[2024-01-24 11:05:24,344] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:24,346] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:24,346] [INFO] DQC Reference Directory: /var/lib/cwl/stga8b72e32-2913-4fdb-8b68-d0234e5dcae4/dqc_reference
[2024-01-24 11:05:25,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:25,948] [INFO] Task started: Prodigal
[2024-01-24 11:05:25,948] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1d9a12d-a667-43e6-96f1-72eee4efa475/GCF_011761355.1_ASM1176135v1_genomic.fna.gz | prodigal -d GCF_011761355.1_ASM1176135v1_genomic.fna/cds.fna -a GCF_011761355.1_ASM1176135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:42,778] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:42,778] [INFO] Task started: HMMsearch
[2024-01-24 11:05:42,779] [INFO] Running command: hmmsearch --tblout GCF_011761355.1_ASM1176135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8b72e32-2913-4fdb-8b68-d0234e5dcae4/dqc_reference/reference_markers.hmm GCF_011761355.1_ASM1176135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:43,130] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:43,132] [INFO] Found 6/6 markers.
[2024-01-24 11:05:43,186] [INFO] Query marker FASTA was written to GCF_011761355.1_ASM1176135v1_genomic.fna/markers.fasta
[2024-01-24 11:05:43,186] [INFO] Task started: Blastn
[2024-01-24 11:05:43,187] [INFO] Running command: blastn -query GCF_011761355.1_ASM1176135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8b72e32-2913-4fdb-8b68-d0234e5dcae4/dqc_reference/reference_markers.fasta -out GCF_011761355.1_ASM1176135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:43,794] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:43,797] [INFO] Selected 12 target genomes.
[2024-01-24 11:05:43,798] [INFO] Target genome list was writen to GCF_011761355.1_ASM1176135v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:43,802] [INFO] Task started: fastANI
[2024-01-24 11:05:43,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d9a12d-a667-43e6-96f1-72eee4efa475/GCF_011761355.1_ASM1176135v1_genomic.fna.gz --refList GCF_011761355.1_ASM1176135v1_genomic.fna/target_genomes.txt --output GCF_011761355.1_ASM1176135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:58,026] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:58,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8b72e32-2913-4fdb-8b68-d0234e5dcae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:58,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8b72e32-2913-4fdb-8b68-d0234e5dcae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:58,041] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:58,041] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:58,042] [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 lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	100.0	2211	2213	95	conclusive
Paenibacillus catalpae	strain=CGMCC 1.10784	GCA_900112695.1	1045775	1045775	type	True	84.1994	1578	2213	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	82.0411	1349	2213	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	82.0002	1310	2213	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	78.7148	391	2213	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	78.691	415	2213	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	78.0182	309	2213	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.6702	259	2213	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	76.989	89	2213	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:58,043] [INFO] DFAST Taxonomy check result was written to GCF_011761355.1_ASM1176135v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:58,044] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:58,044] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:58,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8b72e32-2913-4fdb-8b68-d0234e5dcae4/dqc_reference/checkm_data
[2024-01-24 11:05:58,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:58,104] [INFO] Task started: CheckM
[2024-01-24 11:05:58,104] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011761355.1_ASM1176135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011761355.1_ASM1176135v1_genomic.fna/checkm_input GCF_011761355.1_ASM1176135v1_genomic.fna/checkm_result
[2024-01-24 11:06:49,324] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:49,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:49,349] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:49,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:49,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011761355.1_ASM1176135v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:49,351] [INFO] Task started: Blastn
[2024-01-24 11:06:49,351] [INFO] Running command: blastn -query GCF_011761355.1_ASM1176135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8b72e32-2913-4fdb-8b68-d0234e5dcae4/dqc_reference/reference_markers_gtdb.fasta -out GCF_011761355.1_ASM1176135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:50,135] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:50,140] [INFO] Selected 10 target genomes.
[2024-01-24 11:06:50,140] [INFO] Target genome list was writen to GCF_011761355.1_ASM1176135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:50,149] [INFO] Task started: fastANI
[2024-01-24 11:06:50,150] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d9a12d-a667-43e6-96f1-72eee4efa475/GCF_011761355.1_ASM1176135v1_genomic.fna.gz --refList GCF_011761355.1_ASM1176135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011761355.1_ASM1176135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:01,829] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:01,840] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:01,841] [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_011761355.1	s__Paenibacillus_C lupini	100.0	2211	2213	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112695.1	s__Paenibacillus_C catalpae	84.188	1580	2213	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_000023585.1	s__Paenibacillus_C sp000023585	82.1298	1403	2213	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	81.9908	1320	2213	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_004000805.1	s__Paenibacillus_C glycanilyticus	81.9811	1313	2213	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	97.79	97.79	0.90	0.90	2	-
GCF_014641555.1	s__Paenibacillus_C radicis	78.6805	417	2213	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:01,842] [INFO] GTDB search result was written to GCF_011761355.1_ASM1176135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:01,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:01,845] [INFO] DFAST_QC result json was written to GCF_011761355.1_ASM1176135v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:01,845] [INFO] DFAST_QC completed!
[2024-01-24 11:07:01,845] [INFO] Total running time: 0h1m38s