[2024-01-25 20:25:35,541] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:25:35,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:25:35,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg51c89ba9-385b-4a2a-b8d1-fe30e5477686/dqc_reference
[2024-01-25 20:25:36,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:25:36,783] [INFO] Task started: Prodigal
[2024-01-25 20:25:36,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg809f54e7-b09a-4fc2-bf82-4d5e5909cd4f/GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna.gz | prodigal -d GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/cds.fna -a GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:25:47,276] [INFO] Task succeeded: Prodigal
[2024-01-25 20:25:47,276] [INFO] Task started: HMMsearch
[2024-01-25 20:25:47,276] [INFO] Running command: hmmsearch --tblout GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51c89ba9-385b-4a2a-b8d1-fe30e5477686/dqc_reference/reference_markers.hmm GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:25:47,546] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:25:47,547] [INFO] Found 6/6 markers.
[2024-01-25 20:25:47,587] [INFO] Query marker FASTA was written to GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/markers.fasta
[2024-01-25 20:25:47,587] [INFO] Task started: Blastn
[2024-01-25 20:25:47,587] [INFO] Running command: blastn -query GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51c89ba9-385b-4a2a-b8d1-fe30e5477686/dqc_reference/reference_markers.fasta -out GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:48,152] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:48,155] [INFO] Selected 18 target genomes.
[2024-01-25 20:25:48,156] [INFO] Target genome list was writen to GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/target_genomes.txt
[2024-01-25 20:25:48,172] [INFO] Task started: fastANI
[2024-01-25 20:25:48,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg809f54e7-b09a-4fc2-bf82-4d5e5909cd4f/GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna.gz --refList GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/target_genomes.txt --output GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:07,643] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:07,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51c89ba9-385b-4a2a-b8d1-fe30e5477686/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:07,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51c89ba9-385b-4a2a-b8d1-fe30e5477686/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:07,654] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:26:07,654] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:26:07,654] [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
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	100.0	1860	1861	95	conclusive
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	79.2715	468	1861	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.9661	442	1861	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	78.7227	438	1861	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	78.6966	476	1861	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	78.5155	401	1861	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	78.4935	441	1861	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.4405	403	1861	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	78.3941	417	1861	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	78.3428	453	1861	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	78.206	376	1861	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.0109	200	1861	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	77.9151	247	1861	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	77.7603	266	1861	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.6116	176	1861	95	below_threshold
Neobacillus notoginsengisoli	strain=JCM 30743	GCA_003515685.1	1578198	1578198	type	True	77.2443	123	1861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:07,656] [INFO] DFAST Taxonomy check result was written to GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/tc_result.tsv
[2024-01-25 20:26:07,656] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:07,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:07,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51c89ba9-385b-4a2a-b8d1-fe30e5477686/dqc_reference/checkm_data
[2024-01-25 20:26:07,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:07,714] [INFO] Task started: CheckM
[2024-01-25 20:26:07,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/checkm_input GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/checkm_result
[2024-01-25 20:26:41,971] [INFO] Task succeeded: CheckM
[2024-01-25 20:26:41,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:26:41,989] [INFO] ===== Completeness check finished =====
[2024-01-25 20:26:41,989] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:26:41,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/markers.fasta)
[2024-01-25 20:26:41,990] [INFO] Task started: Blastn
[2024-01-25 20:26:41,990] [INFO] Running command: blastn -query GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51c89ba9-385b-4a2a-b8d1-fe30e5477686/dqc_reference/reference_markers_gtdb.fasta -out GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:42,815] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:42,818] [INFO] Selected 19 target genomes.
[2024-01-25 20:26:42,818] [INFO] Target genome list was writen to GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:26:42,866] [INFO] Task started: fastANI
[2024-01-25 20:26:42,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg809f54e7-b09a-4fc2-bf82-4d5e5909cd4f/GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna.gz --refList GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/target_genomes_gtdb.txt --output GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:04,369] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:04,379] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:27:04,379] [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_001048695.1	s__Neobacillus massiliamazoniensis	100.0	1860	1861	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_001866655.1	s__Neobacillus sp001866655	79.4114	495	1861	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_004358205.1	s__Neobacillus salipaludis	79.2253	471	1861	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	79.0145	462	1861	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_000482325.1	s__Neobacillus sp000482325	78.9898	406	1861	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_001591805.1	s__Neobacillus novalis	78.7382	439	1861	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_900177675.1	s__Neobacillus sp900177675	78.6926	518	1861	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCF_018613065.1	s__Neobacillus sp018613065	78.6239	453	1861	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
GCA_019219025.1	s__Neobacillus sp019219025	78.6017	467	1861	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_000759675.1	s__Neobacillus niacini_A	78.4748	439	1861	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_001026695.1	s__Neobacillus vireti	78.4702	442	1861	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001591665.1	s__Neobacillus soli	78.3181	455	1861	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_014874135.1	s__Neobacillus sp014874135	78.2143	365	1861	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_001591445.1	s__Neobacillus drentensis	78.1682	409	1861	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	78.1295	411	1861	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_001420595.1	s__Cytobacillus solani	78.0133	198	1861	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_900199725.1	s__Cytobacillus massiliigabonensis	77.5762	183	1861	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	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:04,381] [INFO] GTDB search result was written to GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:04,381] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:04,385] [INFO] DFAST_QC result json was written to GCF_001048695.1_PRJEB8581_assembly_1_genomic.fna/dqc_result.json
[2024-01-25 20:27:04,385] [INFO] DFAST_QC completed!
[2024-01-25 20:27:04,385] [INFO] Total running time: 0h1m29s