[2024-01-24 14:30:59,793] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg096a7489-45de-4704-bf57-1a112dc275a5/dqc_reference
[2024-01-24 14:31:01,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:01,214] [INFO] Task started: Prodigal
[2024-01-24 14:31:01,215] [INFO] Running command: gunzip -c /var/lib/cwl/stg50a47bfa-4533-41ff-834b-6e256692760f/GCF_014192015.1_ASM1419201v1_genomic.fna.gz | prodigal -d GCF_014192015.1_ASM1419201v1_genomic.fna/cds.fna -a GCF_014192015.1_ASM1419201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:23,398] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:23,398] [INFO] Task started: HMMsearch
[2024-01-24 14:31:23,398] [INFO] Running command: hmmsearch --tblout GCF_014192015.1_ASM1419201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg096a7489-45de-4704-bf57-1a112dc275a5/dqc_reference/reference_markers.hmm GCF_014192015.1_ASM1419201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:23,871] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:23,873] [INFO] Found 6/6 markers.
[2024-01-24 14:31:23,934] [INFO] Query marker FASTA was written to GCF_014192015.1_ASM1419201v1_genomic.fna/markers.fasta
[2024-01-24 14:31:23,935] [INFO] Task started: Blastn
[2024-01-24 14:31:23,935] [INFO] Running command: blastn -query GCF_014192015.1_ASM1419201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg096a7489-45de-4704-bf57-1a112dc275a5/dqc_reference/reference_markers.fasta -out GCF_014192015.1_ASM1419201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:24,604] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:24,607] [INFO] Selected 22 target genomes.
[2024-01-24 14:31:24,608] [INFO] Target genome list was writen to GCF_014192015.1_ASM1419201v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:24,647] [INFO] Task started: fastANI
[2024-01-24 14:31:24,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg50a47bfa-4533-41ff-834b-6e256692760f/GCF_014192015.1_ASM1419201v1_genomic.fna.gz --refList GCF_014192015.1_ASM1419201v1_genomic.fna/target_genomes.txt --output GCF_014192015.1_ASM1419201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:51,067] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:51,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg096a7489-45de-4704-bf57-1a112dc275a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:51,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg096a7489-45de-4704-bf57-1a112dc275a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:51,091] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:51,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:51,091] [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 rhizosphaerae	strain=CECT 5831	GCA_014192015.1	297318	297318	type	True	100.0	2507	2509	95	conclusive
Paenibacillus chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	79.3702	682	2509	95	below_threshold
Paenibacillus dokdonensis	strain=YH-JAE5	GCA_004916975.1	2567944	2567944	type	True	79.0156	600	2509	95	below_threshold
Paenibacillus lactis	strain=DSM 15596	GCA_017873605.1	228574	228574	type	True	77.8477	426	2509	95	below_threshold
Paenibacillus ihbetae	strain=IHBB 9852	GCA_002741055.1	1870820	1870820	suspected-type	True	77.8444	416	2509	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.7837	234	2509	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	77.6708	174	2509	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	77.476	238	2509	95	below_threshold
Paenibacillus zanthoxyli	strain=JH29	GCA_000520715.1	369399	369399	type	True	77.3769	193	2509	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.354	208	2509	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	77.2495	338	2509	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.225	183	2509	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	77.2163	294	2509	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.2126	349	2509	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	77.2088	325	2509	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.1176	172	2509	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	77.0507	227	2509	95	below_threshold
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	76.9617	277	2509	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.8647	276	2509	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	76.6716	250	2509	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	76.604	191	2509	95	below_threshold
Cohnella panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	76.1959	118	2509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:51,093] [INFO] DFAST Taxonomy check result was written to GCF_014192015.1_ASM1419201v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:51,093] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:51,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:51,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg096a7489-45de-4704-bf57-1a112dc275a5/dqc_reference/checkm_data
[2024-01-24 14:31:51,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:51,173] [INFO] Task started: CheckM
[2024-01-24 14:31:51,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192015.1_ASM1419201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192015.1_ASM1419201v1_genomic.fna/checkm_input GCF_014192015.1_ASM1419201v1_genomic.fna/checkm_result
[2024-01-24 14:32:52,799] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:52,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:52,842] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:52,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:52,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192015.1_ASM1419201v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:52,843] [INFO] Task started: Blastn
[2024-01-24 14:32:52,843] [INFO] Running command: blastn -query GCF_014192015.1_ASM1419201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg096a7489-45de-4704-bf57-1a112dc275a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192015.1_ASM1419201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:53,663] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:53,667] [INFO] Selected 10 target genomes.
[2024-01-24 14:32:53,667] [INFO] Target genome list was writen to GCF_014192015.1_ASM1419201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:53,675] [INFO] Task started: fastANI
[2024-01-24 14:32:53,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg50a47bfa-4533-41ff-834b-6e256692760f/GCF_014192015.1_ASM1419201v1_genomic.fna.gz --refList GCF_014192015.1_ASM1419201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192015.1_ASM1419201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:07,608] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:07,617] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:07,617] [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_014192015.1	s__Paenibacillus rhizosphaerae	100.0	2507	2509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009363095.1	s__Paenibacillus cellulositrophicus_A	92.8817	2046	2509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.73	96.59	0.92	0.91	14	-
GCF_002257645.1	s__Paenibacillus sp002257645	90.5689	2069	2509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009870825.1	s__Paenibacillus albilobatus	79.5999	787	2509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.80	99.80	0.98	0.98	2	-
GCF_018333375.1	s__Paenibacillus cookii	79.5117	748	2509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.09	99.09	0.93	0.93	2	-
GCF_009807035.1	s__Paenibacillus sp009807035	79.4151	583	2509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001045.1	s__Paenibacillus chibensis	79.3837	680	2509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854965.1	s__Paenibacillus sp003854965	77.7837	234	2509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_017086365.1	s__Paenibacillus sp017086365	77.053	229	2509	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 14:33:07,618] [INFO] GTDB search result was written to GCF_014192015.1_ASM1419201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:07,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:07,629] [INFO] DFAST_QC result json was written to GCF_014192015.1_ASM1419201v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:07,629] [INFO] DFAST_QC completed!
[2024-01-24 14:33:07,629] [INFO] Total running time: 0h2m8s