[2024-01-24 14:03:07,143] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:07,146] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:07,146] [INFO] DQC Reference Directory: /var/lib/cwl/stg1666b6f1-8d35-4571-bc83-e96c49bb35ab/dqc_reference
[2024-01-24 14:03:08,499] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:08,500] [INFO] Task started: Prodigal
[2024-01-24 14:03:08,500] [INFO] Running command: gunzip -c /var/lib/cwl/stgcda013e6-4dad-4373-bd9f-ffc86f99187f/GCF_014145585.1_ASM1414558v1_genomic.fna.gz | prodigal -d GCF_014145585.1_ASM1414558v1_genomic.fna/cds.fna -a GCF_014145585.1_ASM1414558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:12,190] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:12,190] [INFO] Task started: HMMsearch
[2024-01-24 14:03:12,190] [INFO] Running command: hmmsearch --tblout GCF_014145585.1_ASM1414558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1666b6f1-8d35-4571-bc83-e96c49bb35ab/dqc_reference/reference_markers.hmm GCF_014145585.1_ASM1414558v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:12,453] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:12,454] [INFO] Found 6/6 markers.
[2024-01-24 14:03:12,473] [INFO] Query marker FASTA was written to GCF_014145585.1_ASM1414558v1_genomic.fna/markers.fasta
[2024-01-24 14:03:12,473] [INFO] Task started: Blastn
[2024-01-24 14:03:12,473] [INFO] Running command: blastn -query GCF_014145585.1_ASM1414558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1666b6f1-8d35-4571-bc83-e96c49bb35ab/dqc_reference/reference_markers.fasta -out GCF_014145585.1_ASM1414558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:13,052] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:13,056] [INFO] Selected 13 target genomes.
[2024-01-24 14:03:13,056] [INFO] Target genome list was writen to GCF_014145585.1_ASM1414558v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:13,083] [INFO] Task started: fastANI
[2024-01-24 14:03:13,083] [INFO] Running command: fastANI --query /var/lib/cwl/stgcda013e6-4dad-4373-bd9f-ffc86f99187f/GCF_014145585.1_ASM1414558v1_genomic.fna.gz --refList GCF_014145585.1_ASM1414558v1_genomic.fna/target_genomes.txt --output GCF_014145585.1_ASM1414558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:18,155] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:18,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1666b6f1-8d35-4571-bc83-e96c49bb35ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:18,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1666b6f1-8d35-4571-bc83-e96c49bb35ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:18,164] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:18,164] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:18,165] [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 agrestis	strain=WF-MT5-A	GCA_014145585.1	2759748	2759748	type	True	100.0	606	610	95	conclusive
Limosilactobacillus balticus	strain=BG-AF3-A	GCA_014145615.1	2759747	2759747	type	True	91.5298	484	610	95	below_threshold
Limosilactobacillus reuteri subsp. rodentium	strain=100-23	GCA_000168255.1	349123	1598	type	True	90.6624	509	610	95	below_threshold
Limosilactobacillus reuteri subsp. murium	strain=lpuph1	GCA_000179455.1	863368	1598	type	True	90.6011	463	610	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_001434615.1	557436	1598	type	True	90.5401	456	610	95	below_threshold
Limosilactobacillus reuteri subsp. suis	strain=ATCC 53608	GCA_000236455.2	927703	1598	type	True	90.5251	488	610	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=JCM 1112	GCA_000010005.1	557436	1598	type	True	90.5065	482	610	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_000016825.1	557436	1598	type	True	90.4514	487	610	95	below_threshold
Limosilactobacillus avistercoris	strain=Sa3CUN2	GCA_014836425.1	2762243	2762243	type	True	79.356	161	610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:18,166] [INFO] DFAST Taxonomy check result was written to GCF_014145585.1_ASM1414558v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:18,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:18,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:18,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1666b6f1-8d35-4571-bc83-e96c49bb35ab/dqc_reference/checkm_data
[2024-01-24 14:03:18,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:18,194] [INFO] Task started: CheckM
[2024-01-24 14:03:18,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014145585.1_ASM1414558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014145585.1_ASM1414558v1_genomic.fna/checkm_input GCF_014145585.1_ASM1414558v1_genomic.fna/checkm_result
[2024-01-24 14:03:37,637] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:37,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:37,665] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:37,666] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:37,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014145585.1_ASM1414558v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:37,667] [INFO] Task started: Blastn
[2024-01-24 14:03:37,667] [INFO] Running command: blastn -query GCF_014145585.1_ASM1414558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1666b6f1-8d35-4571-bc83-e96c49bb35ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_014145585.1_ASM1414558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:38,439] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:38,443] [INFO] Selected 5 target genomes.
[2024-01-24 14:03:38,443] [INFO] Target genome list was writen to GCF_014145585.1_ASM1414558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:38,453] [INFO] Task started: fastANI
[2024-01-24 14:03:38,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgcda013e6-4dad-4373-bd9f-ffc86f99187f/GCF_014145585.1_ASM1414558v1_genomic.fna.gz --refList GCF_014145585.1_ASM1414558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014145585.1_ASM1414558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:03:41,042] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:41,049] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:03:41,050] [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_014145585.1	s__Limosilactobacillus agrestis	100.0	606	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.60	98.25	0.88	0.88	3	conclusive
GCF_014145615.1	s__Limosilactobacillus balticus	91.4944	485	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.51	98.51	0.89	0.89	2	-
GCA_003072625.1	s__Limosilactobacillus reuteri_D	90.4875	473	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	95.43	95.30	0.77	0.72	32	-
GCF_000016825.1	s__Limosilactobacillus reuteri	90.4515	487	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.73	95.25	0.84	0.75	135	-
GCF_013694365.1	s__Limosilactobacillus reuteri_E	89.2837	453	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.28	96.40	0.80	0.72	58	-
--------------------------------------------------------------------------------
[2024-01-24 14:03:41,051] [INFO] GTDB search result was written to GCF_014145585.1_ASM1414558v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:03:41,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:03:41,055] [INFO] DFAST_QC result json was written to GCF_014145585.1_ASM1414558v1_genomic.fna/dqc_result.json
[2024-01-24 14:03:41,055] [INFO] DFAST_QC completed!
[2024-01-24 14:03:41,055] [INFO] Total running time: 0h0m34s