[2024-01-24 12:15:04,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,045] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3b63a4d-626f-4205-90a1-ae0371c66777/dqc_reference
[2024-01-24 12:15:05,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,467] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg730e5fc7-82e7-4717-adde-7e994f412042/GCF_012933385.1_ASM1293338v1_genomic.fna.gz | prodigal -d GCF_012933385.1_ASM1293338v1_genomic.fna/cds.fna -a GCF_012933385.1_ASM1293338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:18,023] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:18,024] [INFO] Task started: HMMsearch
[2024-01-24 12:15:18,024] [INFO] Running command: hmmsearch --tblout GCF_012933385.1_ASM1293338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3b63a4d-626f-4205-90a1-ae0371c66777/dqc_reference/reference_markers.hmm GCF_012933385.1_ASM1293338v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:18,341] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:18,343] [INFO] Found 6/6 markers.
[2024-01-24 12:15:18,395] [INFO] Query marker FASTA was written to GCF_012933385.1_ASM1293338v1_genomic.fna/markers.fasta
[2024-01-24 12:15:18,396] [INFO] Task started: Blastn
[2024-01-24 12:15:18,396] [INFO] Running command: blastn -query GCF_012933385.1_ASM1293338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b63a4d-626f-4205-90a1-ae0371c66777/dqc_reference/reference_markers.fasta -out GCF_012933385.1_ASM1293338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:19,075] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:19,080] [INFO] Selected 19 target genomes.
[2024-01-24 12:15:19,080] [INFO] Target genome list was writen to GCF_012933385.1_ASM1293338v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:19,094] [INFO] Task started: fastANI
[2024-01-24 12:15:19,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg730e5fc7-82e7-4717-adde-7e994f412042/GCF_012933385.1_ASM1293338v1_genomic.fna.gz --refList GCF_012933385.1_ASM1293338v1_genomic.fna/target_genomes.txt --output GCF_012933385.1_ASM1293338v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:38,736] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:38,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3b63a4d-626f-4205-90a1-ae0371c66777/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:38,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3b63a4d-626f-4205-90a1-ae0371c66777/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:38,753] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:38,754] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:38,754] [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 lemnae	strain=L7-75	GCA_012933385.1	1330551	1330551	type	True	100.0	1501	1502	95	conclusive
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	79.5305	518	1502	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	78.8089	354	1502	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	78.5688	318	1502	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	78.4958	332	1502	95	below_threshold
Paenibacillus ihbetae	strain=IHBB 9852	GCA_002741055.1	1870820	1870820	suspected-type	True	78.3768	320	1502	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	78.3595	297	1502	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	78.3282	305	1502	95	below_threshold
Paenibacillus lactis	strain=DSM 15596	GCA_017873605.1	228574	228574	type	True	78.2397	321	1502	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.3829	128	1502	95	below_threshold
Paenibacillus bovis	strain=BD3526	GCA_001421015.2	1616788	1616788	type	True	77.3539	109	1502	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	77.3057	124	1502	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	77.1786	152	1502	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.157	119	1502	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.1424	131	1502	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	77.119	168	1502	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.9206	112	1502	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.9027	155	1502	95	below_threshold
Paenibacillus rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	76.1686	76	1502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:38,755] [INFO] DFAST Taxonomy check result was written to GCF_012933385.1_ASM1293338v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:38,756] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:38,756] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:38,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3b63a4d-626f-4205-90a1-ae0371c66777/dqc_reference/checkm_data
[2024-01-24 12:15:38,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:38,804] [INFO] Task started: CheckM
[2024-01-24 12:15:38,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012933385.1_ASM1293338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012933385.1_ASM1293338v1_genomic.fna/checkm_input GCF_012933385.1_ASM1293338v1_genomic.fna/checkm_result
[2024-01-24 12:16:18,643] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:18,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:18,671] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:18,671] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:18,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012933385.1_ASM1293338v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:18,672] [INFO] Task started: Blastn
[2024-01-24 12:16:18,672] [INFO] Running command: blastn -query GCF_012933385.1_ASM1293338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b63a4d-626f-4205-90a1-ae0371c66777/dqc_reference/reference_markers_gtdb.fasta -out GCF_012933385.1_ASM1293338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:19,497] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:19,502] [INFO] Selected 21 target genomes.
[2024-01-24 12:16:19,502] [INFO] Target genome list was writen to GCF_012933385.1_ASM1293338v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:19,515] [INFO] Task started: fastANI
[2024-01-24 12:16:19,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg730e5fc7-82e7-4717-adde-7e994f412042/GCF_012933385.1_ASM1293338v1_genomic.fna.gz --refList GCF_012933385.1_ASM1293338v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012933385.1_ASM1293338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:40,263] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:40,283] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:40,284] [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_012933385.1	s__Paenibacillus lemnae	100.0	1501	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005577435.1	s__Paenibacillus sp005577435	79.5478	515	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.84	98.84	0.91	0.91	2	-
GCF_000987955.1	s__Paenibacillus sp000987955	79.0634	417	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177425.1	s__Paenibacillus uliginis	78.7972	353	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002573715.1	s__Paenibacillus sp002573715	78.5851	311	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.81	0.89	0.84	4	-
GCF_001373415.1	s__Paenibacillus dakarensis	78.5776	319	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863545.1	s__Paenibacillus lautus_A	78.5413	332	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.37	95.82	0.93	0.90	10	-
GCF_002741055.1	s__Paenibacillus ihbetae	78.3858	321	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.87	98.87	0.95	0.95	2	-
GCF_001277345.1	s__Paenibacillus solani	78.3549	297	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.74	96.74	0.91	0.91	2	-
GCF_900289175.1	s__Paenibacillus sp900289175	78.3235	306	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873605.1	s__Paenibacillus lactis	78.2633	322	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.99	97.11	0.89	0.86	16	-
GCF_001315105.1	s__Paenibacillus sp001315105	78.1447	273	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002272015.1	s__Paenibacillus campinasensis	77.941	307	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.23	99.19	0.91	0.90	3	-
GCF_013359945.1	s__Paenibacillus sp013359945	77.4121	129	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421015.2	s__Paenibacillus_J bovis	77.3158	108	1502	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_003614185.1	s__Paenibacillus_A aceti	77.2943	123	1502	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_000612505.1	s__Paenibacillus sabinae	77.2734	130	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.70	95.69	0.89	0.89	3	-
GCF_003854965.1	s__Paenibacillus sp003854965	77.1424	131	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_000758605.1	s__Paenibacillus sp000758605	77.0872	165	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758665.1	s__Paenibacillus borealis	77.0747	165	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001909055.1	s__Paenibacillus helianthi	76.944	147	1502	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.61	95.31	0.90	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:40,286] [INFO] GTDB search result was written to GCF_012933385.1_ASM1293338v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:40,287] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:40,291] [INFO] DFAST_QC result json was written to GCF_012933385.1_ASM1293338v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:40,291] [INFO] DFAST_QC completed!
[2024-01-24 12:16:40,291] [INFO] Total running time: 0h1m36s