[2024-01-24 15:27:41,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,300] [INFO] DQC Reference Directory: /var/lib/cwl/stgab2f4e77-7961-45a4-b772-4346bebd93aa/dqc_reference
[2024-01-24 15:27:43,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,881] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,881] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc4e304a-3a94-4954-a06e-68077ffaa3a9/GCF_003176895.1_ASM317689v1_genomic.fna.gz | prodigal -d GCF_003176895.1_ASM317689v1_genomic.fna/cds.fna -a GCF_003176895.1_ASM317689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:52,303] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:52,304] [INFO] Task started: HMMsearch
[2024-01-24 15:27:52,304] [INFO] Running command: hmmsearch --tblout GCF_003176895.1_ASM317689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab2f4e77-7961-45a4-b772-4346bebd93aa/dqc_reference/reference_markers.hmm GCF_003176895.1_ASM317689v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:52,610] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:52,612] [INFO] Found 6/6 markers.
[2024-01-24 15:27:52,667] [INFO] Query marker FASTA was written to GCF_003176895.1_ASM317689v1_genomic.fna/markers.fasta
[2024-01-24 15:27:52,668] [INFO] Task started: Blastn
[2024-01-24 15:27:52,668] [INFO] Running command: blastn -query GCF_003176895.1_ASM317689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab2f4e77-7961-45a4-b772-4346bebd93aa/dqc_reference/reference_markers.fasta -out GCF_003176895.1_ASM317689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:53,263] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:53,269] [INFO] Selected 31 target genomes.
[2024-01-24 15:27:53,269] [INFO] Target genome list was writen to GCF_003176895.1_ASM317689v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:53,815] [INFO] Task started: fastANI
[2024-01-24 15:27:53,815] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc4e304a-3a94-4954-a06e-68077ffaa3a9/GCF_003176895.1_ASM317689v1_genomic.fna.gz --refList GCF_003176895.1_ASM317689v1_genomic.fna/target_genomes.txt --output GCF_003176895.1_ASM317689v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:15,509] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:15,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab2f4e77-7961-45a4-b772-4346bebd93aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:15,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab2f4e77-7961-45a4-b772-4346bebd93aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:15,537] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:15,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:15,538] [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 dipsosauri	strain=DD1	GCA_003176895.1	178340	178340	type	True	100.0	1385	1385	95	conclusive
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	78.1862	287	1385	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	78.1396	295	1385	95	below_threshold
Gracilibacillus ureilyticus	strain=CGMCC 1.7727	GCA_900111195.1	531814	531814	type	True	78.1142	242	1385	95	below_threshold
Gracilibacillus oryzae	strain=TD8	GCA_009498735.1	1672701	1672701	type	True	78.0256	251	1385	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	77.8277	74	1385	95	below_threshold
Gracilibacillus orientalis	strain=CGMCC 1.4250	GCA_900114645.1	334253	334253	type	True	77.7809	277	1385	95	below_threshold
Gracilibacillus boraciitolerans	strain=JCM 21714	GCA_000521485.1	307521	307521	type	True	77.6839	194	1385	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.4182	73	1385	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	77.1684	155	1385	95	below_threshold
Aquibacillus halophilus	strain=B6B	GCA_009649745.1	930132	930132	type	True	77.0172	82	1385	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.0011	69	1385	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.9857	87	1385	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.8004	82	1385	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	76.7968	67	1385	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	76.3618	77	1385	95	below_threshold
Oceanobacillus jeddahense	strain=S5	GCA_000750635.1	1462527	1462527	type	True	76.3164	54	1385	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.0216	61	1385	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	75.9167	54	1385	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	75.7784	83	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:15,539] [INFO] DFAST Taxonomy check result was written to GCF_003176895.1_ASM317689v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:15,540] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:15,540] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:15,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab2f4e77-7961-45a4-b772-4346bebd93aa/dqc_reference/checkm_data
[2024-01-24 15:28:15,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:15,579] [INFO] Task started: CheckM
[2024-01-24 15:28:15,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003176895.1_ASM317689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003176895.1_ASM317689v1_genomic.fna/checkm_input GCF_003176895.1_ASM317689v1_genomic.fna/checkm_result
[2024-01-24 15:28:46,637] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:46,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:46,671] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:46,671] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:46,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003176895.1_ASM317689v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:46,672] [INFO] Task started: Blastn
[2024-01-24 15:28:46,672] [INFO] Running command: blastn -query GCF_003176895.1_ASM317689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab2f4e77-7961-45a4-b772-4346bebd93aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003176895.1_ASM317689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:47,514] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:47,519] [INFO] Selected 28 target genomes.
[2024-01-24 15:28:47,519] [INFO] Target genome list was writen to GCF_003176895.1_ASM317689v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:47,542] [INFO] Task started: fastANI
[2024-01-24 15:28:47,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc4e304a-3a94-4954-a06e-68077ffaa3a9/GCF_003176895.1_ASM317689v1_genomic.fna.gz --refList GCF_003176895.1_ASM317689v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003176895.1_ASM317689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:06,331] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:06,350] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:06,350] [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_003176895.1	s__Gracilibacillus dipsosauri	100.0	1385	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.23	99.13	0.93	0.92	3	conclusive
GCF_017599345.1	s__Gracilibacillus sp017599345	78.1919	286	1385	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	78.1568	293	1385	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_900111195.1	s__Gracilibacillus ureilyticus	78.1142	242	1385	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_009498735.1	s__Gracilibacillus sp009498735	78.0256	251	1385	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_000377765.1	s__Gracilibacillus lacisalsi	77.9337	284	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCA_014642895.1	s__Virgibacillus_E populi	77.8485	63	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	98.98	98.88	0.86	0.85	5	-
GCF_900114645.1	s__Gracilibacillus orientalis	77.7893	275	1385	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_010993965.1	s__Gracilibacillus sp010993965	77.7037	221	1385	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_000521485.1	s__Gracilibacillus boraciitolerans	77.6897	195	1385	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	77.5308	146	1385	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_001368815.1	s__Paraliobacillus sp001368815	77.0316	84	1385	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_009649745.1	s__Aquibacillus_A halophilus	76.988	83	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870085.1	s__BH258 sp005870085	76.9857	87	1385	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_900176885.1	s__Oceanobacillus senegalensis	76.7968	67	1385	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_014207435.1	s__Salirhabdus euzebyi	76.6947	64	1385	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_003426025.1	s__Paraliobacillus_A quinghaiensis	76.6058	86	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900184735.1	s__Ornithinibacillus globulus_B	76.5303	69	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.3883	54	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628445.1	s__Oceanobacillus bengalensis	76.3618	77	1385	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_000750635.1	s__Oceanobacillus jeddahense	76.3164	54	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016908235.1	s__Halobacillus_A seohaensis	76.2577	52	1385	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_018919165.1	s__Amphibacillus sp018919165	76.0502	60	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002577655.1	s__Metabacillus sp002577655	75.9823	53	1385	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:06,352] [INFO] GTDB search result was written to GCF_003176895.1_ASM317689v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:06,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:06,357] [INFO] DFAST_QC result json was written to GCF_003176895.1_ASM317689v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:06,357] [INFO] DFAST_QC completed!
[2024-01-24 15:29:06,357] [INFO] Total running time: 0h1m25s