[2024-01-24 13:08:58,484] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg9479e31e-28f3-4d79-b0d2-9a04e0f01ced/dqc_reference
[2024-01-24 13:08:59,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,712] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e02bca5-527a-400e-995d-e72ecb83603e/GCF_010365285.1_ASM1036528v1_genomic.fna.gz | prodigal -d GCF_010365285.1_ASM1036528v1_genomic.fna/cds.fna -a GCF_010365285.1_ASM1036528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:20,875] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:20,875] [INFO] Task started: HMMsearch
[2024-01-24 13:09:20,875] [INFO] Running command: hmmsearch --tblout GCF_010365285.1_ASM1036528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9479e31e-28f3-4d79-b0d2-9a04e0f01ced/dqc_reference/reference_markers.hmm GCF_010365285.1_ASM1036528v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:21,264] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:21,266] [INFO] Found 6/6 markers.
[2024-01-24 13:09:21,326] [INFO] Query marker FASTA was written to GCF_010365285.1_ASM1036528v1_genomic.fna/markers.fasta
[2024-01-24 13:09:21,326] [INFO] Task started: Blastn
[2024-01-24 13:09:21,326] [INFO] Running command: blastn -query GCF_010365285.1_ASM1036528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9479e31e-28f3-4d79-b0d2-9a04e0f01ced/dqc_reference/reference_markers.fasta -out GCF_010365285.1_ASM1036528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:21,951] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:21,955] [INFO] Selected 14 target genomes.
[2024-01-24 13:09:21,956] [INFO] Target genome list was writen to GCF_010365285.1_ASM1036528v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:21,964] [INFO] Task started: fastANI
[2024-01-24 13:09:21,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e02bca5-527a-400e-995d-e72ecb83603e/GCF_010365285.1_ASM1036528v1_genomic.fna.gz --refList GCF_010365285.1_ASM1036528v1_genomic.fna/target_genomes.txt --output GCF_010365285.1_ASM1036528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:40,462] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:40,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9479e31e-28f3-4d79-b0d2-9a04e0f01ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:40,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9479e31e-28f3-4d79-b0d2-9a04e0f01ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:40,480] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:40,480] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:40,480] [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 rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	100.0	2505	2507	95	conclusive
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	84.1393	1517	2507	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	82.5875	1296	2507	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	82.5673	1307	2507	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	82.1069	1224	2507	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	81.2176	1156	2507	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	79.556	718	2507	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	79.3416	757	2507	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	79.3067	692	2507	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.347	328	2507	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.7218	130	2507	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.4513	228	2507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:40,482] [INFO] DFAST Taxonomy check result was written to GCF_010365285.1_ASM1036528v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:40,482] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:40,482] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:40,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9479e31e-28f3-4d79-b0d2-9a04e0f01ced/dqc_reference/checkm_data
[2024-01-24 13:09:40,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:40,551] [INFO] Task started: CheckM
[2024-01-24 13:09:40,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010365285.1_ASM1036528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010365285.1_ASM1036528v1_genomic.fna/checkm_input GCF_010365285.1_ASM1036528v1_genomic.fna/checkm_result
[2024-01-24 13:10:40,785] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:40,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:40,815] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:40,816] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:40,816] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010365285.1_ASM1036528v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:40,817] [INFO] Task started: Blastn
[2024-01-24 13:10:40,817] [INFO] Running command: blastn -query GCF_010365285.1_ASM1036528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9479e31e-28f3-4d79-b0d2-9a04e0f01ced/dqc_reference/reference_markers_gtdb.fasta -out GCF_010365285.1_ASM1036528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:41,680] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:41,684] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:41,685] [INFO] Target genome list was writen to GCF_010365285.1_ASM1036528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:41,760] [INFO] Task started: fastANI
[2024-01-24 13:10:41,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e02bca5-527a-400e-995d-e72ecb83603e/GCF_010365285.1_ASM1036528v1_genomic.fna.gz --refList GCF_010365285.1_ASM1036528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010365285.1_ASM1036528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:55,925] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:55,938] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:55,938] [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_010365285.1	s__Paenibacillus_Z rhizovicinus	100.0	2503	2507	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_010119935.1	s__Paenibacillus_Z lycopersici	84.1418	1513	2507	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_009909195.1	s__Paenibacillus_Z sacheonensis	82.5629	1307	2507	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	82.1175	1222	2507	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	81.0725	1199	2507	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_003268025.1	s__Paenibacillus_Z montanisoli	79.4188	749	2507	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_003386535.1	s__Paenibacillus_Z taihuensis	79.3444	755	2507	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_900110075.1	s__Paenibacillus_Z sp900110075	79.1466	628	2507	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:55,940] [INFO] GTDB search result was written to GCF_010365285.1_ASM1036528v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:55,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:55,943] [INFO] DFAST_QC result json was written to GCF_010365285.1_ASM1036528v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:55,944] [INFO] DFAST_QC completed!
[2024-01-24 13:10:55,944] [INFO] Total running time: 0h1m57s