[2024-01-24 11:51:23,710] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg17e8365a-b75f-42e4-9b5f-798f583f0fa6/dqc_reference
[2024-01-24 11:51:25,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,051] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg19c5e26c-609b-4b5d-9449-7bfd90de8098/GCF_924513355.1_JJ-60_genomic.fna.gz | prodigal -d GCF_924513355.1_JJ-60_genomic.fna/cds.fna -a GCF_924513355.1_JJ-60_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:40,275] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:40,275] [INFO] Task started: HMMsearch
[2024-01-24 11:51:40,275] [INFO] Running command: hmmsearch --tblout GCF_924513355.1_JJ-60_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17e8365a-b75f-42e4-9b5f-798f583f0fa6/dqc_reference/reference_markers.hmm GCF_924513355.1_JJ-60_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:40,638] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:40,639] [INFO] Found 6/6 markers.
[2024-01-24 11:51:40,690] [INFO] Query marker FASTA was written to GCF_924513355.1_JJ-60_genomic.fna/markers.fasta
[2024-01-24 11:51:40,691] [INFO] Task started: Blastn
[2024-01-24 11:51:40,691] [INFO] Running command: blastn -query GCF_924513355.1_JJ-60_genomic.fna/markers.fasta -db /var/lib/cwl/stg17e8365a-b75f-42e4-9b5f-798f583f0fa6/dqc_reference/reference_markers.fasta -out GCF_924513355.1_JJ-60_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:41,346] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:41,350] [INFO] Selected 24 target genomes.
[2024-01-24 11:51:41,351] [INFO] Target genome list was writen to GCF_924513355.1_JJ-60_genomic.fna/target_genomes.txt
[2024-01-24 11:51:41,361] [INFO] Task started: fastANI
[2024-01-24 11:51:41,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c5e26c-609b-4b5d-9449-7bfd90de8098/GCF_924513355.1_JJ-60_genomic.fna.gz --refList GCF_924513355.1_JJ-60_genomic.fna/target_genomes.txt --output GCF_924513355.1_JJ-60_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:10,556] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:10,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17e8365a-b75f-42e4-9b5f-798f583f0fa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:10,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17e8365a-b75f-42e4-9b5f-798f583f0fa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:10,577] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:10,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:10,577] [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 etheri	strain=SH7	GCA_001012825.2	1306852	1306852	type	True	93.7788	1842	2157	95	below_threshold
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	86.1307	1537	2157	95	below_threshold
Paenibacillus albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	79.9245	636	2157	95	below_threshold
Paenibacillus azotifigens	strain=LMG 29963	GCA_008635805.1	2047734	2047734	type	True	79.6435	583	2157	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	79.5965	541	2157	95	below_threshold
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	79.4567	510	2157	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	79.4273	574	2157	95	below_threshold
Paenibacillus graminis	strain=DSM 15220	GCA_000758705.1	189425	189425	type	True	79.3514	599	2157	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	79.3432	511	2157	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	79.3288	591	2157	95	below_threshold
Paenibacillus wynnii	strain=DSM 18334	GCA_000757885.1	268407	268407	type	True	79.3259	527	2157	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.3254	564	2157	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	79.2954	546	2157	95	below_threshold
Paenibacillus jilunlii	strain=DSM 23019	GCA_001546055.1	682956	682956	type	True	79.1379	575	2157	95	below_threshold
Paenibacillus jilunlii	strain=CGMCC 1.10239	GCA_900102965.1	682956	682956	type	True	79.114	582	2157	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	78.5947	425	2157	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.1586	272	2157	95	below_threshold
Paenibacillus pinihumi	strain=DSM 23905	GCA_000422505.1	669462	669462	type	True	76.396	77	2157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:10,580] [INFO] DFAST Taxonomy check result was written to GCF_924513355.1_JJ-60_genomic.fna/tc_result.tsv
[2024-01-24 11:52:10,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:10,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:10,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17e8365a-b75f-42e4-9b5f-798f583f0fa6/dqc_reference/checkm_data
[2024-01-24 11:52:10,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:10,650] [INFO] Task started: CheckM
[2024-01-24 11:52:10,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_924513355.1_JJ-60_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_924513355.1_JJ-60_genomic.fna/checkm_input GCF_924513355.1_JJ-60_genomic.fna/checkm_result
[2024-01-24 11:52:57,913] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:57,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:57,944] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:57,945] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:57,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_924513355.1_JJ-60_genomic.fna/markers.fasta)
[2024-01-24 11:52:57,946] [INFO] Task started: Blastn
[2024-01-24 11:52:57,946] [INFO] Running command: blastn -query GCF_924513355.1_JJ-60_genomic.fna/markers.fasta -db /var/lib/cwl/stg17e8365a-b75f-42e4-9b5f-798f583f0fa6/dqc_reference/reference_markers_gtdb.fasta -out GCF_924513355.1_JJ-60_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:58,761] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:58,764] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:58,765] [INFO] Target genome list was writen to GCF_924513355.1_JJ-60_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:58,775] [INFO] Task started: fastANI
[2024-01-24 11:52:58,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c5e26c-609b-4b5d-9449-7bfd90de8098/GCF_924513355.1_JJ-60_genomic.fna.gz --refList GCF_924513355.1_JJ-60_genomic.fna/target_genomes_gtdb.txt --output GCF_924513355.1_JJ-60_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:10,780] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:10,790] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:10,790] [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_000758545.1	s__Paenibacillus sp000758545	95.1864	1752	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.87	97.65	0.91	0.90	4	conclusive
GCF_001012825.1	s__Paenibacillus etheri	93.7928	1840	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002264395.1	s__Paenibacillus sp002264395	93.5254	1639	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.86	98.86	0.89	0.89	2	-
GCF_000758585.1	s__Paenibacillus sp000758585	91.9873	1670	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.21	98.21	0.91	0.91	2	-
GCA_002438345.1	s__Paenibacillus sp002438345	91.3657	1445	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758725.1	s__Paenibacillus odorifer	86.1363	1537	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.05	97.01	0.93	0.91	32	-
GCF_001637205.1	s__Paenibacillus glacialis	79.1883	230	2157	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:10,792] [INFO] GTDB search result was written to GCF_924513355.1_JJ-60_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:10,792] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:10,796] [INFO] DFAST_QC result json was written to GCF_924513355.1_JJ-60_genomic.fna/dqc_result.json
[2024-01-24 11:53:10,796] [INFO] DFAST_QC completed!
[2024-01-24 11:53:10,796] [INFO] Total running time: 0h1m47s