[2024-01-24 12:31:21,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:21,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:21,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg46eaf37e-75bd-43b3-b3b5-21c8c3b6d524/dqc_reference
[2024-01-24 12:31:22,536] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,537] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg9233f482-4372-4226-bd82-546b95c23b62/GCF_024622425.1_ASM2462242v1_genomic.fna.gz | prodigal -d GCF_024622425.1_ASM2462242v1_genomic.fna/cds.fna -a GCF_024622425.1_ASM2462242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:25,283] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:25,284] [INFO] Task started: HMMsearch
[2024-01-24 12:31:25,284] [INFO] Running command: hmmsearch --tblout GCF_024622425.1_ASM2462242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46eaf37e-75bd-43b3-b3b5-21c8c3b6d524/dqc_reference/reference_markers.hmm GCF_024622425.1_ASM2462242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:25,459] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:25,461] [INFO] Found 6/6 markers.
[2024-01-24 12:31:25,481] [INFO] Query marker FASTA was written to GCF_024622425.1_ASM2462242v1_genomic.fna/markers.fasta
[2024-01-24 12:31:25,481] [INFO] Task started: Blastn
[2024-01-24 12:31:25,481] [INFO] Running command: blastn -query GCF_024622425.1_ASM2462242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46eaf37e-75bd-43b3-b3b5-21c8c3b6d524/dqc_reference/reference_markers.fasta -out GCF_024622425.1_ASM2462242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:26,066] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:26,070] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:26,070] [INFO] Target genome list was writen to GCF_024622425.1_ASM2462242v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:26,087] [INFO] Task started: fastANI
[2024-01-24 12:31:26,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg9233f482-4372-4226-bd82-546b95c23b62/GCF_024622425.1_ASM2462242v1_genomic.fna.gz --refList GCF_024622425.1_ASM2462242v1_genomic.fna/target_genomes.txt --output GCF_024622425.1_ASM2462242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:30,179] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:30,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46eaf37e-75bd-43b3-b3b5-21c8c3b6d524/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:30,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46eaf37e-75bd-43b3-b3b5-21c8c3b6d524/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:30,188] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:30,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:30,188] [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
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	100.0	490	491	95	conclusive
Lactobacillus rodentium	strain=DSM 24759	GCA_003423665.1	947835	947835	type	True	99.9726	489	491	95	conclusive
Lactobacillus hominis	strain=type strain:CRBIP 24.179	GCA_000296835.1	1203033	1203033	type	True	79.8655	193	491	95	below_threshold
Lactobacillus johnsonii	strain=ATCC 33200	GCA_000159355.1	33959	33959	type	True	79.8619	179	491	95	below_threshold
Lactobacillus hominis	strain=DSM 23910	GCA_001436125.1	1203033	1203033	type	True	79.7372	191	491	95	below_threshold
Lactobacillus colini	strain=DSM 101872	GCA_017874575.1	1819254	1819254	type	True	79.6659	149	491	95	below_threshold
Lactobacillus johnsonii	strain=ATCC 33200	GCA_001433975.1	33959	33959	type	True	79.5946	180	491	95	below_threshold
Lactobacillus taiwanensis	strain=DSM 21401	GCA_001436695.1	508451	508451	type	True	79.2868	194	491	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	78.3618	144	491	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	77.5749	67	491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:30,190] [INFO] DFAST Taxonomy check result was written to GCF_024622425.1_ASM2462242v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:30,191] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:30,191] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:30,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46eaf37e-75bd-43b3-b3b5-21c8c3b6d524/dqc_reference/checkm_data
[2024-01-24 12:31:30,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:30,209] [INFO] Task started: CheckM
[2024-01-24 12:31:30,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024622425.1_ASM2462242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024622425.1_ASM2462242v1_genomic.fna/checkm_input GCF_024622425.1_ASM2462242v1_genomic.fna/checkm_result
[2024-01-24 12:31:45,520] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:45,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:45,541] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:45,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:45,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024622425.1_ASM2462242v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:45,542] [INFO] Task started: Blastn
[2024-01-24 12:31:45,542] [INFO] Running command: blastn -query GCF_024622425.1_ASM2462242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46eaf37e-75bd-43b3-b3b5-21c8c3b6d524/dqc_reference/reference_markers_gtdb.fasta -out GCF_024622425.1_ASM2462242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:46,254] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:46,257] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:46,258] [INFO] Target genome list was writen to GCF_024622425.1_ASM2462242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:46,266] [INFO] Task started: fastANI
[2024-01-24 12:31:46,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg9233f482-4372-4226-bd82-546b95c23b62/GCF_024622425.1_ASM2462242v1_genomic.fna.gz --refList GCF_024622425.1_ASM2462242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024622425.1_ASM2462242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:50,564] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:50,576] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:50,576] [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_003423665.1	s__Lactobacillus rodentium	99.9726	489	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014803905.1	s__Lactobacillus sp014803905	87.5412	218	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296835.1	s__Lactobacillus hominis	79.8655	193	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCF_000159355.1	s__Lactobacillus johnsonii	79.8461	180	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.89	95.28	0.86	0.57	61	-
GCF_017874575.1	s__Lactobacillus colini	79.6667	149	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584685.1	s__Lactobacillus paragasseri	79.563	180	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCA_910589175.1	s__Lactobacillus sp910589175	79.4442	180	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803895.1	s__Lactobacillus sp014803895	79.4201	176	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589675.1	s__Lactobacillus sp910589675	79.3313	150	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_001436695.1	s__Lactobacillus taiwanensis	79.2901	193	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCF_002706375.1	s__Lactobacillus amylovorus	78.5421	108	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_001591845.1	s__Lactobacillus acidophilus	78.4598	143	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_000160875.1	s__Lactobacillus iners	78.3072	88	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	-
GCF_001436305.1	s__Lactobacillus ultunensis	78.2816	126	491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:50,578] [INFO] GTDB search result was written to GCF_024622425.1_ASM2462242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:50,579] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:50,585] [INFO] DFAST_QC result json was written to GCF_024622425.1_ASM2462242v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:50,585] [INFO] DFAST_QC completed!
[2024-01-24 12:31:50,585] [INFO] Total running time: 0h0m29s