[2024-01-24 13:25:29,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg63fa859a-7b36-4189-8085-fe7a9af429ba/dqc_reference
[2024-01-24 13:25:30,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:30,520] [INFO] Task started: Prodigal
[2024-01-24 13:25:30,520] [INFO] Running command: gunzip -c /var/lib/cwl/stgca8be702-9b25-4aaf-8e65-216032537c8b/GCF_003429105.1_ASM342910v1_genomic.fna.gz | prodigal -d GCF_003429105.1_ASM342910v1_genomic.fna/cds.fna -a GCF_003429105.1_ASM342910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:42,050] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:42,051] [INFO] Task started: HMMsearch
[2024-01-24 13:25:42,051] [INFO] Running command: hmmsearch --tblout GCF_003429105.1_ASM342910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63fa859a-7b36-4189-8085-fe7a9af429ba/dqc_reference/reference_markers.hmm GCF_003429105.1_ASM342910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:42,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:42,366] [INFO] Found 6/6 markers.
[2024-01-24 13:25:42,407] [INFO] Query marker FASTA was written to GCF_003429105.1_ASM342910v1_genomic.fna/markers.fasta
[2024-01-24 13:25:42,407] [INFO] Task started: Blastn
[2024-01-24 13:25:42,407] [INFO] Running command: blastn -query GCF_003429105.1_ASM342910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63fa859a-7b36-4189-8085-fe7a9af429ba/dqc_reference/reference_markers.fasta -out GCF_003429105.1_ASM342910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:43,025] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:43,030] [INFO] Selected 26 target genomes.
[2024-01-24 13:25:43,030] [INFO] Target genome list was writen to GCF_003429105.1_ASM342910v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:43,040] [INFO] Task started: fastANI
[2024-01-24 13:25:43,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgca8be702-9b25-4aaf-8e65-216032537c8b/GCF_003429105.1_ASM342910v1_genomic.fna.gz --refList GCF_003429105.1_ASM342910v1_genomic.fna/target_genomes.txt --output GCF_003429105.1_ASM342910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:02,528] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:02,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63fa859a-7b36-4189-8085-fe7a9af429ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:02,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63fa859a-7b36-4189-8085-fe7a9af429ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:02,542] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:02,542] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:02,542] [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
Peribacillus glennii	strain=V44-8	GCA_003429105.1	2303991	2303991	type	True	100.0	1473	1474	95	conclusive
Peribacillus cavernae	strain=L5	GCA_003989135.1	1674310	1674310	type	True	78.5398	434	1474	95	below_threshold
Peribacillus kribbensis	strain=DSM 17871	GCA_000430765.1	356658	356658	type	True	78.0774	127	1474	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	77.9809	124	1474	95	below_threshold
Peribacillus muralis	strain=DSM 16288	GCA_001439925.1	264697	264697	type	True	77.5299	154	1474	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_003570705.1	1917180	1917180	type	True	77.5155	86	1474	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	77.4558	95	1474	95	below_threshold
Peribacillus simplex	strain=DSM 1321	GCA_002243645.1	1478	1478	suspected-type	True	77.4383	181	1474	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_013618945.1	1917180	1917180	type	True	77.4173	87	1474	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	77.3354	75	1474	95	below_threshold
Peribacillus simplex	strain=NBRC 15720	GCA_001591785.1	1478	1478	suspected-type	True	77.2262	174	1474	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	77.1706	86	1474	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.1624	57	1474	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.8863	101	1474	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	76.8144	85	1474	95	below_threshold
Metabacillus kandeliae	strain=GX 13764	GCA_021166585.1	2900151	2900151	type	True	76.2019	62	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:02,544] [INFO] DFAST Taxonomy check result was written to GCF_003429105.1_ASM342910v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:02,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:02,545] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:02,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63fa859a-7b36-4189-8085-fe7a9af429ba/dqc_reference/checkm_data
[2024-01-24 13:26:02,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:02,594] [INFO] Task started: CheckM
[2024-01-24 13:26:02,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003429105.1_ASM342910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003429105.1_ASM342910v1_genomic.fna/checkm_input GCF_003429105.1_ASM342910v1_genomic.fna/checkm_result
[2024-01-24 13:26:39,083] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:39,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:39,109] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:39,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:39,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003429105.1_ASM342910v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:39,110] [INFO] Task started: Blastn
[2024-01-24 13:26:39,110] [INFO] Running command: blastn -query GCF_003429105.1_ASM342910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63fa859a-7b36-4189-8085-fe7a9af429ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_003429105.1_ASM342910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:39,928] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:39,932] [INFO] Selected 20 target genomes.
[2024-01-24 13:26:39,933] [INFO] Target genome list was writen to GCF_003429105.1_ASM342910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:39,952] [INFO] Task started: fastANI
[2024-01-24 13:26:39,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgca8be702-9b25-4aaf-8e65-216032537c8b/GCF_003429105.1_ASM342910v1_genomic.fna.gz --refList GCF_003429105.1_ASM342910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003429105.1_ASM342910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:56,288] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:56,303] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:56,303] [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_003429105.1	s__Peribacillus glennii	100.0	1473	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002863565.1	s__Peribacillus sp002863565	83.0612	947	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860285.1	s__Peribacillus_A sp002860285	78.9561	222	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429085.1	s__Peribacillus sp003429085	78.6399	403	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003989135.1	s__Peribacillus cavernae	78.5398	434	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112495.1	s__Peribacillus sp900112495	78.4493	186	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	95.26	95.26	0.85	0.85	2	-
GCF_004006295.1	s__Peribacillus asahii_A	78.3273	152	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542915.1	s__Peribacillus simplex_B	77.8025	156	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	97.35	97.35	0.89	0.89	2	-
GCF_900156045.1	s__Peribacillus simplex_D	77.6664	174	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	95.46	95.05	0.86	0.84	7	-
GCF_001439925.1	s__Peribacillus muralis	77.5462	154	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570705.1	s__Bacillus_AZ zeae	77.5155	86	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	100.00	100.00	1.00	1.00	3	-
GCF_009849585.1	s__Cytobacillus sp009849585	77.4679	91	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002243645.1	s__Peribacillus simplex	77.4373	179	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	99.44	98.94	0.96	0.92	4	-
GCF_018613325.1	s__Peribacillus sp018613325	77.4303	185	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038755.1	s__Cytobacillus firmus_B	77.2409	106	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	97.85	96.97	0.92	0.91	5	-
GCF_002272225.1	s__Cytobacillus sp002272225	77.1024	94	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956215.1	s__Cytobacillus sp001956215	77.0907	102	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000565285.1	s__Cytobacillus firmus_A	76.9953	100	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013396335.1	s__Neobacillus sp013396335	76.8187	74	1474	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:56,305] [INFO] GTDB search result was written to GCF_003429105.1_ASM342910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:56,306] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:56,309] [INFO] DFAST_QC result json was written to GCF_003429105.1_ASM342910v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:56,310] [INFO] DFAST_QC completed!
[2024-01-24 13:26:56,310] [INFO] Total running time: 0h1m27s