[2024-01-24 11:26:54,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,315] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,315] [INFO] DQC Reference Directory: /var/lib/cwl/stg26b2b958-1e78-4937-bd68-8040aaa9e5b1/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,222] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b511936-00c9-47cd-bf51-b71cee65bb0b/GCF_006265175.1_ASM626517v1_genomic.fna.gz | prodigal -d GCF_006265175.1_ASM626517v1_genomic.fna/cds.fna -a GCF_006265175.1_ASM626517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:24,844] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:24,844] [INFO] Task started: HMMsearch
[2024-01-24 11:27:24,845] [INFO] Running command: hmmsearch --tblout GCF_006265175.1_ASM626517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26b2b958-1e78-4937-bd68-8040aaa9e5b1/dqc_reference/reference_markers.hmm GCF_006265175.1_ASM626517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:25,252] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:25,253] [INFO] Found 6/6 markers.
[2024-01-24 11:27:25,330] [INFO] Query marker FASTA was written to GCF_006265175.1_ASM626517v1_genomic.fna/markers.fasta
[2024-01-24 11:27:25,331] [INFO] Task started: Blastn
[2024-01-24 11:27:25,331] [INFO] Running command: blastn -query GCF_006265175.1_ASM626517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26b2b958-1e78-4937-bd68-8040aaa9e5b1/dqc_reference/reference_markers.fasta -out GCF_006265175.1_ASM626517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:25,975] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:25,979] [INFO] Selected 17 target genomes.
[2024-01-24 11:27:25,979] [INFO] Target genome list was writen to GCF_006265175.1_ASM626517v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:25,990] [INFO] Task started: fastANI
[2024-01-24 11:27:25,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b511936-00c9-47cd-bf51-b71cee65bb0b/GCF_006265175.1_ASM626517v1_genomic.fna.gz --refList GCF_006265175.1_ASM626517v1_genomic.fna/target_genomes.txt --output GCF_006265175.1_ASM626517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:47,418] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:47,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26b2b958-1e78-4937-bd68-8040aaa9e5b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:47,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26b2b958-1e78-4937-bd68-8040aaa9e5b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:47,436] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:47,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:47,436] [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 hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	100.0	3135	3143	95	conclusive
Paenibacillus mesophilus	strain=SYSU K30004	GCA_005938385.1	2582849	2582849	type	True	84.0166	1797	3143	95	below_threshold
Paenibacillus ginsengarvi	strain=KCTC 13059	GCA_003626695.1	400777	400777	type	True	80.178	1228	3143	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	79.8409	978	3143	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	79.2045	945	3143	95	below_threshold
Paenibacillus puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	77.0552	204	3143	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	76.8082	215	3143	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.7191	87	3143	95	below_threshold
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	76.7103	161	3143	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	76.7045	238	3143	95	below_threshold
Paenibacillus cisolokensis	strain=LC2-13A	GCA_018403665.1	1658519	1658519	type	True	76.6818	214	3143	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	76.6779	240	3143	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.6657	259	3143	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.6606	160	3143	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.6489	285	3143	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.5254	184	3143	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.0962	127	3143	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:47,438] [INFO] DFAST Taxonomy check result was written to GCF_006265175.1_ASM626517v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:47,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:47,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:47,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26b2b958-1e78-4937-bd68-8040aaa9e5b1/dqc_reference/checkm_data
[2024-01-24 11:27:47,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:47,532] [INFO] Task started: CheckM
[2024-01-24 11:27:47,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006265175.1_ASM626517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006265175.1_ASM626517v1_genomic.fna/checkm_input GCF_006265175.1_ASM626517v1_genomic.fna/checkm_result
[2024-01-24 11:28:59,055] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:59,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:59,083] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:59,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:59,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006265175.1_ASM626517v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:59,085] [INFO] Task started: Blastn
[2024-01-24 11:28:59,085] [INFO] Running command: blastn -query GCF_006265175.1_ASM626517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26b2b958-1e78-4937-bd68-8040aaa9e5b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_006265175.1_ASM626517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:59,878] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:59,882] [INFO] Selected 13 target genomes.
[2024-01-24 11:28:59,883] [INFO] Target genome list was writen to GCF_006265175.1_ASM626517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:59,894] [INFO] Task started: fastANI
[2024-01-24 11:28:59,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b511936-00c9-47cd-bf51-b71cee65bb0b/GCF_006265175.1_ASM626517v1_genomic.fna.gz --refList GCF_006265175.1_ASM626517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006265175.1_ASM626517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:18,246] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:18,267] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:18,267] [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_006265175.1	s__Paenibacillus_AB hemerocallicola	100.0	3135	3143	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005938385.1	s__Paenibacillus_AB mesophilus	84.0142	1797	3143	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626695.1	s__Paenibacillus_AB ginsengarvi	80.1781	1227	3143	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217775.1	s__Paenibacillus_AB flagellatus	79.838	979	3143	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705615.1	s__Paenibacillus_AB sp014705615	79.2208	943	3143	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846885.1	s__Paenibacillus_G puerhi	77.0471	203	3143	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	-
GCF_018918005.1	s__MSJ-34 sp018918005	77.0221	173	3143	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__MSJ-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101595.1	s__Paenibacillus_G sp900101595	76.9953	266	3143	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014212175.1	s__Cohnella xylanilytica	76.8076	215	3143	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_014705655.1	s__Paenibacillus_C sp014705655	76.6395	282	3143	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_900113915.1	s__Paenibacillus_Z sp900113915	76.6347	260	3143	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_017874175.1	s__Cohnella suwonensis	76.4247	184	3143	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705605.1	s__Paenibacillus_D sp014705605	76.3128	191	3143	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 11:29:18,269] [INFO] GTDB search result was written to GCF_006265175.1_ASM626517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:18,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:18,275] [INFO] DFAST_QC result json was written to GCF_006265175.1_ASM626517v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:18,275] [INFO] DFAST_QC completed!
[2024-01-24 11:29:18,275] [INFO] Total running time: 0h2m24s