[2024-01-24 14:05:16,056] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:16,058] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:16,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e350108-2095-4de6-867b-6920b92ca963/dqc_reference
[2024-01-24 14:05:17,379] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,380] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,380] [INFO] Running command: gunzip -c /var/lib/cwl/stga96035bd-be18-4489-83a7-e3a3f068d59e/GCF_003977595.1_ASM397759v1_genomic.fna.gz | prodigal -d GCF_003977595.1_ASM397759v1_genomic.fna/cds.fna -a GCF_003977595.1_ASM397759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:25,440] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:25,440] [INFO] Task started: HMMsearch
[2024-01-24 14:05:25,440] [INFO] Running command: hmmsearch --tblout GCF_003977595.1_ASM397759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e350108-2095-4de6-867b-6920b92ca963/dqc_reference/reference_markers.hmm GCF_003977595.1_ASM397759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:25,753] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:25,755] [INFO] Found 6/6 markers.
[2024-01-24 14:05:25,795] [INFO] Query marker FASTA was written to GCF_003977595.1_ASM397759v1_genomic.fna/markers.fasta
[2024-01-24 14:05:25,796] [INFO] Task started: Blastn
[2024-01-24 14:05:25,796] [INFO] Running command: blastn -query GCF_003977595.1_ASM397759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e350108-2095-4de6-867b-6920b92ca963/dqc_reference/reference_markers.fasta -out GCF_003977595.1_ASM397759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:26,444] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:26,448] [INFO] Selected 29 target genomes.
[2024-01-24 14:05:26,449] [INFO] Target genome list was writen to GCF_003977595.1_ASM397759v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:26,461] [INFO] Task started: fastANI
[2024-01-24 14:05:26,461] [INFO] Running command: fastANI --query /var/lib/cwl/stga96035bd-be18-4489-83a7-e3a3f068d59e/GCF_003977595.1_ASM397759v1_genomic.fna.gz --refList GCF_003977595.1_ASM397759v1_genomic.fna/target_genomes.txt --output GCF_003977595.1_ASM397759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:43,380] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:43,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e350108-2095-4de6-867b-6920b92ca963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:43,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e350108-2095-4de6-867b-6920b92ca963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:43,397] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:43,397] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:43,398] [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
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	79.5215	421	1329	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	79.5138	423	1329	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_002200845.1	561440	561440	type	True	79.2848	336	1329	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	79.093	397	1329	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	78.9878	403	1329	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_000772945.1	1266064	1266064	type	True	78.8605	349	1329	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_002200865.1	1266064	1266064	type	True	78.8359	351	1329	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	78.7959	344	1329	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	78.7959	344	1329	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	78.7006	348	1329	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	78.3145	207	1329	95	below_threshold
Caryophanon tenue	strain=DSM 14152	GCA_001700315.1	33978	33978	type	True	78.1535	190	1329	95	below_threshold
Lysinibacillus agricola	strain=FJAT-51161	GCA_016638705.1	2590012	2590012	type	True	78.1325	226	1329	95	below_threshold
Lysinibacillus fusiformis	strain=ATCC 7055	GCA_003049525.1	28031	28031	type	True	78.0928	214	1329	95	below_threshold
Lysinibacillus fusiformis	strain=NRRL NRS-350	GCA_003367495.1	28031	28031	type	True	77.9899	212	1329	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	77.9198	216	1329	95	below_threshold
Viridibacillus arvi	strain=DSM 16317	GCA_001274945.1	263475	263475	type	True	77.8776	160	1329	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.5601	60	1329	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	76.4957	56	1329	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	76.2855	56	1329	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	75.7173	68	1329	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:43,400] [INFO] DFAST Taxonomy check result was written to GCF_003977595.1_ASM397759v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:43,400] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:43,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:43,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e350108-2095-4de6-867b-6920b92ca963/dqc_reference/checkm_data
[2024-01-24 14:05:43,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:43,447] [INFO] Task started: CheckM
[2024-01-24 14:05:43,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003977595.1_ASM397759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003977595.1_ASM397759v1_genomic.fna/checkm_input GCF_003977595.1_ASM397759v1_genomic.fna/checkm_result
[2024-01-24 14:06:14,521] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:14,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.04%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:14,552] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:14,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:14,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003977595.1_ASM397759v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:14,554] [INFO] Task started: Blastn
[2024-01-24 14:06:14,554] [INFO] Running command: blastn -query GCF_003977595.1_ASM397759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e350108-2095-4de6-867b-6920b92ca963/dqc_reference/reference_markers_gtdb.fasta -out GCF_003977595.1_ASM397759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:15,418] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:15,424] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:15,424] [INFO] Target genome list was writen to GCF_003977595.1_ASM397759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:15,441] [INFO] Task started: fastANI
[2024-01-24 14:06:15,441] [INFO] Running command: fastANI --query /var/lib/cwl/stga96035bd-be18-4489-83a7-e3a3f068d59e/GCF_003977595.1_ASM397759v1_genomic.fna.gz --refList GCF_003977595.1_ASM397759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003977595.1_ASM397759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:26,045] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:26,058] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:26,058] [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_003977595.1	s__Ureibacillus antri	100.0	1324	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	98.58	98.58	0.91	0.91	2	conclusive
GCF_900217795.1	s__Ureibacillus xyleni	81.1137	666	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628435.1	s__Ureibacillus endophyticus	80.8814	573	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966145.1	s__Ureibacillus telephonicus	79.8206	460	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836845.1	s__Ureibacillus sp014836845	79.7527	439	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711845.1	s__Ureibacillus halotolerans	79.7432	426	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005491425.1	s__Ureibacillus sp005491425	79.5492	460	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217295.1	s__Ureibacillus chungkukjangi	79.5242	421	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003515775.1	s__Ureibacillus yapensis	78.6892	345	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073375.1	s__Solibacillus sp003073375	78.0538	252	1329	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:26,061] [INFO] GTDB search result was written to GCF_003977595.1_ASM397759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:26,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:26,067] [INFO] DFAST_QC result json was written to GCF_003977595.1_ASM397759v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:26,068] [INFO] DFAST_QC completed!
[2024-01-24 14:06:26,068] [INFO] Total running time: 0h1m10s