[2024-01-25 19:54:20,444] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:20,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:20,447] [INFO] DQC Reference Directory: /var/lib/cwl/stga2262e2e-5228-4e15-be5b-8cfb2e7da640/dqc_reference
[2024-01-25 19:54:21,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:21,618] [INFO] Task started: Prodigal
[2024-01-25 19:54:21,619] [INFO] Running command: gunzip -c /var/lib/cwl/stgae77ac33-af1d-4a53-ba9a-8e27a8b56b60/GCF_002021565.1_ASM202156v1_genomic.fna.gz | prodigal -d GCF_002021565.1_ASM202156v1_genomic.fna/cds.fna -a GCF_002021565.1_ASM202156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:37,046] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:37,046] [INFO] Task started: HMMsearch
[2024-01-25 19:54:37,046] [INFO] Running command: hmmsearch --tblout GCF_002021565.1_ASM202156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2262e2e-5228-4e15-be5b-8cfb2e7da640/dqc_reference/reference_markers.hmm GCF_002021565.1_ASM202156v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:37,347] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:37,348] [INFO] Found 6/6 markers.
[2024-01-25 19:54:37,403] [INFO] Query marker FASTA was written to GCF_002021565.1_ASM202156v1_genomic.fna/markers.fasta
[2024-01-25 19:54:37,403] [INFO] Task started: Blastn
[2024-01-25 19:54:37,403] [INFO] Running command: blastn -query GCF_002021565.1_ASM202156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2262e2e-5228-4e15-be5b-8cfb2e7da640/dqc_reference/reference_markers.fasta -out GCF_002021565.1_ASM202156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:37,963] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:37,966] [INFO] Selected 25 target genomes.
[2024-01-25 19:54:37,966] [INFO] Target genome list was writen to GCF_002021565.1_ASM202156v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:38,001] [INFO] Task started: fastANI
[2024-01-25 19:54:38,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgae77ac33-af1d-4a53-ba9a-8e27a8b56b60/GCF_002021565.1_ASM202156v1_genomic.fna.gz --refList GCF_002021565.1_ASM202156v1_genomic.fna/target_genomes.txt --output GCF_002021565.1_ASM202156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:04,750] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:04,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2262e2e-5228-4e15-be5b-8cfb2e7da640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:04,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2262e2e-5228-4e15-be5b-8cfb2e7da640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:04,763] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:04,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:04,763] [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 selenitireducens	strain=ES3-24	GCA_002021565.1	1324314	1324314	type	True	100.0	2272	2275	95	conclusive
Paenibacillus terrigena	strain=DSM 21567	GCA_000374845.1	369333	369333	type	True	81.8471	764	2275	95	below_threshold
Paenibacillus guangzhouensis	strain=KCTC 33171	GCA_009363075.1	1473112	1473112	type	True	80.9043	752	2275	95	below_threshold
Paenibacillus wynnii	strain=DSM 18334	GCA_000757885.1	268407	268407	type	True	79.1348	87	2275	95	below_threshold
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	79.1347	143	2275	95	below_threshold
Paenibacillus alvei	strain=DSM 29	GCA_000293805.1	44250	44250	type	True	78.2477	145	2275	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	78.0386	85	2275	95	below_threshold
Paenibacillus castaneae	strain=DSM 19417	GCA_002884445.1	474957	474957	type	True	78.0243	135	2275	95	below_threshold
Paenibacillus xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	77.852	119	2275	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	77.7293	121	2275	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	77.7243	140	2275	95	below_threshold
Paenibacillus amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	77.6903	113	2275	95	below_threshold
Paenibacillus paridis	strain=py1325	GCA_006345825.1	2583376	2583376	type	True	77.5738	112	2275	95	below_threshold
Paenibacillus nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	77.2902	83	2275	95	below_threshold
Paenibacillus barcinonensis	strain=CECT 7022	GCA_003217495.1	198119	198119	type	True	77.2345	92	2275	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	77.1816	65	2275	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.9887	96	2275	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	76.7505	87	2275	95	below_threshold
Paenibacillus xylaniclasticus	strain=NBRC 106381	GCA_004001065.1	588083	588083	type	True	76.5113	55	2275	95	below_threshold
Paenibacillus naphthalenovorans	strain=PR-N1	GCA_900099895.1	162209	162209	type	True	76.3025	51	2275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:04,766] [INFO] DFAST Taxonomy check result was written to GCF_002021565.1_ASM202156v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:04,768] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:04,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:04,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2262e2e-5228-4e15-be5b-8cfb2e7da640/dqc_reference/checkm_data
[2024-01-25 19:55:04,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:04,856] [INFO] Task started: CheckM
[2024-01-25 19:55:04,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002021565.1_ASM202156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002021565.1_ASM202156v1_genomic.fna/checkm_input GCF_002021565.1_ASM202156v1_genomic.fna/checkm_result
[2024-01-25 19:55:51,913] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:51,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:51,941] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:51,942] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:51,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002021565.1_ASM202156v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:51,942] [INFO] Task started: Blastn
[2024-01-25 19:55:51,942] [INFO] Running command: blastn -query GCF_002021565.1_ASM202156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2262e2e-5228-4e15-be5b-8cfb2e7da640/dqc_reference/reference_markers_gtdb.fasta -out GCF_002021565.1_ASM202156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:52,724] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:52,727] [INFO] Selected 24 target genomes.
[2024-01-25 19:55:52,727] [INFO] Target genome list was writen to GCF_002021565.1_ASM202156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:52,752] [INFO] Task started: fastANI
[2024-01-25 19:55:52,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgae77ac33-af1d-4a53-ba9a-8e27a8b56b60/GCF_002021565.1_ASM202156v1_genomic.fna.gz --refList GCF_002021565.1_ASM202156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002021565.1_ASM202156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:21,186] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:21,201] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:21,201] [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_002021565.1	s__Paenibacillus_K selenitireducens	100.0	2272	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_K	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000374845.1	s__Paenibacillus_K terrigena	81.8473	764	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363075.1	s__Paenibacillus_K guangzhouensis	80.9165	751	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014844075.1	s__Paenibacillus sp014844075	79.0784	134	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894745.1	s__Paenibacillus_B sp001894745	78.9918	173	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	96.43	95.29	0.89	0.85	9	-
GCF_000757885.1	s__Paenibacillus wynnii	78.9564	86	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000293805.1	s__Paenibacillus_B alvei	78.2033	146	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	97.68	97.62	0.90	0.89	5	-
GCF_000971975.1	s__Paenibacillus_C algorifonticola	78.172	115	2275	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_000316035.1	s__Paenibacillus sp000316035	78.0577	109	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.8348	N/A	N/A	N/A	N/A	1	-
GCF_017874615.1	s__Paenibacillus xylanexedens	77.8816	118	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.078	N/A	N/A	N/A	N/A	1	-
GCF_016019935.1	s__Paenibacillus_C sp016019935	77.8199	97	2275	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_001514495.1	s__Paenibacillus pabuli	77.7565	120	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614975.1	s__Paenibacillus polymyxa_E	77.6879	123	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918005.1	s__MSJ-34 sp018918005	77.6694	147	2275	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_014534655.1	s__Paenibacillus_E sp014534655	77.6513	94	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359935.1	s__Paenibacillus xylanilyticus	77.406	121	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721045.1	s__Paenibacillus_J nuruki	77.2759	82	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	98.40	98.40	0.93	0.93	2	-
GCF_003583765.1	s__Paenibacillus_C nanensis	77.2285	66	2275	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_001653565.1	s__Paenibacillus_E oryzisoli	77.2274	97	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217495.1	s__Paenibacillus barcinonensis	77.2075	93	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003955665.1	s__Paenibacillus_E whitsoniae	77.1764	94	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829615.1	s__Paenibacillus_E sp007829615	77.0621	89	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874765.1	s__Paenibacillus rhizoplanae	76.9354	99	2275	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:21,203] [INFO] GTDB search result was written to GCF_002021565.1_ASM202156v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:21,203] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:21,208] [INFO] DFAST_QC result json was written to GCF_002021565.1_ASM202156v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:21,208] [INFO] DFAST_QC completed!
[2024-01-25 19:56:21,208] [INFO] Total running time: 0h2m1s