[2024-01-24 11:35:23,410] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b0b3779-2745-40b0-8eee-2f2f840bb071/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,240] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg830f38c3-6ec6-482a-b3fb-06f5917391d5/GCF_001435875.1_ASM143587v1_genomic.fna.gz | prodigal -d GCF_001435875.1_ASM143587v1_genomic.fna/cds.fna -a GCF_001435875.1_ASM143587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:32,577] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:32,578] [INFO] Task started: HMMsearch
[2024-01-24 11:35:32,578] [INFO] Running command: hmmsearch --tblout GCF_001435875.1_ASM143587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b0b3779-2745-40b0-8eee-2f2f840bb071/dqc_reference/reference_markers.hmm GCF_001435875.1_ASM143587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:32,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:32,919] [INFO] Found 6/6 markers.
[2024-01-24 11:35:32,954] [INFO] Query marker FASTA was written to GCF_001435875.1_ASM143587v1_genomic.fna/markers.fasta
[2024-01-24 11:35:32,954] [INFO] Task started: Blastn
[2024-01-24 11:35:32,955] [INFO] Running command: blastn -query GCF_001435875.1_ASM143587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b0b3779-2745-40b0-8eee-2f2f840bb071/dqc_reference/reference_markers.fasta -out GCF_001435875.1_ASM143587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:33,539] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:33,542] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:33,542] [INFO] Target genome list was writen to GCF_001435875.1_ASM143587v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,563] [INFO] Task started: fastANI
[2024-01-24 11:35:33,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg830f38c3-6ec6-482a-b3fb-06f5917391d5/GCF_001435875.1_ASM143587v1_genomic.fna.gz --refList GCF_001435875.1_ASM143587v1_genomic.fna/target_genomes.txt --output GCF_001435875.1_ASM143587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:42,087] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:42,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b0b3779-2745-40b0-8eee-2f2f840bb071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:42,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b0b3779-2745-40b0-8eee-2f2f840bb071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:42,099] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:42,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:42,100] [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
Lentilactobacillus farraginis	strain=DSM 18382	GCA_001435875.1	390841	390841	type	True	100.0	882	887	95	conclusive
Lentilactobacillus farraginis	strain=JCM 14108	GCA_000583655.1	390841	390841	type	True	99.9567	848	887	95	conclusive
Lentilactobacillus hilgardii	strain=ATCC 8290	GCA_004354795.1	1588	1588	type	True	80.976	475	887	95	below_threshold
Lentilactobacillus hilgardii	strain=ATCC 8290	GCA_000159315.1	1588	1588	type	True	80.9751	472	887	95	below_threshold
Lentilactobacillus hilgardii	strain=DSM 20176	GCA_001434655.1	1588	1588	type	True	80.9343	463	887	95	below_threshold
Lentilactobacillus parafarraginis	strain=JCM 14109	GCA_001311355.1	390842	390842	type	True	80.1021	307	887	95	below_threshold
Lentilactobacillus parafarraginis	strain=DSM 18390	GCA_001435895.1	390842	390842	type	True	80.0366	307	887	95	below_threshold
Lentilactobacillus raoultii	strain=Marseille-P4006	GCA_900411375.1	1987503	1987503	type	True	79.7584	418	887	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_000415925.1	481720	481720	type	True	79.4674	179	887	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	79.4606	179	887	95	below_threshold
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	79.3714	181	887	95	below_threshold
Lentilactobacillus kefiri	strain=NBRC 15888	GCA_007989105.1	33962	33962	type	True	79.2292	201	887	95	below_threshold
Lentilactobacillus kefiri	strain=DSM 20587	GCA_001436175.1	33962	33962	type	True	79.2162	184	887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:42,103] [INFO] DFAST Taxonomy check result was written to GCF_001435875.1_ASM143587v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:42,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:42,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:42,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b0b3779-2745-40b0-8eee-2f2f840bb071/dqc_reference/checkm_data
[2024-01-24 11:35:42,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:42,140] [INFO] Task started: CheckM
[2024-01-24 11:35:42,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001435875.1_ASM143587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001435875.1_ASM143587v1_genomic.fna/checkm_input GCF_001435875.1_ASM143587v1_genomic.fna/checkm_result
[2024-01-24 11:36:08,222] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:08,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:08,242] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:08,243] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:08,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001435875.1_ASM143587v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:08,243] [INFO] Task started: Blastn
[2024-01-24 11:36:08,244] [INFO] Running command: blastn -query GCF_001435875.1_ASM143587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b0b3779-2745-40b0-8eee-2f2f840bb071/dqc_reference/reference_markers_gtdb.fasta -out GCF_001435875.1_ASM143587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:08,960] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:08,963] [INFO] Selected 17 target genomes.
[2024-01-24 11:36:08,963] [INFO] Target genome list was writen to GCF_001435875.1_ASM143587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:08,975] [INFO] Task started: fastANI
[2024-01-24 11:36:08,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg830f38c3-6ec6-482a-b3fb-06f5917391d5/GCF_001435875.1_ASM143587v1_genomic.fna.gz --refList GCF_001435875.1_ASM143587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001435875.1_ASM143587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:16,777] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:16,788] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:16,788] [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_000583655.1	s__Lentilactobacillus farraginis	99.9567	848	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_000159315.1	s__Lentilactobacillus hilgardii	80.9613	473	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.37	96.88	0.92	0.87	10	-
GCF_001435895.1	s__Lentilactobacillus parafarraginis	80.0109	308	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.53	97.19	0.92	0.88	5	-
GCF_900411375.1	s__Lentilactobacillus raoultii	79.7584	418	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061365.1	s__Lentilactobacillus sp019061365	79.6162	207	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.43	99.43	0.89	0.89	2	-
GCF_001434145.1	s__Lentilactobacillus otakiensis	79.3714	181	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.95	99.91	1.00	1.00	3	-
GCF_007989105.1	s__Lentilactobacillus kefiri	79.2292	201	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.76	99.64	0.95	0.93	9	-
GCF_018314255.1	s__Lentilactobacillus buchneri	79.1535	196	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.61	97.12	0.94	0.90	27	-
GCF_001435575.1	s__Lentilactobacillus sunkii	78.6072	211	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	96.44	96.44	0.90	0.90	2	-
GCF_001434135.1	s__Lentilactobacillus kisonensis	78.2314	193	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.52	0.95	0.93	3	-
GCF_001436255.1	s__Lentilactobacillus rapi	78.1836	174	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.94	99.89	1.00	1.00	3	-
GCF_016860605.1	s__Lentilactobacillus sp016860605	78.089	175	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946245.1	s__Levilactobacillus cerevisiae	77.5153	50	887	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:16,789] [INFO] GTDB search result was written to GCF_001435875.1_ASM143587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:16,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:16,794] [INFO] DFAST_QC result json was written to GCF_001435875.1_ASM143587v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:16,795] [INFO] DFAST_QC completed!
[2024-01-24 11:36:16,795] [INFO] Total running time: 0h0m53s