[2024-01-24 11:35:34,253] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,256] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,256] [INFO] DQC Reference Directory: /var/lib/cwl/stgd783ffdc-70cc-40c4-9baf-d9796bdbcda0/dqc_reference
[2024-01-24 11:35:35,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,476] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,476] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0b4c558-210a-43c1-bc84-e714ad5a7c2a/GCF_012676905.1_ASM1267690v1_genomic.fna.gz | prodigal -d GCF_012676905.1_ASM1267690v1_genomic.fna/cds.fna -a GCF_012676905.1_ASM1267690v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:49,211] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:49,212] [INFO] Task started: HMMsearch
[2024-01-24 11:35:49,212] [INFO] Running command: hmmsearch --tblout GCF_012676905.1_ASM1267690v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd783ffdc-70cc-40c4-9baf-d9796bdbcda0/dqc_reference/reference_markers.hmm GCF_012676905.1_ASM1267690v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:49,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:49,503] [INFO] Found 6/6 markers.
[2024-01-24 11:35:49,544] [INFO] Query marker FASTA was written to GCF_012676905.1_ASM1267690v1_genomic.fna/markers.fasta
[2024-01-24 11:35:49,545] [INFO] Task started: Blastn
[2024-01-24 11:35:49,545] [INFO] Running command: blastn -query GCF_012676905.1_ASM1267690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd783ffdc-70cc-40c4-9baf-d9796bdbcda0/dqc_reference/reference_markers.fasta -out GCF_012676905.1_ASM1267690v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:50,300] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:50,304] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:50,304] [INFO] Target genome list was writen to GCF_012676905.1_ASM1267690v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:50,310] [INFO] Task started: fastANI
[2024-01-24 11:35:50,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0b4c558-210a-43c1-bc84-e714ad5a7c2a/GCF_012676905.1_ASM1267690v1_genomic.fna.gz --refList GCF_012676905.1_ASM1267690v1_genomic.fna/target_genomes.txt --output GCF_012676905.1_ASM1267690v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:05,690] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:05,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd783ffdc-70cc-40c4-9baf-d9796bdbcda0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:05,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd783ffdc-70cc-40c4-9baf-d9796bdbcda0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:05,709] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:05,710] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:05,710] [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 albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	100.0	1722	1722	95	conclusive
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	90.8794	1423	1722	95	below_threshold
Paenibacillus pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	90.8496	1360	1722	95	below_threshold
Paenibacillus humicus	strain=NBRC 102415	GCA_004000905.1	412861	412861	type	True	81.2421	919	1722	95	below_threshold
Paenibacillus herberti	strain=R33	GCA_002233675.1	1619309	1619309	type	True	79.3587	630	1722	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	78.4627	338	1722	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	78.3135	538	1722	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	78.2189	438	1722	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	78.1131	90	1722	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.5601	443	1722	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.0663	197	1722	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.8962	182	1722	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.4405	193	1722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:05,712] [INFO] DFAST Taxonomy check result was written to GCF_012676905.1_ASM1267690v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:05,712] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:05,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:05,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd783ffdc-70cc-40c4-9baf-d9796bdbcda0/dqc_reference/checkm_data
[2024-01-24 11:36:05,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:05,765] [INFO] Task started: CheckM
[2024-01-24 11:36:05,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012676905.1_ASM1267690v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012676905.1_ASM1267690v1_genomic.fna/checkm_input GCF_012676905.1_ASM1267690v1_genomic.fna/checkm_result
[2024-01-24 11:36:46,400] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:46,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:46,424] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:46,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:46,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012676905.1_ASM1267690v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:46,425] [INFO] Task started: Blastn
[2024-01-24 11:36:46,425] [INFO] Running command: blastn -query GCF_012676905.1_ASM1267690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd783ffdc-70cc-40c4-9baf-d9796bdbcda0/dqc_reference/reference_markers_gtdb.fasta -out GCF_012676905.1_ASM1267690v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:47,528] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:47,532] [INFO] Selected 15 target genomes.
[2024-01-24 11:36:47,532] [INFO] Target genome list was writen to GCF_012676905.1_ASM1267690v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:47,575] [INFO] Task started: fastANI
[2024-01-24 11:36:47,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0b4c558-210a-43c1-bc84-e714ad5a7c2a/GCF_012676905.1_ASM1267690v1_genomic.fna.gz --refList GCF_012676905.1_ASM1267690v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012676905.1_ASM1267690v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:04,678] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:04,702] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:04,702] [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_012676905.1	s__Paenibacillus_O sp012676905	100.0	1722	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000422485.1	s__Paenibacillus_O pasadenensis	90.8794	1423	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.23	98.68	0.94	0.90	4	-
GCF_004000905.1	s__Paenibacillus_O humicus	81.2471	918	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	98.90	98.81	0.93	0.93	3	-
GCF_002243345.2	s__Paenibacillus_O sp002243345	81.0901	940	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.98	99.98	0.98	0.98	4	-
GCA_900105225.1	s__Paenibacillus_O sp900105225	79.5217	601	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002233675.1	s__Paenibacillus_O herberti	79.3892	629	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000961095.1	s__Paenibacillus_O beijingensis	78.5105	339	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	78.1583	441	1722	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_017086365.1	s__Paenibacillus sp017086365	78.1131	90	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124765.1	s__Paenibacillus_Z methanolicus	77.7934	441	1722	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	77.5873	439	1722	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_000987955.1	s__Paenibacillus sp000987955	77.0719	116	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422465.1	s__Paenibacillus_C harenae	76.8108	189	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345425.1	s__Paenibacillus_C sp004345425	76.4681	182	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
GCF_003285005.1	s__YN15 sp003285005	76.0002	111	1722	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__YN15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:04,704] [INFO] GTDB search result was written to GCF_012676905.1_ASM1267690v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:04,704] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:04,708] [INFO] DFAST_QC result json was written to GCF_012676905.1_ASM1267690v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:04,708] [INFO] DFAST_QC completed!
[2024-01-24 11:37:04,708] [INFO] Total running time: 0h1m30s