[2024-01-24 13:49:19,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,073] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,073] [INFO] DQC Reference Directory: /var/lib/cwl/stgb494a1d4-c216-4d0a-9e8a-bc7c1621cd1f/dqc_reference
[2024-01-24 13:49:20,441] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,442] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,442] [INFO] Running command: gunzip -c /var/lib/cwl/stg722ceab4-165c-4124-a930-511526b7dcdd/GCF_001434455.1_ASM143445v1_genomic.fna.gz | prodigal -d GCF_001434455.1_ASM143445v1_genomic.fna/cds.fna -a GCF_001434455.1_ASM143445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:23,499] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:23,499] [INFO] Task started: HMMsearch
[2024-01-24 13:49:23,499] [INFO] Running command: hmmsearch --tblout GCF_001434455.1_ASM143445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb494a1d4-c216-4d0a-9e8a-bc7c1621cd1f/dqc_reference/reference_markers.hmm GCF_001434455.1_ASM143445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:23,741] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:23,742] [INFO] Found 6/6 markers.
[2024-01-24 13:49:23,761] [INFO] Query marker FASTA was written to GCF_001434455.1_ASM143445v1_genomic.fna/markers.fasta
[2024-01-24 13:49:23,761] [INFO] Task started: Blastn
[2024-01-24 13:49:23,762] [INFO] Running command: blastn -query GCF_001434455.1_ASM143445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb494a1d4-c216-4d0a-9e8a-bc7c1621cd1f/dqc_reference/reference_markers.fasta -out GCF_001434455.1_ASM143445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:24,374] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:24,377] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:24,377] [INFO] Target genome list was writen to GCF_001434455.1_ASM143445v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:24,386] [INFO] Task started: fastANI
[2024-01-24 13:49:24,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg722ceab4-165c-4124-a930-511526b7dcdd/GCF_001434455.1_ASM143445v1_genomic.fna.gz --refList GCF_001434455.1_ASM143445v1_genomic.fna/target_genomes.txt --output GCF_001434455.1_ASM143445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:30,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:30,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb494a1d4-c216-4d0a-9e8a-bc7c1621cd1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:30,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb494a1d4-c216-4d0a-9e8a-bc7c1621cd1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:30,143] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:30,143] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:30,143] [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 hayakitensis	strain=DSM 18933	GCA_001434455.1	396716	396716	type	True	100.0	530	533	95	conclusive
Ligilactobacillus hayakitensis	strain=JCM 14209	GCA_000615845.1	396716	396716	type	True	99.9456	503	533	95	conclusive
Ligilactobacillus salivarius	strain=DSM 20554	GCA_002079585.1	1624	1624	type	True	79.2731	181	533	95	below_threshold
Ligilactobacillus agilis	strain=DSM 20509	GCA_001436215.1	1601	1601	type	True	78.8951	82	533	95	below_threshold
Ligilactobacillus salivarius	strain=ATCC 11741	GCA_000159395.1	1624	1624	type	True	78.5787	168	533	95	below_threshold
Ligilactobacillus salivarius	strain=DSM 20555	GCA_001435955.1	1624	1624	type	True	78.5569	163	533	95	below_threshold
Ligilactobacillus ceti	strain=DSM 22408	GCA_001438785.1	395085	395085	type	True	78.1184	95	533	95	below_threshold
Ligilactobacillus ceti	strain=DSM 22408	GCA_000423245.1	395085	395085	type	True	78.0249	96	533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:30,145] [INFO] DFAST Taxonomy check result was written to GCF_001434455.1_ASM143445v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:30,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:30,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:30,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb494a1d4-c216-4d0a-9e8a-bc7c1621cd1f/dqc_reference/checkm_data
[2024-01-24 13:49:30,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:30,167] [INFO] Task started: CheckM
[2024-01-24 13:49:30,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001434455.1_ASM143445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001434455.1_ASM143445v1_genomic.fna/checkm_input GCF_001434455.1_ASM143445v1_genomic.fna/checkm_result
[2024-01-24 13:49:47,754] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:47,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:47,778] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:47,779] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:47,779] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001434455.1_ASM143445v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:47,780] [INFO] Task started: Blastn
[2024-01-24 13:49:47,780] [INFO] Running command: blastn -query GCF_001434455.1_ASM143445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb494a1d4-c216-4d0a-9e8a-bc7c1621cd1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001434455.1_ASM143445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:48,711] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:48,715] [INFO] Selected 24 target genomes.
[2024-01-24 13:49:48,716] [INFO] Target genome list was writen to GCF_001434455.1_ASM143445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:48,735] [INFO] Task started: fastANI
[2024-01-24 13:49:48,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg722ceab4-165c-4124-a930-511526b7dcdd/GCF_001434455.1_ASM143445v1_genomic.fna.gz --refList GCF_001434455.1_ASM143445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001434455.1_ASM143445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:58,964] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:58,974] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:58,974] [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_000615845.1	s__Ligilactobacillus hayakitensis	99.9456	503	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_000615765.1	s__Ligilactobacillus equi	79.5055	82	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.27	98.57	0.92	0.85	3	-
GCF_001436215.1	s__Ligilactobacillus agilis	78.8951	82	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.37	95.88	0.84	0.79	29	-
GCF_001435955.1	s__Ligilactobacillus salivarius	78.5813	162	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.81	97.07	0.87	0.79	193	-
GCF_000423245.1	s__Ligilactobacillus ceti	77.989	97	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900110005.1	s__Ligilactobacillus ruminis_A	77.8155	67	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.72	99.72	0.98	0.98	2	-
GCF_001434845.1	s__Liquorilactobacillus hordei	77.4039	53	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.13	98.13	0.87	0.87	2	-
GCA_019114385.1	s__Ligilactobacillus excrementigallinarum	77.2375	75	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434915.1	s__Liquorilactobacillus capillatus	77.0029	54	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436735.1	s__Liquorilactobacillus cacaonum	76.8845	66	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435235.1	s__Liquorilactobacillus ghanensis	76.6019	56	533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,976] [INFO] GTDB search result was written to GCF_001434455.1_ASM143445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:58,977] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:58,981] [INFO] DFAST_QC result json was written to GCF_001434455.1_ASM143445v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:58,981] [INFO] DFAST_QC completed!
[2024-01-24 13:49:58,982] [INFO] Total running time: 0h0m40s