[2024-01-24 13:19:29,008] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:29,010] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:29,010] [INFO] DQC Reference Directory: /var/lib/cwl/stg2519e4d2-2922-4927-93d0-38d435ca9e76/dqc_reference
[2024-01-24 13:19:30,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:30,380] [INFO] Task started: Prodigal
[2024-01-24 13:19:30,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg3aebdcb6-a45f-4fd0-b36d-185f9e85ed8b/GCF_000378385.1_ASM37838v1_genomic.fna.gz | prodigal -d GCF_000378385.1_ASM37838v1_genomic.fna/cds.fna -a GCF_000378385.1_ASM37838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:53,207] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:53,207] [INFO] Task started: HMMsearch
[2024-01-24 13:19:53,207] [INFO] Running command: hmmsearch --tblout GCF_000378385.1_ASM37838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2519e4d2-2922-4927-93d0-38d435ca9e76/dqc_reference/reference_markers.hmm GCF_000378385.1_ASM37838v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:53,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:53,565] [INFO] Found 6/6 markers.
[2024-01-24 13:19:53,623] [INFO] Query marker FASTA was written to GCF_000378385.1_ASM37838v1_genomic.fna/markers.fasta
[2024-01-24 13:19:53,624] [INFO] Task started: Blastn
[2024-01-24 13:19:53,624] [INFO] Running command: blastn -query GCF_000378385.1_ASM37838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2519e4d2-2922-4927-93d0-38d435ca9e76/dqc_reference/reference_markers.fasta -out GCF_000378385.1_ASM37838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:54,244] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:54,248] [INFO] Selected 33 target genomes.
[2024-01-24 13:19:54,249] [INFO] Target genome list was writen to GCF_000378385.1_ASM37838v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:54,275] [INFO] Task started: fastANI
[2024-01-24 13:19:54,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aebdcb6-a45f-4fd0-b36d-185f9e85ed8b/GCF_000378385.1_ASM37838v1_genomic.fna.gz --refList GCF_000378385.1_ASM37838v1_genomic.fna/target_genomes.txt --output GCF_000378385.1_ASM37838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:27,637] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:27,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2519e4d2-2922-4927-93d0-38d435ca9e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:27,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2519e4d2-2922-4927-93d0-38d435ca9e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:27,669] [INFO] Found 33 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:20:27,670] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:20:27,670] [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
Paenibacillus daejeonensis	strain=DSM 15491	GCA_000378385.1	135193	135193	type	True	100.0	2469	2471	95	conclusive
Paenibacillus pinihumi	strain=DSM 23905	GCA_000422505.1	669462	669462	type	True	77.3282	182	2471	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	77.0901	143	2471	95	below_threshold
Paenibacillus sambharensis	strain=SMB1	GCA_003233845.1	1803190	1803190	type	True	77.0557	173	2471	95	below_threshold
Paenibacillus roseus	strain=MAHUQ-46	GCA_016424485.1	2798579	2798579	type	True	76.9299	156	2471	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	76.8921	149	2471	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	76.8437	183	2471	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.8421	182	2471	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.7731	119	2471	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	76.7683	168	2471	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.7683	133	2471	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	76.7629	69	2471	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.7334	141	2471	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.7309	147	2471	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	76.7023	174	2471	95	below_threshold
Paenibacillus catalpae	strain=CGMCC 1.10784	GCA_900112695.1	1045775	1045775	type	True	76.6901	153	2471	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.6556	73	2471	95	below_threshold
Cohnella faecalis	strain=K2E09-144	GCA_003570905.1	2315694	2315694	type	True	76.6418	74	2471	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	76.6108	65	2471	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	76.5965	177	2471	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	76.5858	157	2471	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	76.5825	163	2471	95	below_threshold
Paenibacillus luteus	strain=R-3	GCA_006542765.1	2545753	2545753	type	True	76.575	150	2471	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	76.5384	185	2471	95	below_threshold
Paenibacillus pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	76.5206	162	2471	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	76.5066	192	2471	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	76.4994	96	2471	95	below_threshold
Paenibacillus humicus	strain=NBRC 102415	GCA_004000905.1	412861	412861	type	True	76.3747	164	2471	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	76.3457	132	2471	95	below_threshold
Paenibacillus dauci	strain=H9	GCA_000971985.1	1567106	1567106	type	True	76.3062	77	2471	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.3041	94	2471	95	below_threshold
Paenibacillus koleovorans	strain=NBRC 103111	GCA_004000845.1	121608	121608	type	True	76.2058	109	2471	95	below_threshold
Thermobacillus composti	strain=KWC4	GCA_000227705.3	377615	377615	type	True	76.1702	116	2471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:27,672] [INFO] DFAST Taxonomy check result was written to GCF_000378385.1_ASM37838v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:27,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:27,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:27,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2519e4d2-2922-4927-93d0-38d435ca9e76/dqc_reference/checkm_data
[2024-01-24 13:20:27,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:27,745] [INFO] Task started: CheckM
[2024-01-24 13:20:27,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000378385.1_ASM37838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000378385.1_ASM37838v1_genomic.fna/checkm_input GCF_000378385.1_ASM37838v1_genomic.fna/checkm_result
[2024-01-24 13:21:32,920] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:32,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:32,945] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:32,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:32,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000378385.1_ASM37838v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:32,946] [INFO] Task started: Blastn
[2024-01-24 13:21:32,947] [INFO] Running command: blastn -query GCF_000378385.1_ASM37838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2519e4d2-2922-4927-93d0-38d435ca9e76/dqc_reference/reference_markers_gtdb.fasta -out GCF_000378385.1_ASM37838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:33,750] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:33,754] [INFO] Selected 24 target genomes.
[2024-01-24 13:21:33,755] [INFO] Target genome list was writen to GCF_000378385.1_ASM37838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:33,777] [INFO] Task started: fastANI
[2024-01-24 13:21:33,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aebdcb6-a45f-4fd0-b36d-185f9e85ed8b/GCF_000378385.1_ASM37838v1_genomic.fna.gz --refList GCF_000378385.1_ASM37838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000378385.1_ASM37838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:01,599] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:01,618] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:01,618] [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_000378385.1	s__Paenibacillus_D daejeonensis	100.0	2469	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003851045.1	s__Paenibacillus_D sp003851045	80.1386	1004	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422505.1	s__Paenibacillus_D pinihumi	77.3121	183	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	99.89	99.89	1.00	1.00	2	-
GCF_009737085.1	s__Paenibacillus_C sp009737085	77.1789	127	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233845.1	s__Paenibacillus_I sambharensis	77.0835	171	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023585.1	s__Paenibacillus_C sp000023585	76.9669	150	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	76.8643	183	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705605.1	s__Paenibacillus_D sp014705605	76.8298	262	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001682865.1	s__Paenibacillus_C sp001682865	76.7833	125	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.12	99.12	0.94	0.94	2	-
GCF_003614185.1	s__Paenibacillus_A aceti	76.7629	69	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000598065.1	s__Paenibacillus_I darwinianus	76.7543	120	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	99.89	99.87	0.94	0.94	3	-
GCF_900113915.1	s__Paenibacillus_Z sp900113915	76.7005	182	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
GCF_900112695.1	s__Paenibacillus_C catalpae	76.6977	156	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116125.1	s__Paenibacillus_Z sp900116125	76.6629	153	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	-
GCF_014192105.1	s__Paenibacillus_Z phyllosphaerae	76.6338	180	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112455.1	s__Paenibacillus_C agaridevorans	76.6209	198	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	96.67	95.87	0.80	0.78	4	-
GCF_006542765.1	s__Paenibacillus_C luteus	76.6022	148	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422485.1	s__Paenibacillus_O pasadenensis	76.5825	163	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.23	98.68	0.94	0.90	4	-
GCF_014779765.1	s__Paenibacillus_T sp014779765	76.5681	131	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403265.1	s__J31TS4 sp018403265	76.5329	83	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__J31TS4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	76.4982	194	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002243345.2	s__Paenibacillus_O sp002243345	76.4888	155	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.98	99.98	0.98	0.98	4	-
GCF_000971985.1	s__Paenibacillus_J dauci	76.3062	77	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	97.87	97.87	0.93	0.93	2	-
GCF_910593845.1	s__Paenibacillus_G solanacearum	76.2449	125	2471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:01,620] [INFO] GTDB search result was written to GCF_000378385.1_ASM37838v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:01,620] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:01,627] [INFO] DFAST_QC result json was written to GCF_000378385.1_ASM37838v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:01,627] [INFO] DFAST_QC completed!
[2024-01-24 13:22:01,628] [INFO] Total running time: 0h2m33s