[2024-01-24 13:27:58,841] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ccea603-8750-4394-8b9a-ebcd60efd603/dqc_reference
[2024-01-24 13:28:00,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:00,051] [INFO] Task started: Prodigal
[2024-01-24 13:28:00,052] [INFO] Running command: gunzip -c /var/lib/cwl/stgc12c1df4-906e-4e2f-b943-0508023cd3b9/GCF_006874425.1_ASM687442v1_genomic.fna.gz | prodigal -d GCF_006874425.1_ASM687442v1_genomic.fna/cds.fna -a GCF_006874425.1_ASM687442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:14,994] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:14,995] [INFO] Task started: HMMsearch
[2024-01-24 13:28:14,995] [INFO] Running command: hmmsearch --tblout GCF_006874425.1_ASM687442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ccea603-8750-4394-8b9a-ebcd60efd603/dqc_reference/reference_markers.hmm GCF_006874425.1_ASM687442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:15,319] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:15,321] [INFO] Found 6/6 markers.
[2024-01-24 13:28:15,374] [INFO] Query marker FASTA was written to GCF_006874425.1_ASM687442v1_genomic.fna/markers.fasta
[2024-01-24 13:28:15,375] [INFO] Task started: Blastn
[2024-01-24 13:28:15,375] [INFO] Running command: blastn -query GCF_006874425.1_ASM687442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ccea603-8750-4394-8b9a-ebcd60efd603/dqc_reference/reference_markers.fasta -out GCF_006874425.1_ASM687442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:16,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:16,005] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:16,006] [INFO] Target genome list was writen to GCF_006874425.1_ASM687442v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:16,016] [INFO] Task started: fastANI
[2024-01-24 13:28:16,016] [INFO] Running command: fastANI --query /var/lib/cwl/stgc12c1df4-906e-4e2f-b943-0508023cd3b9/GCF_006874425.1_ASM687442v1_genomic.fna.gz --refList GCF_006874425.1_ASM687442v1_genomic.fna/target_genomes.txt --output GCF_006874425.1_ASM687442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:29,522] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:29,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ccea603-8750-4394-8b9a-ebcd60efd603/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:29,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ccea603-8750-4394-8b9a-ebcd60efd603/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:29,533] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:29,533] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:29,533] [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 ottowii	strain=MS2379	GCA_006874425.1	2315729	2315729	type	True	100.0	1798	1815	95	conclusive
Paenibacillus polymyxa	strain=NCTC10343	GCA_900454525.1	1406	1406	type	True	92.1903	1571	1815	95	below_threshold
Paenibacillus polymyxa	strain=DSM 36	GCA_015710975.1	1406	1406	type	True	92.188	1574	1815	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_022811565.1	1406	1406	type	True	92.1564	1581	1815	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_000217775.1	1406	1406	type	True	92.1488	1576	1815	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	84.0611	1175	1815	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	77.5569	149	1815	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.554	126	1815	95	below_threshold
Paenibacillus wynnii	strain=DSM 18334	GCA_000757885.1	268407	268407	type	True	77.297	100	1815	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.1727	89	1815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:29,535] [INFO] DFAST Taxonomy check result was written to GCF_006874425.1_ASM687442v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:29,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:29,536] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:29,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ccea603-8750-4394-8b9a-ebcd60efd603/dqc_reference/checkm_data
[2024-01-24 13:28:29,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:29,591] [INFO] Task started: CheckM
[2024-01-24 13:28:29,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006874425.1_ASM687442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006874425.1_ASM687442v1_genomic.fna/checkm_input GCF_006874425.1_ASM687442v1_genomic.fna/checkm_result
[2024-01-24 13:29:19,584] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:19,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:19,602] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:19,602] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:19,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006874425.1_ASM687442v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:19,603] [INFO] Task started: Blastn
[2024-01-24 13:29:19,603] [INFO] Running command: blastn -query GCF_006874425.1_ASM687442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ccea603-8750-4394-8b9a-ebcd60efd603/dqc_reference/reference_markers_gtdb.fasta -out GCF_006874425.1_ASM687442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:20,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:20,381] [INFO] Selected 12 target genomes.
[2024-01-24 13:29:20,381] [INFO] Target genome list was writen to GCF_006874425.1_ASM687442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:20,395] [INFO] Task started: fastANI
[2024-01-24 13:29:20,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgc12c1df4-906e-4e2f-b943-0508023cd3b9/GCF_006874425.1_ASM687442v1_genomic.fna.gz --refList GCF_006874425.1_ASM687442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006874425.1_ASM687442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:34,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:34,574] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:34,575] [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_006874425.1	s__Paenibacillus ottowii	100.0	1797	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.10	96.87	0.92	0.88	5	conclusive
GCF_000237325.1	s__Paenibacillus polymyxa_C	92.7314	1592	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.50	97.87	0.93	0.89	15	-
GCF_015710975.1	s__Paenibacillus polymyxa	92.1748	1575	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.54	98.07	0.94	0.89	44	-
GCF_001709075.1	s__Paenibacillus polymyxa_D	88.9975	1492	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.80	97.93	0.93	0.90	8	-
GCF_001719045.1	s__Paenibacillus polymyxa_B	88.7009	1525	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.14	95.58	0.87	0.84	27	-
GCF_002240415.1	s__Paenibacillus kribbensis	85.6307	1345	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.18	95.13	0.90	0.86	4	-
GCF_009363115.1	s__Paenibacillus brasilensis	85.5133	1376	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.95	97.95	0.90	0.90	2	-
GCF_000236805.1	s__Paenibacillus peoriae	85.2962	1325	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359945.1	s__Paenibacillus sp013359945	77.613	126	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757885.1	s__Paenibacillus wynnii	77.297	100	1815	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001682855.1	s__Paenibacillus sp001682855	77.2868	121	1815	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 13:29:34,576] [INFO] GTDB search result was written to GCF_006874425.1_ASM687442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:34,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:34,580] [INFO] DFAST_QC result json was written to GCF_006874425.1_ASM687442v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:34,580] [INFO] DFAST_QC completed!
[2024-01-24 13:29:34,580] [INFO] Total running time: 0h1m36s