[2024-01-24 13:19:26,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:26,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:26,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg433fbd56-860e-4474-8fa6-a7598f78017c/dqc_reference
[2024-01-24 13:19:27,463] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:27,464] [INFO] Task started: Prodigal
[2024-01-24 13:19:27,464] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e169429-3bb5-46da-8fa6-4830b99cbe3f/GCF_022811565.1_ASM2281156v1_genomic.fna.gz | prodigal -d GCF_022811565.1_ASM2281156v1_genomic.fna/cds.fna -a GCF_022811565.1_ASM2281156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:45,631] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:45,631] [INFO] Task started: HMMsearch
[2024-01-24 13:19:45,631] [INFO] Running command: hmmsearch --tblout GCF_022811565.1_ASM2281156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg433fbd56-860e-4474-8fa6-a7598f78017c/dqc_reference/reference_markers.hmm GCF_022811565.1_ASM2281156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:45,952] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:45,954] [INFO] Found 6/6 markers.
[2024-01-24 13:19:46,008] [INFO] Query marker FASTA was written to GCF_022811565.1_ASM2281156v1_genomic.fna/markers.fasta
[2024-01-24 13:19:46,009] [INFO] Task started: Blastn
[2024-01-24 13:19:46,009] [INFO] Running command: blastn -query GCF_022811565.1_ASM2281156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg433fbd56-860e-4474-8fa6-a7598f78017c/dqc_reference/reference_markers.fasta -out GCF_022811565.1_ASM2281156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:46,608] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:46,614] [INFO] Selected 9 target genomes.
[2024-01-24 13:19:46,615] [INFO] Target genome list was writen to GCF_022811565.1_ASM2281156v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:46,707] [INFO] Task started: fastANI
[2024-01-24 13:19:46,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e169429-3bb5-46da-8fa6-4830b99cbe3f/GCF_022811565.1_ASM2281156v1_genomic.fna.gz --refList GCF_022811565.1_ASM2281156v1_genomic.fna/target_genomes.txt --output GCF_022811565.1_ASM2281156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:58,449] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:58,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg433fbd56-860e-4474-8fa6-a7598f78017c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:58,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg433fbd56-860e-4474-8fa6-a7598f78017c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:58,460] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:19:58,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:58,460] [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 polymyxa	strain=ATCC 842	GCA_022811565.1	1406	1406	type	True	100.0	1988	1988	95	conclusive
Paenibacillus polymyxa	strain=NCTC10343	GCA_900454525.1	1406	1406	type	True	99.9973	1988	1988	95	conclusive
Paenibacillus polymyxa	strain=DSM 36	GCA_015710975.1	1406	1406	type	True	99.9964	1985	1988	95	conclusive
Paenibacillus polymyxa	strain=ATCC 842	GCA_000217775.1	1406	1406	type	True	99.9699	1954	1988	95	conclusive
Paenibacillus ottowii	strain=MS2379	GCA_006874425.1	2315729	2315729	type	True	92.1941	1568	1988	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	84.2501	1183	1988	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	79.201	113	1988	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.1505	94	1988	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.6107	109	1988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:58,462] [INFO] DFAST Taxonomy check result was written to GCF_022811565.1_ASM2281156v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:58,463] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:58,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:58,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg433fbd56-860e-4474-8fa6-a7598f78017c/dqc_reference/checkm_data
[2024-01-24 13:19:58,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:58,528] [INFO] Task started: CheckM
[2024-01-24 13:19:58,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022811565.1_ASM2281156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022811565.1_ASM2281156v1_genomic.fna/checkm_input GCF_022811565.1_ASM2281156v1_genomic.fna/checkm_result
[2024-01-24 13:20:53,850] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:53,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:53,878] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:53,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:53,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022811565.1_ASM2281156v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:53,879] [INFO] Task started: Blastn
[2024-01-24 13:20:53,879] [INFO] Running command: blastn -query GCF_022811565.1_ASM2281156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg433fbd56-860e-4474-8fa6-a7598f78017c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022811565.1_ASM2281156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:54,638] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:54,642] [INFO] Selected 8 target genomes.
[2024-01-24 13:20:54,642] [INFO] Target genome list was writen to GCF_022811565.1_ASM2281156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:54,799] [INFO] Task started: fastANI
[2024-01-24 13:20:54,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e169429-3bb5-46da-8fa6-4830b99cbe3f/GCF_022811565.1_ASM2281156v1_genomic.fna.gz --refList GCF_022811565.1_ASM2281156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022811565.1_ASM2281156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:07,632] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:07,643] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:07,644] [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_015710975.1	s__Paenibacillus polymyxa	99.9964	1985	1988	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.54	98.07	0.94	0.89	44	conclusive
GCF_000237325.1	s__Paenibacillus polymyxa_C	94.6514	1705	1988	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.50	97.87	0.93	0.89	15	-
GCF_006874425.1	s__Paenibacillus ottowii	92.1805	1569	1988	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.10	96.87	0.92	0.88	5	-
GCF_001709075.1	s__Paenibacillus polymyxa_D	89.9289	1556	1988	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	89.8889	1604	1988	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	86.2393	1376	1988	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	86.1597	1357	1988	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	85.8398	1360	1988	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 13:21:07,645] [INFO] GTDB search result was written to GCF_022811565.1_ASM2281156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:07,646] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:07,649] [INFO] DFAST_QC result json was written to GCF_022811565.1_ASM2281156v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:07,649] [INFO] DFAST_QC completed!
[2024-01-24 13:21:07,649] [INFO] Total running time: 0h1m41s