[2024-01-24 13:27:46,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,389] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,389] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc233805-547d-4e52-aa97-d5c7117e7d00/dqc_reference
[2024-01-24 13:27:47,952] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,953] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg82b87815-9d44-499b-baca-f53e30212b83/GCF_000227705.2_ASM22770v3_genomic.fna.gz | prodigal -d GCF_000227705.2_ASM22770v3_genomic.fna/cds.fna -a GCF_000227705.2_ASM22770v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:01,630] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:01,631] [INFO] Task started: HMMsearch
[2024-01-24 13:28:01,631] [INFO] Running command: hmmsearch --tblout GCF_000227705.2_ASM22770v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc233805-547d-4e52-aa97-d5c7117e7d00/dqc_reference/reference_markers.hmm GCF_000227705.2_ASM22770v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:02,009] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:02,010] [INFO] Found 6/6 markers.
[2024-01-24 13:28:02,051] [INFO] Query marker FASTA was written to GCF_000227705.2_ASM22770v3_genomic.fna/markers.fasta
[2024-01-24 13:28:02,052] [INFO] Task started: Blastn
[2024-01-24 13:28:02,052] [INFO] Running command: blastn -query GCF_000227705.2_ASM22770v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc233805-547d-4e52-aa97-d5c7117e7d00/dqc_reference/reference_markers.fasta -out GCF_000227705.2_ASM22770v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:02,754] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:02,768] [INFO] Selected 19 target genomes.
[2024-01-24 13:28:02,769] [INFO] Target genome list was writen to GCF_000227705.2_ASM22770v3_genomic.fna/target_genomes.txt
[2024-01-24 13:28:02,785] [INFO] Task started: fastANI
[2024-01-24 13:28:02,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b87815-9d44-499b-baca-f53e30212b83/GCF_000227705.2_ASM22770v3_genomic.fna.gz --refList GCF_000227705.2_ASM22770v3_genomic.fna/target_genomes.txt --output GCF_000227705.2_ASM22770v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:22,503] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:22,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc233805-547d-4e52-aa97-d5c7117e7d00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:22,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc233805-547d-4e52-aa97-d5c7117e7d00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:22,519] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:22,519] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:28:22,520] [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
Thermobacillus composti	strain=KWC4	GCA_000227705.3	377615	377615	type	True	100.0	1450	1451	95	inconclusive
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	97.5567	1123	1451	95	inconclusive
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	78.4764	347	1451	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	78.1695	239	1451	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	78.0997	382	1451	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	78.0595	353	1451	95	below_threshold
Cohnella laeviribosi	strain=DSM 21336	GCA_000378425.1	380174	380174	type	True	78.0551	282	1451	95	below_threshold
Paenibacillus pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	78.0018	383	1451	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	77.7505	296	1451	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.728	403	1451	95	below_threshold
Paenibacillus cisolokensis	strain=LC2-13A	GCA_018403665.1	1658519	1658519	type	True	77.7144	307	1451	95	below_threshold
Paenibacillus antri	strain=SYSU K30003	GCA_005765165.1	2582848	2582848	type	True	77.6991	270	1451	95	below_threshold
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	77.691	251	1451	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	77.4381	323	1451	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	77.3372	319	1451	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	77.3007	304	1451	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.062	314	1451	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.8736	177	1451	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.5152	140	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:22,522] [INFO] DFAST Taxonomy check result was written to GCF_000227705.2_ASM22770v3_genomic.fna/tc_result.tsv
[2024-01-24 13:28:22,522] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:22,522] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:22,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc233805-547d-4e52-aa97-d5c7117e7d00/dqc_reference/checkm_data
[2024-01-24 13:28:22,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:22,574] [INFO] Task started: CheckM
[2024-01-24 13:28:22,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000227705.2_ASM22770v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000227705.2_ASM22770v3_genomic.fna/checkm_input GCF_000227705.2_ASM22770v3_genomic.fna/checkm_result
[2024-01-24 13:29:04,391] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:04,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:04,414] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:04,414] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:04,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000227705.2_ASM22770v3_genomic.fna/markers.fasta)
[2024-01-24 13:29:04,415] [INFO] Task started: Blastn
[2024-01-24 13:29:04,415] [INFO] Running command: blastn -query GCF_000227705.2_ASM22770v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc233805-547d-4e52-aa97-d5c7117e7d00/dqc_reference/reference_markers_gtdb.fasta -out GCF_000227705.2_ASM22770v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:05,427] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:05,432] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:05,432] [INFO] Target genome list was writen to GCF_000227705.2_ASM22770v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:05,456] [INFO] Task started: fastANI
[2024-01-24 13:29:05,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b87815-9d44-499b-baca-f53e30212b83/GCF_000227705.2_ASM22770v3_genomic.fna.gz --refList GCF_000227705.2_ASM22770v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000227705.2_ASM22770v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:23,613] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:23,628] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:23,628] [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_907165215.1	s__Thermobacillus xylanilyticus	97.5567	1123	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	conclusive
GCA_002159085.1	s__Thermobacillus sp002159085	85.4623	919	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012676905.1	s__Paenibacillus_O sp012676905	78.4639	343	1451	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_000598065.1	s__Paenibacillus_I darwinianus	78.1695	239	1451	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_014212175.1	s__Cohnella xylanilytica	78.0686	352	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_000422485.1	s__Paenibacillus_O pasadenensis	78.0678	386	1451	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_900113915.1	s__Paenibacillus_Z sp900113915	77.7953	399	1451	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_000429825.1	s__Cohnella thermotolerans	77.7574	296	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403665.1	s__Paenibacillus_AH cisolokensis	77.7376	305	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_AH	95.0	98.86	98.86	0.88	0.88	2	-
GCF_003713065.1	s__Cohnella candidum	77.7324	252	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005765165.1	s__Paenibacillus_AE antri	77.7022	271	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002159065.1	s__ZCTH02-B3 sp002159065	77.6904	225	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__ZCTH02-B3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212125.1	s__Cohnella nanjingensis	77.4469	322	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212055.1	s__Cohnella zeiphila	77.3275	302	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124765.1	s__Paenibacillus_Z methanolicus	77.3222	320	1451	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_014705655.1	s__Paenibacillus_C sp014705655	77.263	311	1451	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_009909185.1	s__Paenibacillus_Z glycinis	77.07	314	1451	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_003851045.1	s__Paenibacillus_D sp003851045	76.9833	286	1451	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 13:29:23,630] [INFO] GTDB search result was written to GCF_000227705.2_ASM22770v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:23,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:23,635] [INFO] DFAST_QC result json was written to GCF_000227705.2_ASM22770v3_genomic.fna/dqc_result.json
[2024-01-24 13:29:23,636] [INFO] DFAST_QC completed!
[2024-01-24 13:29:23,636] [INFO] Total running time: 0h1m37s