[2024-01-24 12:05:58,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:58,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:58,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg98f1921e-8809-4a25-b285-db114275f7b3/dqc_reference
[2024-01-24 12:06:00,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:00,320] [INFO] Task started: Prodigal
[2024-01-24 12:06:00,320] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf0e3822-5246-4d95-b802-64cef5f0ac99/GCF_002237775.1_ASM223777v1_genomic.fna.gz | prodigal -d GCF_002237775.1_ASM223777v1_genomic.fna/cds.fna -a GCF_002237775.1_ASM223777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:10,851] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:10,851] [INFO] Task started: HMMsearch
[2024-01-24 12:06:10,851] [INFO] Running command: hmmsearch --tblout GCF_002237775.1_ASM223777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98f1921e-8809-4a25-b285-db114275f7b3/dqc_reference/reference_markers.hmm GCF_002237775.1_ASM223777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:11,172] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:11,173] [INFO] Found 6/6 markers.
[2024-01-24 12:06:11,206] [INFO] Query marker FASTA was written to GCF_002237775.1_ASM223777v1_genomic.fna/markers.fasta
[2024-01-24 12:06:11,207] [INFO] Task started: Blastn
[2024-01-24 12:06:11,208] [INFO] Running command: blastn -query GCF_002237775.1_ASM223777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f1921e-8809-4a25-b285-db114275f7b3/dqc_reference/reference_markers.fasta -out GCF_002237775.1_ASM223777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:11,926] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:11,929] [INFO] Selected 10 target genomes.
[2024-01-24 12:06:11,930] [INFO] Target genome list was writen to GCF_002237775.1_ASM223777v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:11,934] [INFO] Task started: fastANI
[2024-01-24 12:06:11,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf0e3822-5246-4d95-b802-64cef5f0ac99/GCF_002237775.1_ASM223777v1_genomic.fna.gz --refList GCF_002237775.1_ASM223777v1_genomic.fna/target_genomes.txt --output GCF_002237775.1_ASM223777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:19,517] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:19,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98f1921e-8809-4a25-b285-db114275f7b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:19,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98f1921e-8809-4a25-b285-db114275f7b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:19,526] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:06:19,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:19,527] [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
Domibacillus enclensis	strain=DSM 25145	GCA_002237775.1	1017273	1017273	type	True	100.0	1265	1267	95	conclusive
Domibacillus enclensis	strain=NIO-1016	GCA_900156125.1	1017273	1017273	type	True	100.0	1265	1267	95	conclusive
Domibacillus enclensis	strain=NIO-1016	GCA_000966185.1	1017273	1017273	type	True	99.9586	1216	1267	95	conclusive
Domibacillus iocasae	strain=DSM 29979	GCA_001750285.1	1714016	1714016	type	True	81.0235	585	1267	95	below_threshold
Domibacillus tundrae	strain=PAMC 80007	GCA_000970675.1	1587527	1587527	type	True	81.0033	558	1267	95	below_threshold
Domibacillus indicus	strain=SD 111	GCA_000970685.1	1437523	1437523	type	True	79.8646	555	1267	95	below_threshold
Domibacillus epiphyticus	strain=SAB 38	GCA_001975785.1	1714355	1714355	type	True	79.0624	320	1267	95	below_threshold
Bacillus wudalianchiensis	strain=FJAT-27215	GCA_001685015.1	1743143	1743143	type	True	76.6879	88	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:19,529] [INFO] DFAST Taxonomy check result was written to GCF_002237775.1_ASM223777v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:19,530] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:19,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:19,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98f1921e-8809-4a25-b285-db114275f7b3/dqc_reference/checkm_data
[2024-01-24 12:06:19,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:19,574] [INFO] Task started: CheckM
[2024-01-24 12:06:19,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002237775.1_ASM223777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002237775.1_ASM223777v1_genomic.fna/checkm_input GCF_002237775.1_ASM223777v1_genomic.fna/checkm_result
[2024-01-24 12:06:54,762] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:54,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:54,784] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:54,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:54,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002237775.1_ASM223777v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:54,785] [INFO] Task started: Blastn
[2024-01-24 12:06:54,786] [INFO] Running command: blastn -query GCF_002237775.1_ASM223777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f1921e-8809-4a25-b285-db114275f7b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002237775.1_ASM223777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:55,514] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:55,519] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:55,519] [INFO] Target genome list was writen to GCF_002237775.1_ASM223777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:55,531] [INFO] Task started: fastANI
[2024-01-24 12:06:55,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf0e3822-5246-4d95-b802-64cef5f0ac99/GCF_002237775.1_ASM223777v1_genomic.fna.gz --refList GCF_002237775.1_ASM223777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002237775.1_ASM223777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:07,019] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:07,042] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:07,042] [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_900156125.1	s__Domibacillus enclensis	100.0	1265	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	100.00	99.99	1.00	1.00	3	conclusive
GCF_001750285.1	s__Domibacillus iocasae	81.0169	586	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970675.1	s__Domibacillus tundrae	80.985	561	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970685.1	s__Domibacillus indicus	79.8646	555	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000966195.1	s__Domibacillus robiginosus	79.6811	528	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001936625.1	s__Domibacillus antri	79.428	381	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975785.1	s__Domibacillus epiphyticus	79.0713	319	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001906925.1	s__Domibacillus mangrovi	78.6418	291	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668575.1	s__Falsibacillus albus	76.7625	53	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-25281;g__Falsibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685015.1	s__Pseudobacillus wudalianchiensis	76.7135	87	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_000430765.1	s__Bacillus_AI kribbensis	76.5986	53	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909175.1	s__Bacillus_AI deserti	76.4354	50	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:07,044] [INFO] GTDB search result was written to GCF_002237775.1_ASM223777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:07,045] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:07,050] [INFO] DFAST_QC result json was written to GCF_002237775.1_ASM223777v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:07,050] [INFO] DFAST_QC completed!
[2024-01-24 12:07:07,051] [INFO] Total running time: 0h1m8s