[2024-01-24 12:22:34,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg53ea7713-cc1f-4764-8097-228c0ff551b6/dqc_reference
[2024-01-24 12:22:35,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,713] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,714] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a8294f9-481e-45e6-882b-9733425be460/GCF_017873435.1_ASM1787343v1_genomic.fna.gz | prodigal -d GCF_017873435.1_ASM1787343v1_genomic.fna/cds.fna -a GCF_017873435.1_ASM1787343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:44,384] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:44,384] [INFO] Task started: HMMsearch
[2024-01-24 12:22:44,384] [INFO] Running command: hmmsearch --tblout GCF_017873435.1_ASM1787343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53ea7713-cc1f-4764-8097-228c0ff551b6/dqc_reference/reference_markers.hmm GCF_017873435.1_ASM1787343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:44,615] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:44,616] [INFO] Found 6/6 markers.
[2024-01-24 12:22:44,651] [INFO] Query marker FASTA was written to GCF_017873435.1_ASM1787343v1_genomic.fna/markers.fasta
[2024-01-24 12:22:44,652] [INFO] Task started: Blastn
[2024-01-24 12:22:44,652] [INFO] Running command: blastn -query GCF_017873435.1_ASM1787343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53ea7713-cc1f-4764-8097-228c0ff551b6/dqc_reference/reference_markers.fasta -out GCF_017873435.1_ASM1787343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:45,181] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:45,184] [INFO] Selected 22 target genomes.
[2024-01-24 12:22:45,184] [INFO] Target genome list was writen to GCF_017873435.1_ASM1787343v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:45,269] [INFO] Task started: fastANI
[2024-01-24 12:22:45,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a8294f9-481e-45e6-882b-9733425be460/GCF_017873435.1_ASM1787343v1_genomic.fna.gz --refList GCF_017873435.1_ASM1787343v1_genomic.fna/target_genomes.txt --output GCF_017873435.1_ASM1787343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:09,657] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:09,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53ea7713-cc1f-4764-8097-228c0ff551b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:09,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53ea7713-cc1f-4764-8097-228c0ff551b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:09,667] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:09,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:09,668] [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 turicensis	strain=DSM 14349	GCA_017873435.1	160487	160487	type	True	100.0	1566	1568	95	conclusive
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	80.5931	142	1568	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	80.4657	143	1568	95	below_threshold
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	78.0047	167	1568	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	77.8058	128	1568	95	below_threshold
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	77.7683	99	1568	95	below_threshold
Paenibacillus shirakamiensis	strain=DSM 26806	GCA_017874255.1	1265935	1265935	type	True	77.6038	90	1568	95	below_threshold
Paenibacillus lutimineralis	strain=MBLB1234	GCA_003991425.1	2707005	2707005	type	True	77.6025	107	1568	95	below_threshold
Fontibacillus solani	strain=CECT 8693	GCA_014138385.1	1572857	1572857	type	True	77.5435	147	1568	95	below_threshold
Paenibacillus anaericanus	strain=DSM 15890	GCA_003994475.1	170367	170367	type	True	77.5287	162	1568	95	below_threshold
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	77.4687	86	1568	95	below_threshold
Paenibacillus polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	77.3641	98	1568	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	77.2539	95	1568	95	below_threshold
Paenibacillus peoriae	strain=KCTC 3763	GCA_000236805.2	59893	59893	suspected-type	True	76.9885	76	1568	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	76.917	60	1568	95	below_threshold
Paenibacillus nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	76.7729	96	1568	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:09,669] [INFO] DFAST Taxonomy check result was written to GCF_017873435.1_ASM1787343v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:09,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:09,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:09,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53ea7713-cc1f-4764-8097-228c0ff551b6/dqc_reference/checkm_data
[2024-01-24 12:23:09,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:09,716] [INFO] Task started: CheckM
[2024-01-24 12:23:09,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873435.1_ASM1787343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873435.1_ASM1787343v1_genomic.fna/checkm_input GCF_017873435.1_ASM1787343v1_genomic.fna/checkm_result
[2024-01-24 12:23:38,856] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:38,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:38,873] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:38,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:38,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873435.1_ASM1787343v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:38,874] [INFO] Task started: Blastn
[2024-01-24 12:23:38,874] [INFO] Running command: blastn -query GCF_017873435.1_ASM1787343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53ea7713-cc1f-4764-8097-228c0ff551b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873435.1_ASM1787343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:39,666] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:39,668] [INFO] Selected 24 target genomes.
[2024-01-24 12:23:39,669] [INFO] Target genome list was writen to GCF_017873435.1_ASM1787343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:39,696] [INFO] Task started: fastANI
[2024-01-24 12:23:39,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a8294f9-481e-45e6-882b-9733425be460/GCF_017873435.1_ASM1787343v1_genomic.fna.gz --refList GCF_017873435.1_ASM1787343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873435.1_ASM1787343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:03,328] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:03,340] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:03,341] [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_017873435.1	s__Paenibacillus_A turicensis	100.0	1566	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003614185.1	s__Paenibacillus_A aceti	80.5931	142	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014639155.1	s__Paenibacillus_A segetis	78.0047	167	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381905.1	s__Paenibacillus_A fonticola	77.82	130	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874765.1	s__Paenibacillus rhizoplanae	77.7072	66	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991425.1	s__Paenibacillus_A lutimineralis	77.6499	107	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084145.1	s__Paenibacillus_A faecis	77.6444	91	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.85	97.85	0.92	0.92	2	-
GCF_003994475.1	s__Paenibacillus_A anaericanus	77.5518	160	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060825.1	s__Paenibacillus_A sp003060825	77.4956	94	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359945.1	s__Paenibacillus sp013359945	77.4809	61	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007680605.1	s__Paenibacillus xylanexedens_B	77.3302	103	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.13	99.13	0.96	0.96	2	-
GCF_003268635.1	s__Paenibacillus sp003268635	77.3001	98	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836635.1	s__Paenibacillus sp014836635	77.2707	94	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002439285.1	s__Paenibacillus_A sp002439285	77.2261	87	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001709075.1	s__Paenibacillus polymyxa_D	77.1261	71	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.80	97.93	0.93	0.90	8	-
GCF_001315105.1	s__Paenibacillus sp001315105	77.1212	59	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116105.1	s__Paenibacillus sp900116105	77.1183	71	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000237325.1	s__Paenibacillus polymyxa_C	77.1027	77	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.50	97.87	0.93	0.89	15	-
GCF_001955535.1	s__Paenibacillus sp001955535	77.0595	78	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.62	98.62	0.85	0.85	2	-
GCA_017512705.1	s__Paenibacillus sp017512705	76.8692	98	1568	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	76.7526	94	1568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	98.40	98.40	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:03,342] [INFO] GTDB search result was written to GCF_017873435.1_ASM1787343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:03,342] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:03,346] [INFO] DFAST_QC result json was written to GCF_017873435.1_ASM1787343v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:03,346] [INFO] DFAST_QC completed!
[2024-01-24 12:24:03,346] [INFO] Total running time: 0h1m29s