[2024-01-24 13:22:15,854] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:15,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:15,856] [INFO] DQC Reference Directory: /var/lib/cwl/stgd415f064-fb71-4b64-8c84-3b38ce7caddb/dqc_reference
[2024-01-24 13:22:17,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:17,141] [INFO] Task started: Prodigal
[2024-01-24 13:22:17,142] [INFO] Running command: gunzip -c /var/lib/cwl/stge3390f9d-0d92-4a8c-9389-99efda878942/GCF_001591685.1_ASM159168v1_genomic.fna.gz | prodigal -d GCF_001591685.1_ASM159168v1_genomic.fna/cds.fna -a GCF_001591685.1_ASM159168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:21,532] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:21,533] [INFO] Task started: HMMsearch
[2024-01-24 13:22:21,533] [INFO] Running command: hmmsearch --tblout GCF_001591685.1_ASM159168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd415f064-fb71-4b64-8c84-3b38ce7caddb/dqc_reference/reference_markers.hmm GCF_001591685.1_ASM159168v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:21,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:21,790] [INFO] Found 6/6 markers.
[2024-01-24 13:22:21,813] [INFO] Query marker FASTA was written to GCF_001591685.1_ASM159168v1_genomic.fna/markers.fasta
[2024-01-24 13:22:21,814] [INFO] Task started: Blastn
[2024-01-24 13:22:21,814] [INFO] Running command: blastn -query GCF_001591685.1_ASM159168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd415f064-fb71-4b64-8c84-3b38ce7caddb/dqc_reference/reference_markers.fasta -out GCF_001591685.1_ASM159168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:22,427] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:22,433] [INFO] Selected 9 target genomes.
[2024-01-24 13:22:22,433] [INFO] Target genome list was writen to GCF_001591685.1_ASM159168v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:22,447] [INFO] Task started: fastANI
[2024-01-24 13:22:22,448] [INFO] Running command: fastANI --query /var/lib/cwl/stge3390f9d-0d92-4a8c-9389-99efda878942/GCF_001591685.1_ASM159168v1_genomic.fna.gz --refList GCF_001591685.1_ASM159168v1_genomic.fna/target_genomes.txt --output GCF_001591685.1_ASM159168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:26,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:26,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd415f064-fb71-4b64-8c84-3b38ce7caddb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:26,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd415f064-fb71-4b64-8c84-3b38ce7caddb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:26,219] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:26,219] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:26,219] [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 murinus	strain=NBRC 14221	GCA_001591685.1	1622	1622	suspected-type	True	100.0	640	641	95	conclusive
Ligilactobacillus murinus	strain=DSM 20452	GCA_001436015.1	1622	1622	type	True	99.9952	638	641	95	conclusive
Ligilactobacillus animalis	strain=DSM 20602	GCA_001434535.1	1605	1605	type	True	91.8151	499	641	95	below_threshold
Ligilactobacillus animalis	strain=KCTC 3501	GCA_000183825.1	1605	1605	type	True	91.7964	503	641	95	below_threshold
Ligilactobacillus apodemi	strain=DSM 16634	GCA_001434405.1	307126	307126	type	True	81.1966	307	641	95	below_threshold
Ligilactobacillus ceti	strain=DSM 22408	GCA_000423245.1	395085	395085	type	True	78.3146	54	641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:26,221] [INFO] DFAST Taxonomy check result was written to GCF_001591685.1_ASM159168v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:26,228] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:26,228] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:26,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd415f064-fb71-4b64-8c84-3b38ce7caddb/dqc_reference/checkm_data
[2024-01-24 13:22:26,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:26,261] [INFO] Task started: CheckM
[2024-01-24 13:22:26,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591685.1_ASM159168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591685.1_ASM159168v1_genomic.fna/checkm_input GCF_001591685.1_ASM159168v1_genomic.fna/checkm_result
[2024-01-24 13:22:48,350] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:48,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:48,369] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:48,370] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:48,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591685.1_ASM159168v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:48,371] [INFO] Task started: Blastn
[2024-01-24 13:22:48,371] [INFO] Running command: blastn -query GCF_001591685.1_ASM159168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd415f064-fb71-4b64-8c84-3b38ce7caddb/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591685.1_ASM159168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:49,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:49,179] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:49,179] [INFO] Target genome list was writen to GCF_001591685.1_ASM159168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:49,187] [INFO] Task started: fastANI
[2024-01-24 13:22:49,187] [INFO] Running command: fastANI --query /var/lib/cwl/stge3390f9d-0d92-4a8c-9389-99efda878942/GCF_001591685.1_ASM159168v1_genomic.fna.gz --refList GCF_001591685.1_ASM159168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591685.1_ASM159168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:53,549] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:53,556] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:53,557] [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_001591685.1	s__Ligilactobacillus murinus	100.0	640	641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.01	96.68	0.83	0.78	62	conclusive
GCA_910587695.1	s__Ligilactobacillus sp910587695	92.3146	519	641	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	91.8151	499	641	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	81.1969	307	641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900110005.1	s__Ligilactobacillus ruminis_A	78.4382	88	641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.72	99.72	0.98	0.98	2	-
GCF_000423245.1	s__Ligilactobacillus ceti	78.3146	54	641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:53,558] [INFO] GTDB search result was written to GCF_001591685.1_ASM159168v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:53,563] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:53,566] [INFO] DFAST_QC result json was written to GCF_001591685.1_ASM159168v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:53,566] [INFO] DFAST_QC completed!
[2024-01-24 13:22:53,566] [INFO] Total running time: 0h0m38s