[2024-01-24 12:37:37,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,929] [INFO] DQC Reference Directory: /var/lib/cwl/stgbde140e3-1e8e-4dd3-96cc-ac0eee568e3a/dqc_reference
[2024-01-24 12:37:41,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,021] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,021] [INFO] Running command: gunzip -c /var/lib/cwl/stg27f9eadf-16a6-413a-bb63-b53f2afa4475/GCF_014705655.1_ASM1470565v1_genomic.fna.gz | prodigal -d GCF_014705655.1_ASM1470565v1_genomic.fna/cds.fna -a GCF_014705655.1_ASM1470565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:59,645] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:59,646] [INFO] Task started: HMMsearch
[2024-01-24 12:37:59,646] [INFO] Running command: hmmsearch --tblout GCF_014705655.1_ASM1470565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbde140e3-1e8e-4dd3-96cc-ac0eee568e3a/dqc_reference/reference_markers.hmm GCF_014705655.1_ASM1470565v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:59,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:59,977] [INFO] Found 6/6 markers.
[2024-01-24 12:38:00,039] [INFO] Query marker FASTA was written to GCF_014705655.1_ASM1470565v1_genomic.fna/markers.fasta
[2024-01-24 12:38:00,040] [INFO] Task started: Blastn
[2024-01-24 12:38:00,040] [INFO] Running command: blastn -query GCF_014705655.1_ASM1470565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbde140e3-1e8e-4dd3-96cc-ac0eee568e3a/dqc_reference/reference_markers.fasta -out GCF_014705655.1_ASM1470565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:00,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:00,672] [INFO] Selected 22 target genomes.
[2024-01-24 12:38:00,673] [INFO] Target genome list was writen to GCF_014705655.1_ASM1470565v1_genomic.fna/target_genomes.txt
[2024-01-24 12:38:00,696] [INFO] Task started: fastANI
[2024-01-24 12:38:00,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg27f9eadf-16a6-413a-bb63-b53f2afa4475/GCF_014705655.1_ASM1470565v1_genomic.fna.gz --refList GCF_014705655.1_ASM1470565v1_genomic.fna/target_genomes.txt --output GCF_014705655.1_ASM1470565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:25,466] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:25,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbde140e3-1e8e-4dd3-96cc-ac0eee568e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:25,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbde140e3-1e8e-4dd3-96cc-ac0eee568e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:25,483] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:38:25,483] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:38:25,484] [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 harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	81.6208	1187	2317	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	79.7428	706	2317	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	79.6404	660	2317	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	79.0361	514	2317	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	78.4804	537	2317	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	78.4636	395	2317	95	below_threshold
Paenibacillus paridis	strain=py1325	GCA_006345825.1	2583376	2583376	type	True	78.353	512	2317	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	78.2431	606	2317	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	78.0303	513	2317	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	78.0254	512	2317	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	78.0039	312	2317	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.9571	392	2317	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	77.8096	336	2317	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	77.782	398	2317	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	77.7806	397	2317	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.7731	317	2317	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.5985	269	2317	95	below_threshold
Paenibacillus protaetiae	strain=FW100M-2	GCA_004135365.1	2509456	2509456	type	True	77.4362	306	2317	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	77.4005	347	2317	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	77.3666	324	2317	95	below_threshold
Paenibacillus algorifonticola	strain=XJ259	GCA_000971975.1	684063	684063	type	True	77.3636	322	2317	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.6294	239	2317	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:25,486] [INFO] DFAST Taxonomy check result was written to GCF_014705655.1_ASM1470565v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:25,487] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:25,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:25,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbde140e3-1e8e-4dd3-96cc-ac0eee568e3a/dqc_reference/checkm_data
[2024-01-24 12:38:25,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:25,568] [INFO] Task started: CheckM
[2024-01-24 12:38:25,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014705655.1_ASM1470565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014705655.1_ASM1470565v1_genomic.fna/checkm_input GCF_014705655.1_ASM1470565v1_genomic.fna/checkm_result
[2024-01-24 12:39:19,397] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:19,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:19,421] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:19,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:19,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014705655.1_ASM1470565v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:19,423] [INFO] Task started: Blastn
[2024-01-24 12:39:19,423] [INFO] Running command: blastn -query GCF_014705655.1_ASM1470565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbde140e3-1e8e-4dd3-96cc-ac0eee568e3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014705655.1_ASM1470565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:20,357] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:20,360] [INFO] Selected 16 target genomes.
[2024-01-24 12:39:20,360] [INFO] Target genome list was writen to GCF_014705655.1_ASM1470565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:20,378] [INFO] Task started: fastANI
[2024-01-24 12:39:20,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg27f9eadf-16a6-413a-bb63-b53f2afa4475/GCF_014705655.1_ASM1470565v1_genomic.fna.gz --refList GCF_014705655.1_ASM1470565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014705655.1_ASM1470565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:38,734] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:38,756] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:38,757] [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_014705655.1	s__Paenibacillus_C sp014705655	100.0	2313	2317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000422465.1	s__Paenibacillus_C harenae	81.6167	1188	2317	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_003217535.1	s__Paenibacillus_C sp003217535	79.1738	664	2317	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_001428245.1	s__Paenibacillus_C sp001428245	79.1629	651	2317	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_003583765.1	s__Paenibacillus_C nanensis	79.0394	514	2317	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_012935325.2	s__Paenibacillus_C sp012935325	78.892	710	2317	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_003605435.1	s__Paenibacillus_C pinisoli	78.4492	397	2317	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_003112455.1	s__Paenibacillus_C agaridevorans	78.4205	471	2317	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_900113915.1	s__Paenibacillus_Z sp900113915	78.2807	597	2317	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_003388735.1	s__Paenibacillus_C paeoniae	77.9981	312	2317	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_012676905.1	s__Paenibacillus_O sp012676905	77.9485	393	2317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641555.1	s__Paenibacillus_C radicis	77.8096	336	2317	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_000513275.1	s__Paenibacillus_C gorillae	77.7731	317	2317	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_004135365.1	s__Paenibacillus_C protaetiae	77.4421	305	2317	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_000971975.1	s__Paenibacillus_C algorifonticola	77.37	322	2317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014705605.1	s__Paenibacillus_D sp014705605	77.1227	362	2317	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:38,758] [INFO] GTDB search result was written to GCF_014705655.1_ASM1470565v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:38,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:38,763] [INFO] DFAST_QC result json was written to GCF_014705655.1_ASM1470565v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:38,764] [INFO] DFAST_QC completed!
[2024-01-24 12:39:38,764] [INFO] Total running time: 0h2m1s