[2024-01-24 13:59:42,342] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:59:42,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:59:42,344] [INFO] DQC Reference Directory: /var/lib/cwl/stgabe70d34-3f89-40e1-b642-ac7a363f2e48/dqc_reference
[2024-01-24 13:59:43,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:59:43,602] [INFO] Task started: Prodigal
[2024-01-24 13:59:43,602] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d43d309-a5b1-4c37-b628-28dc238f8d01/GCF_004358205.1_ASM435820v1_genomic.fna.gz | prodigal -d GCF_004358205.1_ASM435820v1_genomic.fna/cds.fna -a GCF_004358205.1_ASM435820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:56,600] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:56,601] [INFO] Task started: HMMsearch
[2024-01-24 13:59:56,601] [INFO] Running command: hmmsearch --tblout GCF_004358205.1_ASM435820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabe70d34-3f89-40e1-b642-ac7a363f2e48/dqc_reference/reference_markers.hmm GCF_004358205.1_ASM435820v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:56,939] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:56,941] [INFO] Found 6/6 markers.
[2024-01-24 13:59:56,991] [INFO] Query marker FASTA was written to GCF_004358205.1_ASM435820v1_genomic.fna/markers.fasta
[2024-01-24 13:59:56,992] [INFO] Task started: Blastn
[2024-01-24 13:59:56,992] [INFO] Running command: blastn -query GCF_004358205.1_ASM435820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabe70d34-3f89-40e1-b642-ac7a363f2e48/dqc_reference/reference_markers.fasta -out GCF_004358205.1_ASM435820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:57,593] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:57,597] [INFO] Selected 27 target genomes.
[2024-01-24 13:59:57,598] [INFO] Target genome list was writen to GCF_004358205.1_ASM435820v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:57,613] [INFO] Task started: fastANI
[2024-01-24 13:59:57,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d43d309-a5b1-4c37-b628-28dc238f8d01/GCF_004358205.1_ASM435820v1_genomic.fna.gz --refList GCF_004358205.1_ASM435820v1_genomic.fna/target_genomes.txt --output GCF_004358205.1_ASM435820v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:00:21,598] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:21,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabe70d34-3f89-40e1-b642-ac7a363f2e48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:00:21,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabe70d34-3f89-40e1-b642-ac7a363f2e48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:00:21,617] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:00:21,617] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:00:21,618] [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
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	100.0	2015	2019	95	conclusive
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	79.1324	494	2019	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	78.8934	509	2019	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.7381	402	2019	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	78.6628	483	2019	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	78.6125	428	2019	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	78.5549	391	2019	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.5486	482	2019	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	78.4833	471	2019	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	78.4773	463	2019	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	78.4303	447	2019	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	78.3394	422	2019	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	78.3162	427	2019	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	78.3159	397	2019	95	below_threshold
Neobacillus niacini	strain=NBRC 15566	GCA_001591505.1	86668	86668	suspected-type	True	78.2859	410	2019	95	below_threshold
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	78.1256	275	2019	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.8036	201	2019	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.3251	179	2019	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.0144	165	2019	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.89	142	2019	95	below_threshold
Bacillus vallismortis	strain=DSM 11031	GCA_004116955.1	72361	72361	type	True	76.8209	66	2019	95	below_threshold
Mesobacillus harenae	strain=Y40	GCA_013343715.1	2213203	2213203	type	True	76.8172	134	2019	95	below_threshold
Bacillus spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	76.727	64	2019	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.6051	99	2019	95	below_threshold
Lederbergia panacisoli	strain=KACC 17503	GCA_024626525.1	1255251	1255251	type	True	76.2816	99	2019	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:00:21,619] [INFO] DFAST Taxonomy check result was written to GCF_004358205.1_ASM435820v1_genomic.fna/tc_result.tsv
[2024-01-24 14:00:21,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:00:21,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:00:21,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabe70d34-3f89-40e1-b642-ac7a363f2e48/dqc_reference/checkm_data
[2024-01-24 14:00:21,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:00:21,680] [INFO] Task started: CheckM
[2024-01-24 14:00:21,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358205.1_ASM435820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358205.1_ASM435820v1_genomic.fna/checkm_input GCF_004358205.1_ASM435820v1_genomic.fna/checkm_result
[2024-01-24 14:01:03,312] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:03,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:03,333] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:03,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:03,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358205.1_ASM435820v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:03,334] [INFO] Task started: Blastn
[2024-01-24 14:01:03,334] [INFO] Running command: blastn -query GCF_004358205.1_ASM435820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabe70d34-3f89-40e1-b642-ac7a363f2e48/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358205.1_ASM435820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:04,128] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:04,131] [INFO] Selected 12 target genomes.
[2024-01-24 14:01:04,132] [INFO] Target genome list was writen to GCF_004358205.1_ASM435820v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:04,143] [INFO] Task started: fastANI
[2024-01-24 14:01:04,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d43d309-a5b1-4c37-b628-28dc238f8d01/GCF_004358205.1_ASM435820v1_genomic.fna.gz --refList GCF_004358205.1_ASM435820v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004358205.1_ASM435820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:19,404] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:19,418] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:19,419] [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_004358205.1	s__Neobacillus salipaludis	100.0	2015	2019	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	conclusive
GCF_000482325.1	s__Neobacillus sp000482325	94.7353	1558	2019	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	-
GCF_016107705.1	s__Neobacillus cucumis_B	93.4175	1626	2019	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	-
GCF_001866655.1	s__Neobacillus sp001866655	84.5625	1301	2019	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	-
GCA_019219025.1	s__Neobacillus sp019219025	79.1843	559	2019	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	-
GCF_001048695.1	s__Neobacillus massiliamazoniensis	79.1622	489	2019	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	-
GCF_002860255.1	s__Neobacillus cucumis_A	78.6791	446	2019	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	-
GCF_009928415.1	s__Neobacillus sp009928415	78.4946	427	2019	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	-
GCF_001591665.1	s__Neobacillus soli	78.4482	466	2019	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011250555.1	s__Neobacillus sp011250555	78.3697	437	2019	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004124315.1	s__Bacillus cabrialesii	77.136	64	2019	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCF_002835735.1	s__Cytobacillus horneckiae	77.078	165	2019	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.87	98.22	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:19,420] [INFO] GTDB search result was written to GCF_004358205.1_ASM435820v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:19,421] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:19,425] [INFO] DFAST_QC result json was written to GCF_004358205.1_ASM435820v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:19,425] [INFO] DFAST_QC completed!
[2024-01-24 14:01:19,426] [INFO] Total running time: 0h1m37s