastANI
[2024-01-24 13:26:32,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dfdac09-d9ec-4960-8c65-b7024446c226/GCF_007989665.1_ASM798966v1_genomic.fna.gz --refList GCF_007989665.1_ASM798966v1_genomic.fna/target_genomes.txt --output GCF_007989665.1_ASM798966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:38,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:38,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdcba67a-69b5-4c52-a00c-fd0afe0a3ad7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:38,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdcba67a-69b5-4c52-a00c-fd0afe0a3ad7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:38,613] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:38,613] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:38,614] [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 aviarius	strain=NBRC 102162	GCA_007989665.1	1606	1606	type	True	100.0	520	524	95	conclusive
Ligilactobacillus aviarius	strain=DSM 20655	GCA_001436315.1	1606	1606	type	True	99.9901	523	524	95	conclusive
Ligilactobacillus araffinosus	strain=DSM 20653	GCA_001435375.1	147809	147809	type	True	89.3172	399	524	95	below_threshold
Ligilactobacillus animalis	strain=KCTC 3501	GCA_000183825.1	1605	1605	type	True	78.5905	55	524	95	below_threshold
Ligilactobacillus animalis	strain=DSM 20602	GCA_001434535.1	1605	1605	type	True	78.1504	54	524	95	below_threshold
Ligilactobacillus apodemi	strain=DSM 16634	GCA_001434405.1	307126	307126	type	True	78.1349	63	524	95	below_threshold
Ligilactobacillus apodemi	strain=JCM 16172	GCA_000615885.1	307126	307126	type	True	77.9774	64	524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:38,615] [INFO] DFAST Taxonomy check result was written to GCF_007989665.1_ASM798966v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:38,616] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:38,616] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:38,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdcba67a-69b5-4c52-a00c-fd0afe0a3ad7/dqc_reference/checkm_data
[2024-01-24 13:26:38,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:38,677] [INFO] Task started: CheckM
[2024-01-24 13:26:38,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989665.1_ASM798966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989665.1_ASM798966v1_genomic.fna/checkm_input GCF_007989665.1_ASM798966v1_genomic.fna/checkm_result
[2024-01-24 13:26:57,843] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:57,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:57,862] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:57,863] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:57,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989665.1_ASM798966v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:57,863] [INFO] Task started: Blastn
[2024-01-24 13:26:57,864] [INFO] Running command: blastn -query GCF_007989665.1_ASM798966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdcba67a-69b5-4c52-a00c-fd0afe0a3ad7/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989665.1_ASM798966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:58,584] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:58,588] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:58,588] [INFO] Target genome list was writen to GCF_007989665.1_ASM798966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:58,877] [INFO] Task started: fastANI
[2024-01-24 13:26:58,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dfdac09-d9ec-4960-8c65-b7024446c226/GCF_007989665.1_ASM798966v1_genomic.fna.gz --refList GCF_007989665.1_ASM798966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989665.1_ASM798966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:03,158] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:03,167] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:03,167] [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_001436315.1	s__Ligilactobacillus aviarius	99.9901	523	524	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.10	96.00	0.94	0.89	5	conclusive
GCF_001654615.1	s__Ligilactobacillus aviarius_B	94.4129	429	524	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.09	96.72	0.90	0.88	16	-
GCA_019120355.1	s__Ligilactobacillus faecavium	92.7915	329	524	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435375.1	s__Ligilactobacillus araffinosus	89.344	398	524	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114385.1	s__Ligilactobacillus excrementigallinarum	79.0862	172	524	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	78.1349	63	524	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:03,169] [INFO] GTDB search result was written to GCF_007989665.1_ASM798966v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:03,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:03,176] [INFO] DFAST_QC result json was written to GCF_007989665.1_ASM798966v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:03,176] [INFO] DFAST_QC completed!
[2024-01-24 13:27:03,177] [INFO] Total running time: 0h0m37s