[2024-01-24 13:03:19,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:03:19,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:03:19,586] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4543559-3543-42d4-ad18-4d7a14d430ec/dqc_reference
[2024-01-24 13:03:20,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:03:20,845] [INFO] Task started: Prodigal
[2024-01-24 13:03:20,845] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4fb4f5a-9a6c-4d90-9976-b6f495c86495/GCF_000224945.1_PR_1_genomic.fna.gz | prodigal -d GCF_000224945.1_PR_1_genomic.fna/cds.fna -a GCF_000224945.1_PR_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:03:36,962] [INFO] Task succeeded: Prodigal
[2024-01-24 13:03:36,962] [INFO] Task started: HMMsearch
[2024-01-24 13:03:36,963] [INFO] Running command: hmmsearch --tblout GCF_000224945.1_PR_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4543559-3543-42d4-ad18-4d7a14d430ec/dqc_reference/reference_markers.hmm GCF_000224945.1_PR_1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:03:37,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:03:37,313] [INFO] Found 6/6 markers.
[2024-01-24 13:03:37,374] [INFO] Query marker FASTA was written to GCF_000224945.1_PR_1_genomic.fna/markers.fasta
[2024-01-24 13:03:37,374] [INFO] Task started: Blastn
[2024-01-24 13:03:37,374] [INFO] Running command: blastn -query GCF_000224945.1_PR_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4543559-3543-42d4-ad18-4d7a14d430ec/dqc_reference/reference_markers.fasta -out GCF_000224945.1_PR_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:37,971] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:37,976] [INFO] Selected 11 target genomes.
[2024-01-24 13:03:37,977] [INFO] Target genome list was writen to GCF_000224945.1_PR_1_genomic.fna/target_genomes.txt
[2024-01-24 13:03:37,984] [INFO] Task started: fastANI
[2024-01-24 13:03:37,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4fb4f5a-9a6c-4d90-9976-b6f495c86495/GCF_000224945.1_PR_1_genomic.fna.gz --refList GCF_000224945.1_PR_1_genomic.fna/target_genomes.txt --output GCF_000224945.1_PR_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:53,056] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:53,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4543559-3543-42d4-ad18-4d7a14d430ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:53,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4543559-3543-42d4-ad18-4d7a14d430ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:53,076] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:03:53,076] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:03:53,077] [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 riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	100.0	1661	1687	95	inconclusive
Paenibacillus riograndensis		GCA_000981585.1	483937	483937	type	True	99.9756	1687	1687	95	inconclusive
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	96.5215	1477	1687	95	inconclusive
Paenibacillus sonchi	strain=X19-5	GCA_000316285.1	373687	373687	type	True	96.3076	1248	1687	95	inconclusive
Paenibacillus jilunlii	strain=CGMCC 1.10239	GCA_900102965.1	682956	682956	type	True	93.2766	1435	1687	95	below_threshold
Paenibacillus jilunlii	strain=DSM 23019	GCA_001546055.1	682956	682956	type	True	93.2633	1434	1687	95	below_threshold
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	92.0113	1242	1687	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	80.8632	763	1687	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	80.2381	784	1687	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.3684	460	1687	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.6376	353	1687	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:53,079] [INFO] DFAST Taxonomy check result was written to GCF_000224945.1_PR_1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:53,079] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:53,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:53,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4543559-3543-42d4-ad18-4d7a14d430ec/dqc_reference/checkm_data
[2024-01-24 13:03:53,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:53,178] [INFO] Task started: CheckM
[2024-01-24 13:03:53,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000224945.1_PR_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000224945.1_PR_1_genomic.fna/checkm_input GCF_000224945.1_PR_1_genomic.fna/checkm_result
[2024-01-24 13:04:43,699] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:43,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:43,744] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:43,745] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:43,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000224945.1_PR_1_genomic.fna/markers.fasta)
[2024-01-24 13:04:43,746] [INFO] Task started: Blastn
[2024-01-24 13:04:43,746] [INFO] Running command: blastn -query GCF_000224945.1_PR_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4543559-3543-42d4-ad18-4d7a14d430ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_000224945.1_PR_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:44,539] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:44,543] [INFO] Selected 6 target genomes.
[2024-01-24 13:04:44,544] [INFO] Target genome list was writen to GCF_000224945.1_PR_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:44,554] [INFO] Task started: fastANI
[2024-01-24 13:04:44,555] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4fb4f5a-9a6c-4d90-9976-b6f495c86495/GCF_000224945.1_PR_1_genomic.fna.gz --refList GCF_000224945.1_PR_1_genomic.fna/target_genomes_gtdb.txt --output GCF_000224945.1_PR_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:54,462] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:54,470] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:04:54,470] [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_000981585.1	s__Paenibacillus riograndensis	99.9756	1687	1687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	97.36	97.36	0.91	0.91	2	inconclusive
GCF_016772475.1	s__Paenibacillus sonchi	96.5364	1476	1687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	99.97	99.97	1.00	1.00	2	inconclusive
GCF_900102965.1	s__Paenibacillus jilunlii	93.2766	1435	1687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.98	99.98	1.00	0.99	3	-
GCF_000758705.1	s__Paenibacillus graminis	92.3004	1407	1687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001909055.1	s__Paenibacillus helianthi	84.944	1158	1687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.61	95.31	0.90	0.83	4	-
GCF_000374185.1	s__Paenibacillus sp000374185	83.0349	1055	1687	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 13:04:54,472] [INFO] GTDB search result was written to GCF_000224945.1_PR_1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:54,473] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:54,479] [INFO] DFAST_QC result json was written to GCF_000224945.1_PR_1_genomic.fna/dqc_result.json
[2024-01-24 13:04:54,479] [INFO] DFAST_QC completed!
[2024-01-24 13:04:54,479] [INFO] Total running time: 0h1m35s