[2024-01-24 11:51:37,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg893eabc1-35c9-4dd9-b972-52b0e67e7b8c/dqc_reference
[2024-01-24 11:51:38,461] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,462] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,463] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe05fafb-fbc4-4f1b-b715-3843cef8746d/GCF_008084145.1_ASM808414v1_genomic.fna.gz | prodigal -d GCF_008084145.1_ASM808414v1_genomic.fna/cds.fna -a GCF_008084145.1_ASM808414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:56,038] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:56,038] [INFO] Task started: HMMsearch
[2024-01-24 11:51:56,038] [INFO] Running command: hmmsearch --tblout GCF_008084145.1_ASM808414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg893eabc1-35c9-4dd9-b972-52b0e67e7b8c/dqc_reference/reference_markers.hmm GCF_008084145.1_ASM808414v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:56,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:56,357] [INFO] Found 6/6 markers.
[2024-01-24 11:51:56,406] [INFO] Query marker FASTA was written to GCF_008084145.1_ASM808414v1_genomic.fna/markers.fasta
[2024-01-24 11:51:56,406] [INFO] Task started: Blastn
[2024-01-24 11:51:56,407] [INFO] Running command: blastn -query GCF_008084145.1_ASM808414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg893eabc1-35c9-4dd9-b972-52b0e67e7b8c/dqc_reference/reference_markers.fasta -out GCF_008084145.1_ASM808414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:57,026] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:57,030] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:57,031] [INFO] Target genome list was writen to GCF_008084145.1_ASM808414v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:57,036] [INFO] Task started: fastANI
[2024-01-24 11:51:57,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe05fafb-fbc4-4f1b-b715-3843cef8746d/GCF_008084145.1_ASM808414v1_genomic.fna.gz --refList GCF_008084145.1_ASM808414v1_genomic.fna/target_genomes.txt --output GCF_008084145.1_ASM808414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:13,520] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:13,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg893eabc1-35c9-4dd9-b972-52b0e67e7b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:13,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg893eabc1-35c9-4dd9-b972-52b0e67e7b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:13,534] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:13,534] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:13,534] [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 macerans	strain=NCTC6355	GCA_900454495.1	44252	44252	type	True	79.4138	733	2111	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	79.388	723	2111	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	79.3447	700	2111	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	79.2978	547	2111	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	79.2197	721	2111	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	78.7941	518	2111	95	below_threshold
Paenibacillus barengoltzii	strain=NBRC 101215	GCA_004000745.1	343517	343517	type	True	78.474	401	2111	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	78.4297	527	2111	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	78.4146	365	2111	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	78.3386	418	2111	95	below_threshold
Fontibacillus panacisegetis	strain=DSM 28129	GCA_900102215.1	670482	670482	type	True	78.2187	289	2111	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	78.0397	359	2111	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.4811	229	2111	95	below_threshold
Paenibacillus rhizosphaerae	strain=CECT 5831	GCA_014192015.1	297318	297318	type	True	77.4736	288	2111	95	below_threshold
Paenibacillus chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	77.2931	226	2111	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.5315	171	2111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:13,536] [INFO] DFAST Taxonomy check result was written to GCF_008084145.1_ASM808414v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:13,537] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:13,537] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:13,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg893eabc1-35c9-4dd9-b972-52b0e67e7b8c/dqc_reference/checkm_data
[2024-01-24 11:52:13,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:13,603] [INFO] Task started: CheckM
[2024-01-24 11:52:13,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008084145.1_ASM808414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008084145.1_ASM808414v1_genomic.fna/checkm_input GCF_008084145.1_ASM808414v1_genomic.fna/checkm_result
[2024-01-24 11:53:05,085] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:05,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:05,107] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:05,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:05,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008084145.1_ASM808414v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:05,108] [INFO] Task started: Blastn
[2024-01-24 11:53:05,108] [INFO] Running command: blastn -query GCF_008084145.1_ASM808414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg893eabc1-35c9-4dd9-b972-52b0e67e7b8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_008084145.1_ASM808414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:05,929] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:05,932] [INFO] Selected 16 target genomes.
[2024-01-24 11:53:05,932] [INFO] Target genome list was writen to GCF_008084145.1_ASM808414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:05,945] [INFO] Task started: fastANI
[2024-01-24 11:53:05,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe05fafb-fbc4-4f1b-b715-3843cef8746d/GCF_008084145.1_ASM808414v1_genomic.fna.gz --refList GCF_008084145.1_ASM808414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008084145.1_ASM808414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:26,594] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:26,611] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:26,611] [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_008084145.1	s__Paenibacillus_A faecis	100.0	2111	2111	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.85	97.85	0.92	0.92	2	conclusive
GCF_003337355.1	s__Paenibacillus_A phaseoli	80.0495	770	2111	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_018403325.1	s__Paenibacillus_A vini	79.8269	687	2111	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.00	98.00	0.91	0.91	2	-
GCA_002439285.1	s__Paenibacillus_A sp002439285	79.5367	556	2111	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_900454495.1	s__Paenibacillus_A macerans	79.4295	731	2111	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.51	99.09	0.97	0.93	8	-
GCF_003863965.1	s__Paenibacillus_A oralis	79.1935	723	2111	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_009725205.1	s__Paenibacillus_A timonensis	78.7714	451	2111	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.34	98.12	0.92	0.92	3	-
GCA_900766135.1	s__Paenibacillus_A sp900766135	78.6853	523	2111	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_004000745.1	s__Paenibacillus_A barengoltzii	78.4684	401	2111	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.39	97.66	0.91	0.90	5	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	78.444	528	2111	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018919145.1	s__Paenibacillus_A sp018919145	78.4014	368	2111	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_001403875.1	s__Paenibacillus_A ihumii	78.3444	420	2111	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002272015.1	s__Paenibacillus campinasensis	77.558	210	2111	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.23	99.19	0.91	0.90	3	-
GCF_009870825.1	s__Paenibacillus albilobatus	77.4578	326	2111	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.80	99.80	0.98	0.98	2	-
GCF_004001045.1	s__Paenibacillus chibensis	77.2921	224	2111	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 11:53:26,613] [INFO] GTDB search result was written to GCF_008084145.1_ASM808414v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:26,613] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:26,617] [INFO] DFAST_QC result json was written to GCF_008084145.1_ASM808414v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:26,617] [INFO] DFAST_QC completed!
[2024-01-24 11:53:26,618] [INFO] Total running time: 0h1m49s