[2024-01-24 13:48:59,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg16386b3f-99a2-40fa-a32e-992ad6ad9f1a/dqc_reference
[2024-01-24 13:49:01,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,011] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg66dd188e-2beb-4201-9f46-6b315873fffd/GCF_003388735.1_ASM338873v1_genomic.fna.gz | prodigal -d GCF_003388735.1_ASM338873v1_genomic.fna/cds.fna -a GCF_003388735.1_ASM338873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:17,226] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:17,227] [INFO] Task started: HMMsearch
[2024-01-24 13:49:17,227] [INFO] Running command: hmmsearch --tblout GCF_003388735.1_ASM338873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16386b3f-99a2-40fa-a32e-992ad6ad9f1a/dqc_reference/reference_markers.hmm GCF_003388735.1_ASM338873v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:17,523] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:17,524] [INFO] Found 6/6 markers.
[2024-01-24 13:49:17,573] [INFO] Query marker FASTA was written to GCF_003388735.1_ASM338873v1_genomic.fna/markers.fasta
[2024-01-24 13:49:17,574] [INFO] Task started: Blastn
[2024-01-24 13:49:17,574] [INFO] Running command: blastn -query GCF_003388735.1_ASM338873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16386b3f-99a2-40fa-a32e-992ad6ad9f1a/dqc_reference/reference_markers.fasta -out GCF_003388735.1_ASM338873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:18,195] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:18,198] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:18,198] [INFO] Target genome list was writen to GCF_003388735.1_ASM338873v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:18,205] [INFO] Task started: fastANI
[2024-01-24 13:49:18,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg66dd188e-2beb-4201-9f46-6b315873fffd/GCF_003388735.1_ASM338873v1_genomic.fna.gz --refList GCF_003388735.1_ASM338873v1_genomic.fna/target_genomes.txt --output GCF_003388735.1_ASM338873v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:38,100] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:38,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16386b3f-99a2-40fa-a32e-992ad6ad9f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:38,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16386b3f-99a2-40fa-a32e-992ad6ad9f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:38,115] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:38,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:38,115] [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 paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	100.0	1921	1922	95	conclusive
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	83.4016	1274	1922	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	79.5685	477	1922	95	below_threshold
Paenibacillus oryzae	strain=1DrF-4	GCA_001675045.1	1844972	1844972	type	True	78.3927	293	1922	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	78.3786	273	1922	95	below_threshold
Paenibacillus luteus	strain=R-3	GCA_006542765.1	2545753	2545753	type	True	78.2849	301	1922	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	78.2014	331	1922	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	78.0699	268	1922	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	77.9909	305	1922	95	below_threshold
Paenibacillus protaetiae	strain=FW100M-2	GCA_004135365.1	2509456	2509456	type	True	77.8821	182	1922	95	below_threshold
Paenibacillus lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	77.8108	213	1922	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	77.6382	253	1922	95	below_threshold
Paenibacillus algorifonticola	strain=XJ259	GCA_000971975.1	684063	684063	type	True	77.2739	239	1922	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	77.2541	239	1922	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.1775	152	1922	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	76.9277	73	1922	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.8745	171	1922	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.6922	78	1922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:38,117] [INFO] DFAST Taxonomy check result was written to GCF_003388735.1_ASM338873v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:38,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:38,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:38,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16386b3f-99a2-40fa-a32e-992ad6ad9f1a/dqc_reference/checkm_data
[2024-01-24 13:49:38,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:38,174] [INFO] Task started: CheckM
[2024-01-24 13:49:38,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003388735.1_ASM338873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003388735.1_ASM338873v1_genomic.fna/checkm_input GCF_003388735.1_ASM338873v1_genomic.fna/checkm_result
[2024-01-24 13:50:31,239] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:31,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:31,260] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:31,260] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:31,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003388735.1_ASM338873v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:31,261] [INFO] Task started: Blastn
[2024-01-24 13:50:31,262] [INFO] Running command: blastn -query GCF_003388735.1_ASM338873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16386b3f-99a2-40fa-a32e-992ad6ad9f1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003388735.1_ASM338873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:32,114] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:32,117] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:32,117] [INFO] Target genome list was writen to GCF_003388735.1_ASM338873v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:32,125] [INFO] Task started: fastANI
[2024-01-24 13:50:32,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg66dd188e-2beb-4201-9f46-6b315873fffd/GCF_003388735.1_ASM338873v1_genomic.fna.gz --refList GCF_003388735.1_ASM338873v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003388735.1_ASM338873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:45,834] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:45,854] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:45,854] [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_003388735.1	s__Paenibacillus_C paeoniae	100.0	1921	1922	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_003591485.1	s__Paenibacillus_C sp003591485	84.8406	1269	1922	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_003605435.1	s__Paenibacillus_C pinisoli	83.4086	1273	1922	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_003583765.1	s__Paenibacillus_C nanensis	79.5558	480	1922	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_003112455.1	s__Paenibacillus_C agaridevorans	78.4739	379	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	96.67	95.87	0.80	0.78	4	-
GCF_001675045.1	s__Paenibacillus_C oryzae	78.381	294	1922	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_011947265.1	s__Paenibacillus_C sp011947265	78.1209	334	1922	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_005222705.1	s__Paenibacillus_C sp005222705	78.0736	266	1922	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_002741035.1	s__Paenibacillus_C sp002741035	77.7397	250	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	95.68	95.68	0.84	0.84	2	-
GCF_014192105.1	s__Paenibacillus_Z phyllosphaerae	77.2975	181	1922	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_000971975.1	s__Paenibacillus_C algorifonticola	77.2907	238	1922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,856] [INFO] GTDB search result was written to GCF_003388735.1_ASM338873v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:45,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:45,860] [INFO] DFAST_QC result json was written to GCF_003388735.1_ASM338873v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:45,861] [INFO] DFAST_QC completed!
[2024-01-24 13:50:45,861] [INFO] Total running time: 0h1m46s