[2024-01-24 10:57:07,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,621] [INFO] DQC Reference Directory: /var/lib/cwl/stge556989b-e9a6-4263-9366-31ecf57ac4f4/dqc_reference
[2024-01-24 10:57:10,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:10,645] [INFO] Task started: Prodigal
[2024-01-24 10:57:10,645] [INFO] Running command: gunzip -c /var/lib/cwl/stge64851ff-bbfd-424c-889c-2a24b18e1444/GCF_013184075.1_ASM1318407v1_genomic.fna.gz | prodigal -d GCF_013184075.1_ASM1318407v1_genomic.fna/cds.fna -a GCF_013184075.1_ASM1318407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:13,736] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:13,737] [INFO] Task started: HMMsearch
[2024-01-24 10:57:13,737] [INFO] Running command: hmmsearch --tblout GCF_013184075.1_ASM1318407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge556989b-e9a6-4263-9366-31ecf57ac4f4/dqc_reference/reference_markers.hmm GCF_013184075.1_ASM1318407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:14,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:14,144] [INFO] Found 6/6 markers.
[2024-01-24 10:57:14,177] [INFO] Query marker FASTA was written to GCF_013184075.1_ASM1318407v1_genomic.fna/markers.fasta
[2024-01-24 10:57:14,178] [INFO] Task started: Blastn
[2024-01-24 10:57:14,178] [INFO] Running command: blastn -query GCF_013184075.1_ASM1318407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge556989b-e9a6-4263-9366-31ecf57ac4f4/dqc_reference/reference_markers.fasta -out GCF_013184075.1_ASM1318407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:17,730] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:17,733] [INFO] Selected 25 target genomes.
[2024-01-24 10:57:17,733] [INFO] Target genome list was writen to GCF_013184075.1_ASM1318407v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:18,219] [INFO] Task started: fastANI
[2024-01-24 10:57:18,220] [INFO] Running command: fastANI --query /var/lib/cwl/stge64851ff-bbfd-424c-889c-2a24b18e1444/GCF_013184075.1_ASM1318407v1_genomic.fna.gz --refList GCF_013184075.1_ASM1318407v1_genomic.fna/target_genomes.txt --output GCF_013184075.1_ASM1318407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:28,380] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:28,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge556989b-e9a6-4263-9366-31ecf57ac4f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:28,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge556989b-e9a6-4263-9366-31ecf57ac4f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:28,402] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:28,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:28,402] [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 kribbianus	strain=YH-lac9	GCA_013184075.1	2729622	2729622	type	True	100.0	500	501	95	conclusive
Lentilactobacillus senioris	strain=JCM 17472	GCA_001312065.1	931534	931534	type	True	79.5405	172	501	95	below_threshold
Lentilactobacillus senioris	strain=DSM 24302	GCA_001436555.1	931534	931534	type	True	79.5372	178	501	95	below_threshold
Apilactobacillus bombintestini	strain=BHWM-4	GCA_003627035.1	2419772	2419772	type	True	79.3507	53	501	95	below_threshold
Lentilactobacillus curieae	strain=CCTCC M 2011381	GCA_000785105.2	1138822	1138822	type	True	79.2996	81	501	95	below_threshold
Lentilactobacillus parakefiri	strain=DSM 10551	GCA_004354625.1	152332	152332	type	True	79.2835	51	501	95	below_threshold
Lentilactobacillus parakefiri	strain=JCM 8573	GCA_002157585.1	152332	152332	type	True	79.0142	52	501	95	below_threshold
Lentilactobacillus laojiaonis	strain=IM3328	GCA_020616595.1	2883998	2883998	type	True	79.011	104	501	95	below_threshold
Lentilactobacillus kosonis	strain=NBRC111893	GCA_003864335.1	2810561	2810561	type	True	78.6611	71	501	95	below_threshold
Lentilactobacillus kisonensis	strain=DSM 19906	GCA_001434135.1	481722	481722	type	True	78.6189	69	501	95	below_threshold
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	78.5876	66	501	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	78.4669	67	501	95	below_threshold
Lentilactobacillus kefiri	strain=NBRC 15888	GCA_007989105.1	33962	33962	type	True	78.3733	72	501	95	below_threshold
Lentilactobacillus kefiri	strain=DSM 20587	GCA_001436175.1	33962	33962	type	True	78.2901	65	501	95	below_threshold
Apilactobacillus xinyiensis	strain=F575-4	GCA_019656235.1	2841032	2841032	type	True	78.0958	54	501	95	below_threshold
Lentilactobacillus fungorum	strain=YK48G	GCA_016860605.1	2201250	2201250	type	True	77.9284	70	501	95	below_threshold
Apilactobacillus quenuiae	strain=HV_6	GCA_002994005.1	2008377	2008377	type	True	77.8179	59	501	95	below_threshold
Lentilactobacillus raoultii	strain=Marseille-P4006	GCA_900411375.1	1987503	1987503	type	True	77.6643	70	501	95	below_threshold
Apilactobacillus timberlakei	strain=HV_12	GCA_002993965.1	2008380	2008380	type	True	77.4518	56	501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:28,404] [INFO] DFAST Taxonomy check result was written to GCF_013184075.1_ASM1318407v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:28,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:28,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:28,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge556989b-e9a6-4263-9366-31ecf57ac4f4/dqc_reference/checkm_data
[2024-01-24 10:57:28,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:28,425] [INFO] Task started: CheckM
[2024-01-24 10:57:28,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013184075.1_ASM1318407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013184075.1_ASM1318407v1_genomic.fna/checkm_input GCF_013184075.1_ASM1318407v1_genomic.fna/checkm_result
[2024-01-24 10:57:46,129] [INFO] Task succeeded: CheckM
[2024-01-24 10:57:46,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:57:46,149] [INFO] ===== Completeness check finished =====
[2024-01-24 10:57:46,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:57:46,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013184075.1_ASM1318407v1_genomic.fna/markers.fasta)
[2024-01-24 10:57:46,150] [INFO] Task started: Blastn
[2024-01-24 10:57:46,150] [INFO] Running command: blastn -query GCF_013184075.1_ASM1318407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge556989b-e9a6-4263-9366-31ecf57ac4f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013184075.1_ASM1318407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:47,080] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:47,084] [INFO] Selected 25 target genomes.
[2024-01-24 10:57:47,084] [INFO] Target genome list was writen to GCF_013184075.1_ASM1318407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:57:47,116] [INFO] Task started: fastANI
[2024-01-24 10:57:47,116] [INFO] Running command: fastANI --query /var/lib/cwl/stge64851ff-bbfd-424c-889c-2a24b18e1444/GCF_013184075.1_ASM1318407v1_genomic.fna.gz --refList GCF_013184075.1_ASM1318407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013184075.1_ASM1318407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:57:56,577] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:56,594] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:57:56,594] [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_013184075.1	s__Lentilactobacillus kribbianus	100.0	500	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001436555.1	s__Lentilactobacillus senioris	79.5372	178	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.88	99.77	1.00	1.00	3	-
GCF_003627035.1	s__Apilactobacillus bombintestini	79.3086	53	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785105.2	s__Lentilactobacillus curieae	79.098	80	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157585.1	s__Lentilactobacillus parakefiri	79.0123	52	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.39	0.94	0.92	4	-
GCF_003864335.1	s__Lentilactobacillus curieae_A	78.6611	71	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434135.1	s__Lentilactobacillus kisonensis	78.6189	69	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.52	0.95	0.93	3	-
GCF_001434145.1	s__Lentilactobacillus otakiensis	78.5876	66	501	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	78.3733	72	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.76	99.64	0.95	0.93	9	-
GCF_002993975.1	s__Apilactobacillus micheneri	78.2951	58	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	-
GCF_016860605.1	s__Lentilactobacillus sp016860605	77.9284	70	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994005.1	s__Apilactobacillus quenuiae	77.8179	59	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900411375.1	s__Lentilactobacillus raoultii	77.6643	70	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434255.1	s__Lentilactobacillus diolivorans	77.638	78	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.05	98.10	0.95	0.90	3	-
GCF_002993965.1	s__Apilactobacillus timberlakei	77.4518	56	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-24 10:57:56,596] [INFO] GTDB search result was written to GCF_013184075.1_ASM1318407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:57:56,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:57:56,606] [INFO] DFAST_QC result json was written to GCF_013184075.1_ASM1318407v1_genomic.fna/dqc_result.json
[2024-01-24 10:57:56,606] [INFO] DFAST_QC completed!
[2024-01-24 10:57:56,606] [INFO] Total running time: 0h0m49s