[2024-01-25 19:01:05,500] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:05,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:05,502] [INFO] DQC Reference Directory: /var/lib/cwl/stg902a9a3e-76a8-4a41-8deb-b33fe60b84da/dqc_reference
[2024-01-25 19:01:06,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:06,646] [INFO] Task started: Prodigal
[2024-01-25 19:01:06,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ad97ace-805a-4752-bb40-f5aa5436dc69/GCF_001027985.1_ASM102798v1_genomic.fna.gz | prodigal -d GCF_001027985.1_ASM102798v1_genomic.fna/cds.fna -a GCF_001027985.1_ASM102798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:10,670] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:10,670] [INFO] Task started: HMMsearch
[2024-01-25 19:01:10,670] [INFO] Running command: hmmsearch --tblout GCF_001027985.1_ASM102798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg902a9a3e-76a8-4a41-8deb-b33fe60b84da/dqc_reference/reference_markers.hmm GCF_001027985.1_ASM102798v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:10,846] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:10,847] [INFO] Found 6/6 markers.
[2024-01-25 19:01:10,868] [INFO] Query marker FASTA was written to GCF_001027985.1_ASM102798v1_genomic.fna/markers.fasta
[2024-01-25 19:01:10,868] [INFO] Task started: Blastn
[2024-01-25 19:01:10,869] [INFO] Running command: blastn -query GCF_001027985.1_ASM102798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg902a9a3e-76a8-4a41-8deb-b33fe60b84da/dqc_reference/reference_markers.fasta -out GCF_001027985.1_ASM102798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:11,416] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:11,419] [INFO] Selected 16 target genomes.
[2024-01-25 19:01:11,419] [INFO] Target genome list was writen to GCF_001027985.1_ASM102798v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:11,433] [INFO] Task started: fastANI
[2024-01-25 19:01:11,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ad97ace-805a-4752-bb40-f5aa5436dc69/GCF_001027985.1_ASM102798v1_genomic.fna.gz --refList GCF_001027985.1_ASM102798v1_genomic.fna/target_genomes.txt --output GCF_001027985.1_ASM102798v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:17,846] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:17,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg902a9a3e-76a8-4a41-8deb-b33fe60b84da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:17,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg902a9a3e-76a8-4a41-8deb-b33fe60b84da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:17,854] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:01:17,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:17,854] [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
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	100.0	594	601	95	conclusive
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	99.9256	564	601	95	conclusive
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	80.1816	250	601	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_000160835.1	227943	227943	type	True	80.1288	276	601	95	below_threshold
Limosilactobacillus frumenti	strain=DSM 13145	GCA_001436045.1	104955	104955	type	True	80.0108	136	601	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	79.9996	265	601	95	below_threshold
Limosilactobacillus pontis	strain=DSM 8475	GCA_001435345.1	35787	35787	type	True	79.5766	198	601	95	below_threshold
Limosilactobacillus avistercoris	strain=Sa3CUN2	GCA_014836425.1	2762243	2762243	type	True	79.4615	129	601	95	below_threshold
Limosilactobacillus secaliphilus	strain=DSM 17896	GCA_001437055.1	396268	396268	type	True	78.611	100	601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:17,856] [INFO] DFAST Taxonomy check result was written to GCF_001027985.1_ASM102798v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:17,856] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:17,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:17,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg902a9a3e-76a8-4a41-8deb-b33fe60b84da/dqc_reference/checkm_data
[2024-01-25 19:01:17,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:17,881] [INFO] Task started: CheckM
[2024-01-25 19:01:17,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001027985.1_ASM102798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001027985.1_ASM102798v1_genomic.fna/checkm_input GCF_001027985.1_ASM102798v1_genomic.fna/checkm_result
[2024-01-25 19:01:36,080] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:36,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:36,107] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:36,107] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:36,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001027985.1_ASM102798v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:36,107] [INFO] Task started: Blastn
[2024-01-25 19:01:36,107] [INFO] Running command: blastn -query GCF_001027985.1_ASM102798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg902a9a3e-76a8-4a41-8deb-b33fe60b84da/dqc_reference/reference_markers_gtdb.fasta -out GCF_001027985.1_ASM102798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:36,934] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:36,936] [INFO] Selected 13 target genomes.
[2024-01-25 19:01:36,936] [INFO] Target genome list was writen to GCF_001027985.1_ASM102798v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:36,949] [INFO] Task started: fastANI
[2024-01-25 19:01:36,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ad97ace-805a-4752-bb40-f5aa5436dc69/GCF_001027985.1_ASM102798v1_genomic.fna.gz --refList GCF_001027985.1_ASM102798v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001027985.1_ASM102798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:41,744] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:41,751] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:01:41,752] [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_001435935.1	s__Limosilactobacillus panis	99.9256	564	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.95	99.95	0.95	0.95	2	conclusive
GCA_905214235.1	s__Limosilactobacillus sp905214235	93.0595	491	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902834055.1	s__Limosilactobacillus sp902834055	87.8939	188	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434465.1	s__Limosilactobacillus oris	80.1816	250	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	-
GCF_000160835.1	s__Limosilactobacillus antri	80.1509	274	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.98	99.98	0.99	0.99	3	-
GCA_019118405.1	s__Limosilactobacillus gallistercoris	79.3566	140	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.70	98.67	0.88	0.83	3	-
GCF_002940945.1	s__Limosilactobacillus pontis_A	79.2989	176	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156885.1	s__Limosilactobacillus sp900156885	79.224	183	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299975.1	s__Limosilactobacillus sp002299975	78.6922	141	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.38	99.38	0.84	0.84	2	-
GCF_001437055.1	s__Limosilactobacillus secaliphilus	78.6292	99	601	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:41,753] [INFO] GTDB search result was written to GCF_001027985.1_ASM102798v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:41,754] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:41,756] [INFO] DFAST_QC result json was written to GCF_001027985.1_ASM102798v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:41,756] [INFO] DFAST_QC completed!
[2024-01-25 19:01:41,756] [INFO] Total running time: 0h0m36s