[2024-01-25 20:04:20,762] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:20,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:20,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bcc2119-8cd8-49fb-95e8-95c6838536c5/dqc_reference
[2024-01-25 20:04:21,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:21,910] [INFO] Task started: Prodigal
[2024-01-25 20:04:21,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg88262ed6-f4dc-4429-ad61-3498482fa076/GCF_000772965.1_ASM77296v1_genomic.fna.gz | prodigal -d GCF_000772965.1_ASM77296v1_genomic.fna/cds.fna -a GCF_000772965.1_ASM77296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:28,353] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:28,353] [INFO] Task started: HMMsearch
[2024-01-25 20:04:28,353] [INFO] Running command: hmmsearch --tblout GCF_000772965.1_ASM77296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bcc2119-8cd8-49fb-95e8-95c6838536c5/dqc_reference/reference_markers.hmm GCF_000772965.1_ASM77296v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:28,620] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:28,621] [INFO] Found 6/6 markers.
[2024-01-25 20:04:28,652] [INFO] Query marker FASTA was written to GCF_000772965.1_ASM77296v1_genomic.fna/markers.fasta
[2024-01-25 20:04:28,652] [INFO] Task started: Blastn
[2024-01-25 20:04:28,652] [INFO] Running command: blastn -query GCF_000772965.1_ASM77296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bcc2119-8cd8-49fb-95e8-95c6838536c5/dqc_reference/reference_markers.fasta -out GCF_000772965.1_ASM77296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:29,218] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:29,221] [INFO] Selected 14 target genomes.
[2024-01-25 20:04:29,221] [INFO] Target genome list was writen to GCF_000772965.1_ASM77296v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:29,266] [INFO] Task started: fastANI
[2024-01-25 20:04:29,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg88262ed6-f4dc-4429-ad61-3498482fa076/GCF_000772965.1_ASM77296v1_genomic.fna.gz --refList GCF_000772965.1_ASM77296v1_genomic.fna/target_genomes.txt --output GCF_000772965.1_ASM77296v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:39,060] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:39,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bcc2119-8cd8-49fb-95e8-95c6838536c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:39,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bcc2119-8cd8-49fb-95e8-95c6838536c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:39,068] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:04:39,068] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:39,068] [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 massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	100.0	1262	1265	95	conclusive
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	100.0	1262	1265	95	conclusive
Ureibacillus manganicus	strain=DSM 26584	GCA_002200865.1	1266064	1266064	type	True	79.6263	431	1265	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_000772945.1	1266064	1266064	type	True	79.6143	432	1265	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	79.533	457	1265	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	79.5045	340	1265	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	79.1278	350	1265	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	79.117	349	1265	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.0457	69	1265	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	75.9749	63	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:39,074] [INFO] DFAST Taxonomy check result was written to GCF_000772965.1_ASM77296v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:39,074] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:39,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:39,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bcc2119-8cd8-49fb-95e8-95c6838536c5/dqc_reference/checkm_data
[2024-01-25 20:04:39,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:39,124] [INFO] Task started: CheckM
[2024-01-25 20:04:39,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000772965.1_ASM77296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000772965.1_ASM77296v1_genomic.fna/checkm_input GCF_000772965.1_ASM77296v1_genomic.fna/checkm_result
[2024-01-25 20:05:02,823] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:02,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:02,841] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:02,841] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:02,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000772965.1_ASM77296v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:02,842] [INFO] Task started: Blastn
[2024-01-25 20:05:02,842] [INFO] Running command: blastn -query GCF_000772965.1_ASM77296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bcc2119-8cd8-49fb-95e8-95c6838536c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000772965.1_ASM77296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:03,608] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:03,611] [INFO] Selected 14 target genomes.
[2024-01-25 20:05:03,611] [INFO] Target genome list was writen to GCF_000772965.1_ASM77296v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:03,630] [INFO] Task started: fastANI
[2024-01-25 20:05:03,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg88262ed6-f4dc-4429-ad61-3498482fa076/GCF_000772965.1_ASM77296v1_genomic.fna.gz --refList GCF_000772965.1_ASM77296v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000772965.1_ASM77296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:13,772] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:13,780] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:13,781] [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_000772965.1	s__Ureibacillus massiliensis	100.0	1262	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900291985.1	s__Ureibacillus timonensis	80.1396	566	1265	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_000772945.1	s__Ureibacillus manganicus	79.6022	433	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900220965.1	s__Ureibacillus acetophenoni	79.5265	458	1265	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	79.1347	383	1265	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_016908465.1	s__Ureibacillus composti	79.1274	350	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003628435.1	s__Ureibacillus endophyticus	79.0127	321	1265	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_003977595.1	s__Ureibacillus antri	78.9346	331	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	98.58	98.58	0.91	0.91	2	-
GCF_014836845.1	s__Ureibacillus sp014836845	78.79	343	1265	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_900217795.1	s__Ureibacillus xyleni	78.7336	357	1265	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_014595895.1	s__Lysinibacillus_B odysseyi_A	78.1225	144	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844575.1	s__Margalitia camelliae	75.9749	63	1265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.53	99.53	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:13,782] [INFO] GTDB search result was written to GCF_000772965.1_ASM77296v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:13,783] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:13,785] [INFO] DFAST_QC result json was written to GCF_000772965.1_ASM77296v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:13,785] [INFO] DFAST_QC completed!
[2024-01-25 20:05:13,785] [INFO] Total running time: 0h0m53s