[2024-01-24 12:29:26,690] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:26,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:26,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg191f1920-b7e1-4d1c-8fb4-2e912357a5bc/dqc_reference
[2024-01-24 12:29:27,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:27,951] [INFO] Task started: Prodigal
[2024-01-24 12:29:27,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg78b3b95c-3507-461e-aed1-00e26f7b556d/GCF_010119935.1_ASM1011993v1_genomic.fna.gz | prodigal -d GCF_010119935.1_ASM1011993v1_genomic.fna/cds.fna -a GCF_010119935.1_ASM1011993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:47,312] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:47,312] [INFO] Task started: HMMsearch
[2024-01-24 12:29:47,312] [INFO] Running command: hmmsearch --tblout GCF_010119935.1_ASM1011993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg191f1920-b7e1-4d1c-8fb4-2e912357a5bc/dqc_reference/reference_markers.hmm GCF_010119935.1_ASM1011993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:47,727] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:47,729] [INFO] Found 6/6 markers.
[2024-01-24 12:29:47,796] [INFO] Query marker FASTA was written to GCF_010119935.1_ASM1011993v1_genomic.fna/markers.fasta
[2024-01-24 12:29:47,797] [INFO] Task started: Blastn
[2024-01-24 12:29:47,797] [INFO] Running command: blastn -query GCF_010119935.1_ASM1011993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg191f1920-b7e1-4d1c-8fb4-2e912357a5bc/dqc_reference/reference_markers.fasta -out GCF_010119935.1_ASM1011993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:48,450] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:48,453] [INFO] Selected 10 target genomes.
[2024-01-24 12:29:48,454] [INFO] Target genome list was writen to GCF_010119935.1_ASM1011993v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:48,458] [INFO] Task started: fastANI
[2024-01-24 12:29:48,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg78b3b95c-3507-461e-aed1-00e26f7b556d/GCF_010119935.1_ASM1011993v1_genomic.fna.gz --refList GCF_010119935.1_ASM1011993v1_genomic.fna/target_genomes.txt --output GCF_010119935.1_ASM1011993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:02,709] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:02,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg191f1920-b7e1-4d1c-8fb4-2e912357a5bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:02,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg191f1920-b7e1-4d1c-8fb4-2e912357a5bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:02,720] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:02,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:02,720] [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 lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	100.0	2247	2247	95	conclusive
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	84.0688	1514	2247	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	82.5927	1138	2247	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	82.4774	1230	2247	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	82.2733	1237	2247	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	82.266	1232	2247	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	78.1017	425	2247	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.6934	258	2247	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.3177	346	2247	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.9363	207	2247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:02,723] [INFO] DFAST Taxonomy check result was written to GCF_010119935.1_ASM1011993v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:02,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:02,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:02,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg191f1920-b7e1-4d1c-8fb4-2e912357a5bc/dqc_reference/checkm_data
[2024-01-24 12:30:02,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:02,787] [INFO] Task started: CheckM
[2024-01-24 12:30:02,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119935.1_ASM1011993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119935.1_ASM1011993v1_genomic.fna/checkm_input GCF_010119935.1_ASM1011993v1_genomic.fna/checkm_result
[2024-01-24 12:31:00,560] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:00,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:00,596] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:00,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:00,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119935.1_ASM1011993v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:00,597] [INFO] Task started: Blastn
[2024-01-24 12:31:00,597] [INFO] Running command: blastn -query GCF_010119935.1_ASM1011993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg191f1920-b7e1-4d1c-8fb4-2e912357a5bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119935.1_ASM1011993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:01,559] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:01,565] [INFO] Selected 5 target genomes.
[2024-01-24 12:31:01,565] [INFO] Target genome list was writen to GCF_010119935.1_ASM1011993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:01,572] [INFO] Task started: fastANI
[2024-01-24 12:31:01,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg78b3b95c-3507-461e-aed1-00e26f7b556d/GCF_010119935.1_ASM1011993v1_genomic.fna.gz --refList GCF_010119935.1_ASM1011993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119935.1_ASM1011993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:11,323] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:11,332] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:11,332] [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_010119935.1	s__Paenibacillus_Z lycopersici	100.0	2247	2247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010365285.1	s__Paenibacillus_Z rhizovicinus	84.0822	1514	2247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	82.5909	1138	2247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113915.1	s__Paenibacillus_Z sp900113915	82.4753	1218	2247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
GCF_009909195.1	s__Paenibacillus_Z sacheonensis	82.2787	1230	2247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:11,334] [INFO] GTDB search result was written to GCF_010119935.1_ASM1011993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:11,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:11,337] [INFO] DFAST_QC result json was written to GCF_010119935.1_ASM1011993v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:11,337] [INFO] DFAST_QC completed!
[2024-01-24 12:31:11,337] [INFO] Total running time: 0h1m45s