[2024-01-24 12:21:54,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:54,265] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:54,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg580b11ee-9195-4f86-a78f-abc45163b335/dqc_reference
[2024-01-24 12:21:55,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:55,468] [INFO] Task started: Prodigal
[2024-01-24 12:21:55,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bb63b1b-27a6-4074-8962-cc014199f2c6/GCF_002802965.1_ASM280296v1_genomic.fna.gz | prodigal -d GCF_002802965.1_ASM280296v1_genomic.fna/cds.fna -a GCF_002802965.1_ASM280296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:05,337] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:05,337] [INFO] Task started: HMMsearch
[2024-01-24 12:22:05,337] [INFO] Running command: hmmsearch --tblout GCF_002802965.1_ASM280296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg580b11ee-9195-4f86-a78f-abc45163b335/dqc_reference/reference_markers.hmm GCF_002802965.1_ASM280296v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:05,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:05,600] [INFO] Found 6/6 markers.
[2024-01-24 12:22:05,632] [INFO] Query marker FASTA was written to GCF_002802965.1_ASM280296v1_genomic.fna/markers.fasta
[2024-01-24 12:22:05,633] [INFO] Task started: Blastn
[2024-01-24 12:22:05,633] [INFO] Running command: blastn -query GCF_002802965.1_ASM280296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg580b11ee-9195-4f86-a78f-abc45163b335/dqc_reference/reference_markers.fasta -out GCF_002802965.1_ASM280296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:06,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:06,260] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:06,260] [INFO] Target genome list was writen to GCF_002802965.1_ASM280296v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:06,280] [INFO] Task started: fastANI
[2024-01-24 12:22:06,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb63b1b-27a6-4074-8962-cc014199f2c6/GCF_002802965.1_ASM280296v1_genomic.fna.gz --refList GCF_002802965.1_ASM280296v1_genomic.fna/target_genomes.txt --output GCF_002802965.1_ASM280296v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:15,290] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:15,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg580b11ee-9195-4f86-a78f-abc45163b335/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:15,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg580b11ee-9195-4f86-a78f-abc45163b335/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:15,299] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:15,300] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:15,300] [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
Sporolactobacillus pectinivorans	strain=GD201205	GCA_002802965.1	1591408	1591408	type	True	99.9944	1297	1303	95	conclusive
Sporolactobacillus shoreae	strain=BK92	GCA_004684935.1	1465501	1465501	type	True	80.3482	589	1303	95	below_threshold
Sporolactobacillus putidus	strain=JCM 15325	GCA_014647035.1	492735	492735	type	True	79.5857	262	1303	95	below_threshold
Sporolactobacillus nakayamae	strain=ATCC 700379	GCA_900113325.1	269670	269670	type	True	79.0772	171	1303	95	below_threshold
Sporolactobacillus laevolacticus	strain=DSM 442	GCA_000497245.1	33018	33018	type	True	78.765	205	1303	95	below_threshold
Sporolactobacillus vineae	strain=DSM 21990	GCA_000377985.1	444463	444463	type	True	77.8298	195	1303	95	below_threshold
Sporolactobacillus shoreicorticis	strain=LMG 29111	GCA_024125445.1	1923877	1923877	type	True	77.6721	152	1303	95	below_threshold
Sporolactobacillus vineae	strain=SL153	GCA_000246965.2	444463	444463	type	True	77.6618	204	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:15,304] [INFO] DFAST Taxonomy check result was written to GCF_002802965.1_ASM280296v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:15,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:15,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:15,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg580b11ee-9195-4f86-a78f-abc45163b335/dqc_reference/checkm_data
[2024-01-24 12:22:15,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:15,348] [INFO] Task started: CheckM
[2024-01-24 12:22:15,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002802965.1_ASM280296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002802965.1_ASM280296v1_genomic.fna/checkm_input GCF_002802965.1_ASM280296v1_genomic.fna/checkm_result
[2024-01-24 12:22:49,355] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:49,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:49,380] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:49,380] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:49,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002802965.1_ASM280296v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:49,381] [INFO] Task started: Blastn
[2024-01-24 12:22:49,381] [INFO] Running command: blastn -query GCF_002802965.1_ASM280296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg580b11ee-9195-4f86-a78f-abc45163b335/dqc_reference/reference_markers_gtdb.fasta -out GCF_002802965.1_ASM280296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:50,174] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:50,177] [INFO] Selected 20 target genomes.
[2024-01-24 12:22:50,178] [INFO] Target genome list was writen to GCF_002802965.1_ASM280296v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:50,204] [INFO] Task started: fastANI
[2024-01-24 12:22:50,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb63b1b-27a6-4074-8962-cc014199f2c6/GCF_002802965.1_ASM280296v1_genomic.fna.gz --refList GCF_002802965.1_ASM280296v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002802965.1_ASM280296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:01,315] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:01,323] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:01,324] [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_002802965.1	s__Sporolactobacillus pectinivorans	99.9944	1298	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009718825.1	s__Terrilactibacillus tamarindi	82.5829	52	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Terrilactibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684935.1	s__Sporolactobacillus shoreae	80.3552	587	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647035.1	s__Sporolactobacillus putidus	79.5856	262	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153165.1	s__Sporolactobacillus sp004153165	79.0479	175	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497245.1	s__Sporolactobacillus laevolacticus	78.7456	206	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377985.1	s__Sporolactobacillus vineae	77.8343	194	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_004153225.1	s__Sporolactobacillus sp004153225	77.2942	115	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543345.1	s__Sporolactobacillus sp900543345	76.7221	73	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:01,329] [INFO] GTDB search result was written to GCF_002802965.1_ASM280296v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:01,331] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:01,336] [INFO] DFAST_QC result json was written to GCF_002802965.1_ASM280296v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:01,339] [INFO] DFAST_QC completed!
[2024-01-24 12:23:01,339] [INFO] Total running time: 0h1m7s