[2024-01-24 13:17:26,756] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:26,758] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:26,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg6585a397-fea1-49e4-9769-1411b1993f43/dqc_reference
[2024-01-24 13:17:27,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:27,947] [INFO] Task started: Prodigal
[2024-01-24 13:17:27,948] [INFO] Running command: gunzip -c /var/lib/cwl/stge258dfb1-852c-4137-bf02-7eebe5372498/GCF_019656235.1_ASM1965623v1_genomic.fna.gz | prodigal -d GCF_019656235.1_ASM1965623v1_genomic.fna/cds.fna -a GCF_019656235.1_ASM1965623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:30,284] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:30,285] [INFO] Task started: HMMsearch
[2024-01-24 13:17:30,285] [INFO] Running command: hmmsearch --tblout GCF_019656235.1_ASM1965623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6585a397-fea1-49e4-9769-1411b1993f43/dqc_reference/reference_markers.hmm GCF_019656235.1_ASM1965623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:30,496] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:30,497] [INFO] Found 6/6 markers.
[2024-01-24 13:17:30,517] [INFO] Query marker FASTA was written to GCF_019656235.1_ASM1965623v1_genomic.fna/markers.fasta
[2024-01-24 13:17:30,518] [INFO] Task started: Blastn
[2024-01-24 13:17:30,518] [INFO] Running command: blastn -query GCF_019656235.1_ASM1965623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6585a397-fea1-49e4-9769-1411b1993f43/dqc_reference/reference_markers.fasta -out GCF_019656235.1_ASM1965623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:31,160] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:31,164] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:31,164] [INFO] Target genome list was writen to GCF_019656235.1_ASM1965623v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:31,189] [INFO] Task started: fastANI
[2024-01-24 13:17:31,190] [INFO] Running command: fastANI --query /var/lib/cwl/stge258dfb1-852c-4137-bf02-7eebe5372498/GCF_019656235.1_ASM1965623v1_genomic.fna.gz --refList GCF_019656235.1_ASM1965623v1_genomic.fna/target_genomes.txt --output GCF_019656235.1_ASM1965623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:37,015] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:37,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6585a397-fea1-49e4-9769-1411b1993f43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:37,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6585a397-fea1-49e4-9769-1411b1993f43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:37,028] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:37,028] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:37,028] [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
Apilactobacillus xinyiensis	strain=F575-4	GCA_019656235.1	2841032	2841032	type	True	100.0	460	461	95	conclusive
Apilactobacillus ozensis	strain=JCM 17196	GCA_001311485.1	866801	866801	type	True	84.576	337	461	95	below_threshold
Apilactobacillus ozensis	strain=DSM 23829	GCA_001435995.1	866801	866801	type	True	84.5675	353	461	95	below_threshold
Apilactobacillus micheneri	strain=Hlig3	GCA_002993975.1	1899430	1899430	type	True	79.4593	164	461	95	below_threshold
Apilactobacillus quenuiae	strain=HV_6	GCA_002994005.1	2008377	2008377	type	True	79.3326	163	461	95	below_threshold
Apilactobacillus kunkeei	strain=YH-15	GCA_001281265.1	148814	148814	suspected-type	True	79.1159	99	461	95	below_threshold
Apilactobacillus timberlakei	strain=HV_12	GCA_002993965.1	2008380	2008380	type	True	79.068	179	461	95	below_threshold
Apilactobacillus kunkeei	strain=DSM 12361	GCA_001433825.1	148814	148814	suspected-type	True	78.9815	98	461	95	below_threshold
Fructilactobacillus sanfranciscensis	strain=JCM 5668	GCA_003369815.1	1625	1625	type	True	78.0805	62	461	95	below_threshold
Fructilactobacillus sanfranciscensis	strain=TMW 1.53	GCA_002907365.1	1625	1625	type	True	78.0339	62	461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:37,030] [INFO] DFAST Taxonomy check result was written to GCF_019656235.1_ASM1965623v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:37,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:37,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:37,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6585a397-fea1-49e4-9769-1411b1993f43/dqc_reference/checkm_data
[2024-01-24 13:17:37,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:37,048] [INFO] Task started: CheckM
[2024-01-24 13:17:37,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019656235.1_ASM1965623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019656235.1_ASM1965623v1_genomic.fna/checkm_input GCF_019656235.1_ASM1965623v1_genomic.fna/checkm_result
[2024-01-24 13:17:52,258] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:52,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:52,275] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:52,276] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:52,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019656235.1_ASM1965623v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:52,277] [INFO] Task started: Blastn
[2024-01-24 13:17:52,277] [INFO] Running command: blastn -query GCF_019656235.1_ASM1965623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6585a397-fea1-49e4-9769-1411b1993f43/dqc_reference/reference_markers_gtdb.fasta -out GCF_019656235.1_ASM1965623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:53,260] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:53,264] [INFO] Selected 23 target genomes.
[2024-01-24 13:17:53,264] [INFO] Target genome list was writen to GCF_019656235.1_ASM1965623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:53,279] [INFO] Task started: fastANI
[2024-01-24 13:17:53,279] [INFO] Running command: fastANI --query /var/lib/cwl/stge258dfb1-852c-4137-bf02-7eebe5372498/GCF_019656235.1_ASM1965623v1_genomic.fna.gz --refList GCF_019656235.1_ASM1965623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019656235.1_ASM1965623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:01,292] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:01,302] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:18:01,303] [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_001435995.1	s__Apilactobacillus ozensis	84.5675	353	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	99.83	99.83	1.00	1.00	2	-
GCF_002993975.1	s__Apilactobacillus micheneri	79.4593	164	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	-
GCF_002994005.1	s__Apilactobacillus quenuiae	79.3326	163	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627035.1	s__Apilactobacillus bombintestini	79.2568	134	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281265.1	s__Apilactobacillus kunkeei	79.1159	99	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	97.63	95.32	0.94	0.90	8	-
GCF_002993965.1	s__Apilactobacillus timberlakei	79.08	178	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	-
GCF_001308205.1	s__Apilactobacillus kunkeei_B	78.9896	101	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930915.1	s__Apilactobacillus kunkeei_D	78.9088	101	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.78	97.92	0.96	0.94	5	-
GCF_001281175.1	s__Apilactobacillus apinorum	78.8534	132	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930975.1	s__Apilactobacillus kunkeei_E	78.7788	106	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184075.1	s__Lentilactobacillus kribbianus	77.7825	54	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436035.1	s__Fructilactobacillus sanfranciscensis	77.7786	58	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.31	98.98	0.96	0.90	32	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:01,304] [INFO] GTDB search result was written to GCF_019656235.1_ASM1965623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:01,304] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:01,307] [INFO] DFAST_QC result json was written to GCF_019656235.1_ASM1965623v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:01,308] [INFO] DFAST_QC completed!
[2024-01-24 13:18:01,308] [INFO] Total running time: 0h0m35s