[2024-01-24 15:02:07,448] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,450] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c68fd3d-9922-4f0a-8891-b4cf893f1542/dqc_reference
[2024-01-24 15:02:09,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,600] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg73cb9042-e482-4582-b65e-067cc3cd0e68/GCF_004764705.1_ASM476470v1_genomic.fna.gz | prodigal -d GCF_004764705.1_ASM476470v1_genomic.fna/cds.fna -a GCF_004764705.1_ASM476470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:38,425] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:38,425] [INFO] Task started: HMMsearch
[2024-01-24 15:02:38,425] [INFO] Running command: hmmsearch --tblout GCF_004764705.1_ASM476470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c68fd3d-9922-4f0a-8891-b4cf893f1542/dqc_reference/reference_markers.hmm GCF_004764705.1_ASM476470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:38,755] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:38,756] [INFO] Found 6/6 markers.
[2024-01-24 15:02:38,824] [INFO] Query marker FASTA was written to GCF_004764705.1_ASM476470v1_genomic.fna/markers.fasta
[2024-01-24 15:02:38,824] [INFO] Task started: Blastn
[2024-01-24 15:02:38,825] [INFO] Running command: blastn -query GCF_004764705.1_ASM476470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c68fd3d-9922-4f0a-8891-b4cf893f1542/dqc_reference/reference_markers.fasta -out GCF_004764705.1_ASM476470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:39,543] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:39,547] [INFO] Selected 21 target genomes.
[2024-01-24 15:02:39,548] [INFO] Target genome list was writen to GCF_004764705.1_ASM476470v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:39,563] [INFO] Task started: fastANI
[2024-01-24 15:02:39,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg73cb9042-e482-4582-b65e-067cc3cd0e68/GCF_004764705.1_ASM476470v1_genomic.fna.gz --refList GCF_004764705.1_ASM476470v1_genomic.fna/target_genomes.txt --output GCF_004764705.1_ASM476470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:08,841] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:08,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c68fd3d-9922-4f0a-8891-b4cf893f1542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:08,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c68fd3d-9922-4f0a-8891-b4cf893f1542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:08,858] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:08,858] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:08,858] [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 cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	100.0	3105	3108	95	conclusive
Paenibacillus koleovorans	strain=NBRC 103111	GCA_004000845.1	121608	121608	type	True	77.7952	410	3108	95	below_threshold
Paenibacillus ginsengarvi	strain=KCTC 13059	GCA_003626695.1	400777	400777	type	True	77.3419	383	3108	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	77.2798	518	3108	95	below_threshold
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	77.1792	358	3108	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	77.0284	328	3108	95	below_threshold
Paenibacillus athensensis	strain=MEC069	GCA_004514475.2	1967502	1967502	type	True	77.0016	287	3108	95	below_threshold
Paenibacillus mesophilus	strain=SYSU K30004	GCA_005938385.1	2582849	2582849	type	True	76.9723	337	3108	95	below_threshold
Paenibacillus contaminans	strain=CKOBP-6	GCA_003285015.1	450362	450362	type	True	76.9048	438	3108	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.8926	301	3108	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	76.8843	348	3108	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.8774	422	3108	95	below_threshold
Paenibacillus pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	76.8541	353	3108	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	76.6655	222	3108	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.6004	328	3108	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.5855	309	3108	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.4318	174	3108	95	below_threshold
Paenibacillus thalictri	strain=N2SHLJ1	GCA_004307995.1	2527873	2527873	type	True	76.4003	275	3108	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	76.3503	153	3108	95	below_threshold
Xylanibacillus composti	strain=K13	GCA_018403685.1	1572762	1572762	type	True	76.0577	93	3108	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.0034	142	3108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:08,860] [INFO] DFAST Taxonomy check result was written to GCF_004764705.1_ASM476470v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:08,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:08,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:08,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c68fd3d-9922-4f0a-8891-b4cf893f1542/dqc_reference/checkm_data
[2024-01-24 15:03:08,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:08,945] [INFO] Task started: CheckM
[2024-01-24 15:03:08,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004764705.1_ASM476470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004764705.1_ASM476470v1_genomic.fna/checkm_input GCF_004764705.1_ASM476470v1_genomic.fna/checkm_result
[2024-01-24 15:04:24,558] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:24,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:24,586] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:24,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:24,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004764705.1_ASM476470v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:24,587] [INFO] Task started: Blastn
[2024-01-24 15:04:24,587] [INFO] Running command: blastn -query GCF_004764705.1_ASM476470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c68fd3d-9922-4f0a-8891-b4cf893f1542/dqc_reference/reference_markers_gtdb.fasta -out GCF_004764705.1_ASM476470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:25,539] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:25,542] [INFO] Selected 21 target genomes.
[2024-01-24 15:04:25,543] [INFO] Target genome list was writen to GCF_004764705.1_ASM476470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:25,564] [INFO] Task started: fastANI
[2024-01-24 15:04:25,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg73cb9042-e482-4582-b65e-067cc3cd0e68/GCF_004764705.1_ASM476470v1_genomic.fna.gz --refList GCF_004764705.1_ASM476470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004764705.1_ASM476470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:52,365] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:52,380] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:52,380] [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_004764705.1	s__R196 sp004764705	100.0	3105	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__R196	95.0	95.77	95.77	0.86	0.86	2	conclusive
GCF_004000845.1	s__Paenibacillus_AA koleovorans	77.8091	409	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626695.1	s__Paenibacillus_AB ginsengarvi	77.3352	383	3108	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	77.2939	514	3108	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_000829455.1	s__VKM-B-2647 sp000829455	77.2862	400	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__VKM-B-2647	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265175.1	s__Paenibacillus_AB hemerocallicola	77.1801	357	3108	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_907165215.1	s__Thermobacillus xylanilyticus	77.0652	259	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	-
GCF_004514475.1	s__MEC069 sp004514475	77.0275	287	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__MEC069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380965.1	s__Paenibacillus_M ginsengihumi	77.0197	328	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938385.1	s__Paenibacillus_AB mesophilus	76.972	336	3108	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_003285015.1	s__Paenibacillus_V contaminans	76.9084	434	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_V	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403265.1	s__J31TS4 sp018403265	76.9082	275	3108	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_000422485.1	s__Paenibacillus_O pasadenensis	76.8911	347	3108	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_000961095.1	s__Paenibacillus_O beijingensis	76.8371	223	3108	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_004000985.1	s__Paenibacillus_G validus	76.6655	222	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.29	99.15	0.90	0.89	6	-
GCF_014705655.1	s__Paenibacillus_C sp014705655	76.4467	337	3108	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_004307995.1	s__Paenibacillus_AF thalictri	76.3967	273	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AF	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739915.1	s__Paenibacillus_F chitinolyticus	76.2036	176	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004345425.1	s__Paenibacillus_C sp004345425	76.1843	156	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
GCF_018403685.1	s__Xylanibacillus composti	76.0577	93	3108	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__K13;g__Xylanibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:52,382] [INFO] GTDB search result was written to GCF_004764705.1_ASM476470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:52,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:52,387] [INFO] DFAST_QC result json was written to GCF_004764705.1_ASM476470v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:52,387] [INFO] DFAST_QC completed!
[2024-01-24 15:04:52,387] [INFO] Total running time: 0h2m45s