[2024-01-24 13:17:33,566] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:33,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:33,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg986ce0d8-4b73-499f-8ea7-bfd07ea14d9f/dqc_reference
[2024-01-24 13:17:34,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:34,983] [INFO] Task started: Prodigal
[2024-01-24 13:17:34,984] [INFO] Running command: gunzip -c /var/lib/cwl/stg43c05f67-b5a1-4ecf-b65f-8848083fdd3e/GCF_008087205.1_ASM808720v1_genomic.fna.gz | prodigal -d GCF_008087205.1_ASM808720v1_genomic.fna/cds.fna -a GCF_008087205.1_ASM808720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:44,772] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:44,772] [INFO] Task started: HMMsearch
[2024-01-24 13:17:44,773] [INFO] Running command: hmmsearch --tblout GCF_008087205.1_ASM808720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg986ce0d8-4b73-499f-8ea7-bfd07ea14d9f/dqc_reference/reference_markers.hmm GCF_008087205.1_ASM808720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:45,097] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:45,098] [INFO] Found 6/6 markers.
[2024-01-24 13:17:45,141] [INFO] Query marker FASTA was written to GCF_008087205.1_ASM808720v1_genomic.fna/markers.fasta
[2024-01-24 13:17:45,142] [INFO] Task started: Blastn
[2024-01-24 13:17:45,142] [INFO] Running command: blastn -query GCF_008087205.1_ASM808720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg986ce0d8-4b73-499f-8ea7-bfd07ea14d9f/dqc_reference/reference_markers.fasta -out GCF_008087205.1_ASM808720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:45,839] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:45,842] [INFO] Selected 17 target genomes.
[2024-01-24 13:17:45,843] [INFO] Target genome list was writen to GCF_008087205.1_ASM808720v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:45,854] [INFO] Task started: fastANI
[2024-01-24 13:17:45,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg43c05f67-b5a1-4ecf-b65f-8848083fdd3e/GCF_008087205.1_ASM808720v1_genomic.fna.gz --refList GCF_008087205.1_ASM808720v1_genomic.fna/target_genomes.txt --output GCF_008087205.1_ASM808720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:59,879] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:59,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg986ce0d8-4b73-499f-8ea7-bfd07ea14d9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:59,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg986ce0d8-4b73-499f-8ea7-bfd07ea14d9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:59,892] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:59,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:59,893] [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
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	100.0	1542	1545	95	conclusive
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	99.9993	1537	1545	95	conclusive
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	87.8994	1165	1545	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	78.5716	330	1545	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	78.4873	312	1545	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	78.2954	243	1545	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.9947	164	1545	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	77.9176	185	1545	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.8072	208	1545	95	below_threshold
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	77.6731	170	1545	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.4845	210	1545	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	77.4173	178	1545	95	below_threshold
Oceanobacillus sojae	strain=NBRC 105379	GCA_007991515.1	582851	582851	type	True	77.1321	174	1545	95	below_threshold
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	76.8344	79	1545	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:59,895] [INFO] DFAST Taxonomy check result was written to GCF_008087205.1_ASM808720v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:59,895] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:59,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:59,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg986ce0d8-4b73-499f-8ea7-bfd07ea14d9f/dqc_reference/checkm_data
[2024-01-24 13:17:59,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:59,944] [INFO] Task started: CheckM
[2024-01-24 13:17:59,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008087205.1_ASM808720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008087205.1_ASM808720v1_genomic.fna/checkm_input GCF_008087205.1_ASM808720v1_genomic.fna/checkm_result
[2024-01-24 13:18:34,635] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:34,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:34,660] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:34,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:34,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008087205.1_ASM808720v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:34,661] [INFO] Task started: Blastn
[2024-01-24 13:18:34,662] [INFO] Running command: blastn -query GCF_008087205.1_ASM808720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg986ce0d8-4b73-499f-8ea7-bfd07ea14d9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_008087205.1_ASM808720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:35,464] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:35,468] [INFO] Selected 20 target genomes.
[2024-01-24 13:18:35,468] [INFO] Target genome list was writen to GCF_008087205.1_ASM808720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:35,490] [INFO] Task started: fastANI
[2024-01-24 13:18:35,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg43c05f67-b5a1-4ecf-b65f-8848083fdd3e/GCF_008087205.1_ASM808720v1_genomic.fna.gz --refList GCF_008087205.1_ASM808720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008087205.1_ASM808720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:52,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:52,339] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:52,339] [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_003515705.1	s__Oceanobacillus profundus	99.9993	1537	1545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	conclusive
GCF_008304605.1	s__Oceanobacillus polygoni	87.9097	1163	1545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002153375.1	s__Oceanobacillus rekensis	78.5859	330	1545	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_001618145.1	s__Oceanobacillus damuensis	78.517	311	1545	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_016908155.1	s__Oceanobacillus caeni	78.4547	180	1545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_018333215.1	s__Oceanobacillus sp018333215	78.2994	189	1545	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_000011245.1	s__Oceanobacillus iheyensis	77.9293	185	1545	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_003369565.1	s__Oceanobacillus chungangensis	77.8472	238	1545	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_003628445.1	s__Oceanobacillus bengalensis	77.799	210	1545	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_014645515.1	s__Oceanobacillus neutriphilus	77.6731	170	1545	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_009733865.1	s__Oceanobacillus salinisoli	77.4816	205	1545	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_003628505.1	s__Oceanobacillus halophilus	77.4173	178	1545	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_001659985.1	s__Oceanobacillus sp001659985	77.3889	185	1545	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_001038485.1	s__Ornithinibacillus californiensis	77.3128	123	1545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129485.1	s__Ornithinibacillus halophilus	77.1446	146	1545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991515.1	s__Oceanobacillus sojae	77.1321	174	1545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.95	98.95	0.93	0.93	2	-
GCF_009389585.1	s__Oceanobacillus sp009389585	76.8038	164	1545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:52,341] [INFO] GTDB search result was written to GCF_008087205.1_ASM808720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:52,341] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:52,345] [INFO] DFAST_QC result json was written to GCF_008087205.1_ASM808720v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:52,346] [INFO] DFAST_QC completed!
[2024-01-24 13:18:52,346] [INFO] Total running time: 0h1m19s