[2024-01-24 15:02:07,445] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,447] [INFO] DQC Reference Directory: /var/lib/cwl/stga6651534-3399-43df-8a18-be0456d674ac/dqc_reference
[2024-01-24 15:02:09,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,599] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,599] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc8c3293-7d1e-438a-8b2c-ed19189baa45/GCF_001721045.1_ASM172104v1_genomic.fna.gz | prodigal -d GCF_001721045.1_ASM172104v1_genomic.fna/cds.fna -a GCF_001721045.1_ASM172104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:21,013] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:21,014] [INFO] Task started: HMMsearch
[2024-01-24 15:02:21,014] [INFO] Running command: hmmsearch --tblout GCF_001721045.1_ASM172104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6651534-3399-43df-8a18-be0456d674ac/dqc_reference/reference_markers.hmm GCF_001721045.1_ASM172104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:21,294] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:21,295] [INFO] Found 6/6 markers.
[2024-01-24 15:02:21,346] [INFO] Query marker FASTA was written to GCF_001721045.1_ASM172104v1_genomic.fna/markers.fasta
[2024-01-24 15:02:21,347] [INFO] Task started: Blastn
[2024-01-24 15:02:21,347] [INFO] Running command: blastn -query GCF_001721045.1_ASM172104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6651534-3399-43df-8a18-be0456d674ac/dqc_reference/reference_markers.fasta -out GCF_001721045.1_ASM172104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:21,972] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:21,976] [INFO] Selected 18 target genomes.
[2024-01-24 15:02:21,976] [INFO] Target genome list was writen to GCF_001721045.1_ASM172104v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:21,999] [INFO] Task started: fastANI
[2024-01-24 15:02:21,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc8c3293-7d1e-438a-8b2c-ed19189baa45/GCF_001721045.1_ASM172104v1_genomic.fna.gz --refList GCF_001721045.1_ASM172104v1_genomic.fna/target_genomes.txt --output GCF_001721045.1_ASM172104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:40,949] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:40,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6651534-3399-43df-8a18-be0456d674ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:40,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6651534-3399-43df-8a18-be0456d674ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:40,969] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:40,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:40,970] [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 nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	100.0	1730	1733	95	conclusive
Paenibacillus wulumuqiensis	strain=Y24	GCA_000971965.1	1567107	1567107	type	True	78.2685	331	1733	95	below_threshold
Paenibacillus bovis	strain=BD3526	GCA_001421015.2	1616788	1616788	type	True	78.1478	390	1733	95	below_threshold
Paenibacillus dauci	strain=H9	GCA_000971985.1	1567106	1567106	type	True	78.1059	393	1733	95	below_threshold
Paenibacillus hunanensis	strain=CGMCC 1.8907	GCA_014645615.1	539262	539262	type	True	77.5581	344	1733	95	below_threshold
Paenibacillus antarcticus	strain=CECT 5836	GCA_001637225.1	253703	253703	type	True	77.3868	95	1733	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	77.3743	105	1733	95	below_threshold
Paenibacillus macquariensis subsp. macquariensis	strain=DSM 2	GCA_001637165.1	1468	948756	type	True	77.3099	104	1733	95	below_threshold
Paenibacillus xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	77.1325	121	1733	95	below_threshold
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	77.1158	90	1733	95	below_threshold
Paenibacillus macquariensis	strain=ATCC 23464	GCA_900156375.1	948756	948756	type	True	77.0957	104	1733	95	below_threshold
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	77.0585	110	1733	95	below_threshold
Paenibacillus crassostreae	strain=LPB0068	GCA_001857945.1	1763538	1763538	type	True	76.9803	96	1733	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	76.8482	108	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:40,972] [INFO] DFAST Taxonomy check result was written to GCF_001721045.1_ASM172104v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:40,973] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:40,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:40,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6651534-3399-43df-8a18-be0456d674ac/dqc_reference/checkm_data
[2024-01-24 15:02:40,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:41,034] [INFO] Task started: CheckM
[2024-01-24 15:02:41,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001721045.1_ASM172104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001721045.1_ASM172104v1_genomic.fna/checkm_input GCF_001721045.1_ASM172104v1_genomic.fna/checkm_result
[2024-01-24 15:03:22,858] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:22,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:22,879] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:22,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:22,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001721045.1_ASM172104v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:22,880] [INFO] Task started: Blastn
[2024-01-24 15:03:22,880] [INFO] Running command: blastn -query GCF_001721045.1_ASM172104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6651534-3399-43df-8a18-be0456d674ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_001721045.1_ASM172104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:23,699] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:23,702] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:23,702] [INFO] Target genome list was writen to GCF_001721045.1_ASM172104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:23,718] [INFO] Task started: fastANI
[2024-01-24 15:03:23,718] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc8c3293-7d1e-438a-8b2c-ed19189baa45/GCF_001721045.1_ASM172104v1_genomic.fna.gz --refList GCF_001721045.1_ASM172104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001721045.1_ASM172104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:40,411] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:40,424] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:40,424] [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_001721045.1	s__Paenibacillus_J nuruki	100.0	1730	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	98.40	98.40	0.93	0.93	2	conclusive
GCF_016908805.1	s__Paenibacillus_J nicotianae	87.7111	1481	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971965.1	s__Paenibacillus_J wulumuqiensis	78.2536	332	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421015.2	s__Paenibacillus_J bovis	78.1497	388	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971985.1	s__Paenibacillus_J dauci	78.1047	392	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	97.87	97.87	0.93	0.93	2	-
GCF_014645615.1	s__Paenibacillus_J hunanensis	77.5643	342	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287275.1	s__Paenibacillus taichungensis_A	77.3884	98	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637205.1	s__Paenibacillus glacialis	77.2336	87	1733	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	77.1253	94	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.13	99.13	0.96	0.96	2	-
GCF_009363115.1	s__Paenibacillus brasilensis	76.9833	90	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.95	97.95	0.90	0.90	2	-
GCF_012912005.1	s__Paenibacillus sp012912005	76.9598	123	1733	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	76.7688	106	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719335.1	s__Paenibacillus amylolyticus_D	76.5714	110	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943545.1	s__Paenibacillus terrae_A	76.4914	98	1733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:40,426] [INFO] GTDB search result was written to GCF_001721045.1_ASM172104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:40,426] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:40,430] [INFO] DFAST_QC result json was written to GCF_001721045.1_ASM172104v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:40,430] [INFO] DFAST_QC completed!
[2024-01-24 15:03:40,430] [INFO] Total running time: 0h1m33s