[2024-01-25 17:41:05,577] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:05,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:05,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg861bba76-ddbb-4abf-a2db-274f739a8747/dqc_reference
[2024-01-25 17:41:06,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:06,762] [INFO] Task started: Prodigal
[2024-01-25 17:41:06,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg93207ae3-ab66-4a82-82b1-94814e06d382/GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna.gz | prodigal -d GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/cds.fna -a GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:20,342] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:20,342] [INFO] Task started: HMMsearch
[2024-01-25 17:41:20,342] [INFO] Running command: hmmsearch --tblout GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg861bba76-ddbb-4abf-a2db-274f739a8747/dqc_reference/reference_markers.hmm GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:20,700] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:20,701] [INFO] Found 6/6 markers.
[2024-01-25 17:41:20,751] [INFO] Query marker FASTA was written to GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/markers.fasta
[2024-01-25 17:41:20,751] [INFO] Task started: Blastn
[2024-01-25 17:41:20,751] [INFO] Running command: blastn -query GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg861bba76-ddbb-4abf-a2db-274f739a8747/dqc_reference/reference_markers.fasta -out GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:21,346] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:21,354] [INFO] Selected 15 target genomes.
[2024-01-25 17:41:21,354] [INFO] Target genome list was writen to GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/target_genomes.txt
[2024-01-25 17:41:21,363] [INFO] Task started: fastANI
[2024-01-25 17:41:21,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg93207ae3-ab66-4a82-82b1-94814e06d382/GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna.gz --refList GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/target_genomes.txt --output GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:37,933] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:37,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg861bba76-ddbb-4abf-a2db-274f739a8747/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:37,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg861bba76-ddbb-4abf-a2db-274f739a8747/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:37,943] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:37,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:37,943] [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 phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	100.0	1818	1819	95	conclusive
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	87.058	1237	1819	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	85.457	1272	1819	95	below_threshold
Paenibacillus barengoltzii	strain=NBRC 101215	GCA_004000745.1	343517	343517	type	True	83.1715	1073	1819	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	80.4295	866	1819	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	80.4081	834	1819	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.6874	234	1819	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	77.3969	136	1819	95	below_threshold
Paenibacillus herberti	strain=R33	GCA_002233675.1	1619309	1619309	type	True	77.2408	80	1819	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.1789	114	1819	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.9128	168	1819	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	76.8292	121	1819	95	below_threshold
Paenibacillus turpanensis	strain=YIM B00363	GCA_011421635.1	2689078	2689078	type	True	76.0863	78	1819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:37,945] [INFO] DFAST Taxonomy check result was written to GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/tc_result.tsv
[2024-01-25 17:41:37,945] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:37,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:37,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg861bba76-ddbb-4abf-a2db-274f739a8747/dqc_reference/checkm_data
[2024-01-25 17:41:37,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:38,003] [INFO] Task started: CheckM
[2024-01-25 17:41:38,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/checkm_input GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/checkm_result
[2024-01-25 17:42:17,292] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:17,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:17,311] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:17,311] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:17,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/markers.fasta)
[2024-01-25 17:42:17,312] [INFO] Task started: Blastn
[2024-01-25 17:42:17,312] [INFO] Running command: blastn -query GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg861bba76-ddbb-4abf-a2db-274f739a8747/dqc_reference/reference_markers_gtdb.fasta -out GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:18,199] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:18,202] [INFO] Selected 12 target genomes.
[2024-01-25 17:42:18,202] [INFO] Target genome list was writen to GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:18,217] [INFO] Task started: fastANI
[2024-01-25 17:42:18,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg93207ae3-ab66-4a82-82b1-94814e06d382/GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna.gz --refList GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/target_genomes_gtdb.txt --output GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:29,988] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:29,995] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:29,995] [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_900021165.1	s__Paenibacillus_A phocaensis	100.0	1818	1819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_900766135.1	s__Paenibacillus_A sp900766135	87.1938	1310	1819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	85.4631	1269	1819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009725205.1	s__Paenibacillus_A timonensis	85.3719	1248	1819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.34	98.12	0.92	0.92	3	-
GCF_000159955.1	s__Paenibacillus_A sp000159955	84.2074	1140	1819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900069005.2	s__Paenibacillus_A sp900069005	79.0346	338	1819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.72	99.44	0.97	0.94	3	-
GCF_003614185.1	s__Paenibacillus_A aceti	78.7029	338	1819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900177425.1	s__Paenibacillus uliginis	77.4653	134	1819	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:29,996] [INFO] GTDB search result was written to GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:29,997] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:30,042] [INFO] DFAST_QC result json was written to GCF_900021165.1_Paenibacillus_phoceensis_genomic.fna/dqc_result.json
[2024-01-25 17:42:30,042] [INFO] DFAST_QC completed!
[2024-01-25 17:42:30,042] [INFO] Total running time: 0h1m24s