[2024-01-24 11:05:27,597] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,600] [INFO] DQC Reference Directory: /var/lib/cwl/stge21a48b3-13b7-4a2a-abe2-adc87d5e9ce0/dqc_reference
[2024-01-24 11:05:29,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,022] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,022] [INFO] Running command: gunzip -c /var/lib/cwl/stga6d82553-d7d2-44bc-86fa-e6723132cab0/GCF_017942085.1_ASM1794208v1_genomic.fna.gz | prodigal -d GCF_017942085.1_ASM1794208v1_genomic.fna/cds.fna -a GCF_017942085.1_ASM1794208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:49,877] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:49,877] [INFO] Task started: HMMsearch
[2024-01-24 11:05:49,877] [INFO] Running command: hmmsearch --tblout GCF_017942085.1_ASM1794208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge21a48b3-13b7-4a2a-abe2-adc87d5e9ce0/dqc_reference/reference_markers.hmm GCF_017942085.1_ASM1794208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:50,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:50,286] [INFO] Found 6/6 markers.
[2024-01-24 11:05:50,341] [INFO] Query marker FASTA was written to GCF_017942085.1_ASM1794208v1_genomic.fna/markers.fasta
[2024-01-24 11:05:50,341] [INFO] Task started: Blastn
[2024-01-24 11:05:50,341] [INFO] Running command: blastn -query GCF_017942085.1_ASM1794208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge21a48b3-13b7-4a2a-abe2-adc87d5e9ce0/dqc_reference/reference_markers.fasta -out GCF_017942085.1_ASM1794208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:50,933] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:50,936] [INFO] Selected 13 target genomes.
[2024-01-24 11:05:50,937] [INFO] Target genome list was writen to GCF_017942085.1_ASM1794208v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:50,942] [INFO] Task started: fastANI
[2024-01-24 11:05:50,942] [INFO] Running command: fastANI --query /var/lib/cwl/stga6d82553-d7d2-44bc-86fa-e6723132cab0/GCF_017942085.1_ASM1794208v1_genomic.fna.gz --refList GCF_017942085.1_ASM1794208v1_genomic.fna/target_genomes.txt --output GCF_017942085.1_ASM1794208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:08,443] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:08,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge21a48b3-13b7-4a2a-abe2-adc87d5e9ce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:08,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge21a48b3-13b7-4a2a-abe2-adc87d5e9ce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:08,454] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:08,454] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:08,454] [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 lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	100.0	2327	2413	95	conclusive
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	80.9161	1071	2413	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	79.6114	901	2413	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	79.606	845	2413	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	79.1151	722	2413	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	78.9807	679	2413	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	78.9411	676	2413	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	78.731	652	2413	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	78.7237	611	2413	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	78.2157	586	2413	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	77.0569	71	2413	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.8442	121	2413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:08,456] [INFO] DFAST Taxonomy check result was written to GCF_017942085.1_ASM1794208v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:08,457] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:08,457] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:08,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge21a48b3-13b7-4a2a-abe2-adc87d5e9ce0/dqc_reference/checkm_data
[2024-01-24 11:06:08,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:08,526] [INFO] Task started: CheckM
[2024-01-24 11:06:08,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017942085.1_ASM1794208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017942085.1_ASM1794208v1_genomic.fna/checkm_input GCF_017942085.1_ASM1794208v1_genomic.fna/checkm_result
[2024-01-24 11:07:07,415] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:07,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:07,441] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:07,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:07,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017942085.1_ASM1794208v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:07,442] [INFO] Task started: Blastn
[2024-01-24 11:07:07,442] [INFO] Running command: blastn -query GCF_017942085.1_ASM1794208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge21a48b3-13b7-4a2a-abe2-adc87d5e9ce0/dqc_reference/reference_markers_gtdb.fasta -out GCF_017942085.1_ASM1794208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:08,325] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:08,329] [INFO] Selected 8 target genomes.
[2024-01-24 11:07:08,329] [INFO] Target genome list was writen to GCF_017942085.1_ASM1794208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:08,337] [INFO] Task started: fastANI
[2024-01-24 11:07:08,337] [INFO] Running command: fastANI --query /var/lib/cwl/stga6d82553-d7d2-44bc-86fa-e6723132cab0/GCF_017942085.1_ASM1794208v1_genomic.fna.gz --refList GCF_017942085.1_ASM1794208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017942085.1_ASM1794208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:20,248] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:20,260] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:20,260] [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_900116125.1	s__Paenibacillus_Z sp900116125	95.3161	2091	2413	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	conclusive
GCF_900106745.1	s__Paenibacillus_Z sp900106745	88.5547	1870	2413	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_003268025.1	s__Paenibacillus_Z montanisoli	80.9166	1071	2413	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_004342525.1	s__Paenibacillus_Z sp004342525	79.7969	850	2413	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_003952225.1	s__Paenibacillus_Z albus	79.627	842	2413	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	79.6148	900	2413	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	78.9863	677	2413	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_010119935.1	s__Paenibacillus_Z lycopersici	78.7241	611	2413	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 11:07:20,262] [INFO] GTDB search result was written to GCF_017942085.1_ASM1794208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:20,262] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:20,265] [INFO] DFAST_QC result json was written to GCF_017942085.1_ASM1794208v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:20,265] [INFO] DFAST_QC completed!
[2024-01-24 11:07:20,265] [INFO] Total running time: 0h1m53s