[2024-01-24 12:13:05,262] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:05,264] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:05,264] [INFO] DQC Reference Directory: /var/lib/cwl/stgb77fc433-d05e-4a20-8acb-3e77af470ef4/dqc_reference
[2024-01-24 12:13:06,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:06,488] [INFO] Task started: Prodigal
[2024-01-24 12:13:06,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe9fa759-393f-42bc-80d6-c50ee6192672/GCF_000615765.1_ASM61576v1_genomic.fna.gz | prodigal -d GCF_000615765.1_ASM61576v1_genomic.fna/cds.fna -a GCF_000615765.1_ASM61576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:10,495] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:10,495] [INFO] Task started: HMMsearch
[2024-01-24 12:13:10,495] [INFO] Running command: hmmsearch --tblout GCF_000615765.1_ASM61576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb77fc433-d05e-4a20-8acb-3e77af470ef4/dqc_reference/reference_markers.hmm GCF_000615765.1_ASM61576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:10,659] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:10,660] [INFO] Found 6/6 markers.
[2024-01-24 12:13:10,681] [INFO] Query marker FASTA was written to GCF_000615765.1_ASM61576v1_genomic.fna/markers.fasta
[2024-01-24 12:13:10,682] [INFO] Task started: Blastn
[2024-01-24 12:13:10,682] [INFO] Running command: blastn -query GCF_000615765.1_ASM61576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb77fc433-d05e-4a20-8acb-3e77af470ef4/dqc_reference/reference_markers.fasta -out GCF_000615765.1_ASM61576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:11,295] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:11,299] [INFO] Selected 28 target genomes.
[2024-01-24 12:13:11,299] [INFO] Target genome list was writen to GCF_000615765.1_ASM61576v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:11,592] [INFO] Task started: fastANI
[2024-01-24 12:13:11,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe9fa759-393f-42bc-80d6-c50ee6192672/GCF_000615765.1_ASM61576v1_genomic.fna.gz --refList GCF_000615765.1_ASM61576v1_genomic.fna/target_genomes.txt --output GCF_000615765.1_ASM61576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:19,591] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:19,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb77fc433-d05e-4a20-8acb-3e77af470ef4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:19,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb77fc433-d05e-4a20-8acb-3e77af470ef4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:19,599] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:13:19,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:19,600] [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 equi	strain=JCM 10991	GCA_000615765.1	137357	137357	type	True	100.0	668	676	95	conclusive
Ligilactobacillus equi	strain=DSM 15833	GCA_001435735.1	137357	137357	type	True	99.9636	668	676	95	conclusive
Ligilactobacillus agilis	strain=DSM 20509	GCA_001436215.1	1601	1601	type	True	79.5887	96	676	95	below_threshold
Ligilactobacillus hayakitensis	strain=JCM 14209	GCA_000615845.1	396716	396716	type	True	79.5764	86	676	95	below_threshold
Ligilactobacillus hayakitensis	strain=DSM 18933	GCA_001434455.1	396716	396716	type	True	79.4486	82	676	95	below_threshold
Ligilactobacillus animalis	strain=KCTC 3501	GCA_000183825.1	1605	1605	type	True	78.5349	56	676	95	below_threshold
Ligilactobacillus animalis	strain=DSM 20602	GCA_001434535.1	1605	1605	type	True	78.2671	53	676	95	below_threshold
Ligilactobacillus apodemi	strain=DSM 16634	GCA_001434405.1	307126	307126	type	True	78.2187	65	676	95	below_threshold
Ligilactobacillus apodemi	strain=JCM 16172	GCA_000615885.1	307126	307126	type	True	78.0579	63	676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:19,601] [INFO] DFAST Taxonomy check result was written to GCF_000615765.1_ASM61576v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:19,601] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:19,602] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:19,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb77fc433-d05e-4a20-8acb-3e77af470ef4/dqc_reference/checkm_data
[2024-01-24 12:13:19,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:19,625] [INFO] Task started: CheckM
[2024-01-24 12:13:19,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000615765.1_ASM61576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000615765.1_ASM61576v1_genomic.fna/checkm_input GCF_000615765.1_ASM61576v1_genomic.fna/checkm_result
[2024-01-24 12:13:37,942] [INFO] Task succeeded: CheckM
[2024-01-24 12:13:37,943] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:13:37,964] [INFO] ===== Completeness check finished =====
[2024-01-24 12:13:37,965] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:13:37,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000615765.1_ASM61576v1_genomic.fna/markers.fasta)
[2024-01-24 12:13:37,965] [INFO] Task started: Blastn
[2024-01-24 12:13:37,965] [INFO] Running command: blastn -query GCF_000615765.1_ASM61576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb77fc433-d05e-4a20-8acb-3e77af470ef4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000615765.1_ASM61576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:38,937] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:38,942] [INFO] Selected 31 target genomes.
[2024-01-24 12:13:38,942] [INFO] Target genome list was writen to GCF_000615765.1_ASM61576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:13:38,962] [INFO] Task started: fastANI
[2024-01-24 12:13:38,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe9fa759-393f-42bc-80d6-c50ee6192672/GCF_000615765.1_ASM61576v1_genomic.fna.gz --refList GCF_000615765.1_ASM61576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000615765.1_ASM61576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:13:48,881] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:48,889] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:13:48,890] [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_000615765.1	s__Ligilactobacillus equi	100.0	668	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.27	98.57	0.92	0.85	3	conclusive
GCF_001436215.1	s__Ligilactobacillus agilis	79.5887	96	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.37	95.88	0.84	0.79	29	-
GCF_000615845.1	s__Ligilactobacillus hayakitensis	79.5764	86	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_001591685.1	s__Ligilactobacillus murinus	78.6648	56	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.01	96.68	0.83	0.78	62	-
GCA_910587695.1	s__Ligilactobacillus sp910587695	78.3329	51	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434535.1	s__Ligilactobacillus animalis	78.2671	53	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.99	95.79	0.93	0.90	12	-
GCF_001434405.1	s__Ligilactobacillus apodemi	78.2187	65	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	1.00	1.00	2	-
GCA_905204935.1	s__Ligilactobacillus sp900765635	78.2133	60	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.92	0.92	2	-
GCF_000423265.1	s__Ligilactobacillus saerimneri	77.3251	55	676	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.58	97.67	0.92	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:13:48,891] [INFO] GTDB search result was written to GCF_000615765.1_ASM61576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:13:48,892] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:13:48,895] [INFO] DFAST_QC result json was written to GCF_000615765.1_ASM61576v1_genomic.fna/dqc_result.json
[2024-01-24 12:13:48,895] [INFO] DFAST_QC completed!
[2024-01-24 12:13:48,895] [INFO] Total running time: 0h0m44s