[2024-01-24 13:40:43,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,813] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,813] [INFO] DQC Reference Directory: /var/lib/cwl/stg29d25817-29ed-4a0f-8c1f-c30be15c23a9/dqc_reference
[2024-01-24 13:40:45,186] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,187] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,187] [INFO] Running command: gunzip -c /var/lib/cwl/stg010d7a44-c58f-4046-95c5-c1408f93e148/GCF_009498735.1_ASM949873v1_genomic.fna.gz | prodigal -d GCF_009498735.1_ASM949873v1_genomic.fna/cds.fna -a GCF_009498735.1_ASM949873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:55,768] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:55,768] [INFO] Task started: HMMsearch
[2024-01-24 13:40:55,768] [INFO] Running command: hmmsearch --tblout GCF_009498735.1_ASM949873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29d25817-29ed-4a0f-8c1f-c30be15c23a9/dqc_reference/reference_markers.hmm GCF_009498735.1_ASM949873v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:56,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:56,120] [INFO] Found 6/6 markers.
[2024-01-24 13:40:56,166] [INFO] Query marker FASTA was written to GCF_009498735.1_ASM949873v1_genomic.fna/markers.fasta
[2024-01-24 13:40:56,167] [INFO] Task started: Blastn
[2024-01-24 13:40:56,167] [INFO] Running command: blastn -query GCF_009498735.1_ASM949873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29d25817-29ed-4a0f-8c1f-c30be15c23a9/dqc_reference/reference_markers.fasta -out GCF_009498735.1_ASM949873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:56,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:56,805] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:56,805] [INFO] Target genome list was writen to GCF_009498735.1_ASM949873v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:56,811] [INFO] Task started: fastANI
[2024-01-24 13:40:56,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg010d7a44-c58f-4046-95c5-c1408f93e148/GCF_009498735.1_ASM949873v1_genomic.fna.gz --refList GCF_009498735.1_ASM949873v1_genomic.fna/target_genomes.txt --output GCF_009498735.1_ASM949873v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:10,575] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:10,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29d25817-29ed-4a0f-8c1f-c30be15c23a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:10,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29d25817-29ed-4a0f-8c1f-c30be15c23a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:10,590] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:10,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:10,590] [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
Gracilibacillus oryzae	strain=TD8	GCA_009498735.1	1672701	1672701	type	True	100.0	1517	1519	95	conclusive
Gracilibacillus ureilyticus	strain=CGMCC 1.7727	GCA_900111195.1	531814	531814	type	True	79.9472	635	1519	95	below_threshold
Gracilibacillus massiliensis	strain=Awa-1	GCA_001458115.1	1564956	1564956	type	True	77.8579	253	1519	95	below_threshold
Gracilibacillus dipsosauri	strain=DD1	GCA_003176895.1	178340	178340	type	True	77.8195	267	1519	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	77.7492	286	1519	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	77.6787	292	1519	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.1119	87	1519	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	76.9731	115	1519	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.8395	109	1519	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	76.7165	126	1519	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	76.4791	103	1519	95	below_threshold
Salirhabdus euzebyi	strain=DSM 19612	GCA_014207435.1	394506	394506	type	True	76.4348	62	1519	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	76.1899	75	1519	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.1401	69	1519	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	75.9582	55	1519	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	75.5434	51	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:10,592] [INFO] DFAST Taxonomy check result was written to GCF_009498735.1_ASM949873v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:10,592] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:10,592] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:10,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29d25817-29ed-4a0f-8c1f-c30be15c23a9/dqc_reference/checkm_data
[2024-01-24 13:41:10,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:10,640] [INFO] Task started: CheckM
[2024-01-24 13:41:10,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009498735.1_ASM949873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009498735.1_ASM949873v1_genomic.fna/checkm_input GCF_009498735.1_ASM949873v1_genomic.fna/checkm_result
[2024-01-24 13:41:47,600] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:47,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,625] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:47,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:47,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009498735.1_ASM949873v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:47,626] [INFO] Task started: Blastn
[2024-01-24 13:41:47,626] [INFO] Running command: blastn -query GCF_009498735.1_ASM949873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29d25817-29ed-4a0f-8c1f-c30be15c23a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009498735.1_ASM949873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:48,459] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:48,463] [INFO] Selected 23 target genomes.
[2024-01-24 13:41:48,463] [INFO] Target genome list was writen to GCF_009498735.1_ASM949873v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:48,474] [INFO] Task started: fastANI
[2024-01-24 13:41:48,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg010d7a44-c58f-4046-95c5-c1408f93e148/GCF_009498735.1_ASM949873v1_genomic.fna.gz --refList GCF_009498735.1_ASM949873v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009498735.1_ASM949873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:03,859] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:03,883] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:03,883] [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_009498735.1	s__Gracilibacillus sp009498735	100.0	1517	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111195.1	s__Gracilibacillus ureilyticus	79.9472	635	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458115.1	s__Gracilibacillus massiliensis	77.847	251	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003176895.1	s__Gracilibacillus dipsosauri	77.8319	266	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.23	99.13	0.93	0.92	3	-
GCF_017599345.1	s__Gracilibacillus sp017599345	77.7601	285	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650095.1	s__Gracilibacillus sp002797295	77.6722	295	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_010993965.1	s__Gracilibacillus sp010993965	77.3429	213	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909015.1	s__Gracilibacillus alcaliphilus	77.0956	159	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	77.0845	88	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	76.9731	115	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870085.1	s__BH258 sp005870085	76.8608	108	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162665.1	s__Oceanobacillus sojae_A	76.6767	65	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612865.1	s__Virgibacillus picturae	76.5342	73	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	97.99	95.34	0.93	0.90	5	-
GCF_014207435.1	s__Salirhabdus euzebyi	76.5273	63	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003268595.1	s__Paraliobacillus_A zengyii	76.4843	104	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_018333235.1	s__Ornithinibacillus bavariensis	76.3974	54	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	98.72	98.72	0.93	0.93	2	-
GCF_016908235.1	s__Halobacillus_A seohaensis	76.3796	50	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340475.1	s__Oceanobacillus kimchii	76.1916	83	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.20	99.13	0.93	0.91	5	-
GCF_001048695.1	s__Neobacillus massiliamazoniensis	75.8784	54	1519	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_016879755.1	s__Bacillus_AZ sp016879755	75.7626	50	1519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:03,885] [INFO] GTDB search result was written to GCF_009498735.1_ASM949873v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:03,885] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:03,892] [INFO] DFAST_QC result json was written to GCF_009498735.1_ASM949873v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:03,893] [INFO] DFAST_QC completed!
[2024-01-24 13:42:03,893] [INFO] Total running time: 0h1m20s