[2024-01-24 14:19:18,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:18,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:18,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8b20975-3b62-4d98-9310-de9f9662efd9/dqc_reference
[2024-01-24 14:19:19,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:19,915] [INFO] Task started: Prodigal
[2024-01-24 14:19:19,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a80af6b-1ec0-41ba-b070-6963173f929a/GCF_024623455.1_ASM2462345v1_genomic.fna.gz | prodigal -d GCF_024623455.1_ASM2462345v1_genomic.fna/cds.fna -a GCF_024623455.1_ASM2462345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:39,432] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:39,433] [INFO] Task started: HMMsearch
[2024-01-24 14:19:39,433] [INFO] Running command: hmmsearch --tblout GCF_024623455.1_ASM2462345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8b20975-3b62-4d98-9310-de9f9662efd9/dqc_reference/reference_markers.hmm GCF_024623455.1_ASM2462345v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:39,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:39,794] [INFO] Found 6/6 markers.
[2024-01-24 14:19:39,854] [INFO] Query marker FASTA was written to GCF_024623455.1_ASM2462345v1_genomic.fna/markers.fasta
[2024-01-24 14:19:39,855] [INFO] Task started: Blastn
[2024-01-24 14:19:39,855] [INFO] Running command: blastn -query GCF_024623455.1_ASM2462345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8b20975-3b62-4d98-9310-de9f9662efd9/dqc_reference/reference_markers.fasta -out GCF_024623455.1_ASM2462345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:40,518] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:40,522] [INFO] Selected 16 target genomes.
[2024-01-24 14:19:40,522] [INFO] Target genome list was writen to GCF_024623455.1_ASM2462345v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:40,528] [INFO] Task started: fastANI
[2024-01-24 14:19:40,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a80af6b-1ec0-41ba-b070-6963173f929a/GCF_024623455.1_ASM2462345v1_genomic.fna.gz --refList GCF_024623455.1_ASM2462345v1_genomic.fna/target_genomes.txt --output GCF_024623455.1_ASM2462345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:57,330] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:57,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8b20975-3b62-4d98-9310-de9f9662efd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:57,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8b20975-3b62-4d98-9310-de9f9662efd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:57,345] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:19:57,345] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:19:57,345] [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 nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	80.9002	971	2252	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	79.8199	616	2252	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	79.5648	488	2252	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	78.5164	504	2252	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	78.0772	404	2252	95	below_threshold
Paenibacillus oryzae	strain=1DrF-4	GCA_001675045.1	1844972	1844972	type	True	78.0695	328	2252	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	77.9425	283	2252	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.7292	272	2252	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.6688	398	2252	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.3162	204	2252	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.9991	218	2252	95	below_threshold
Paenibacillus algorifonticola	strain=XJ259	GCA_000971975.1	684063	684063	type	True	76.8904	254	2252	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	76.8606	253	2252	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	76.8115	228	2252	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.798	175	2252	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.6027	162	2252	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:57,347] [INFO] DFAST Taxonomy check result was written to GCF_024623455.1_ASM2462345v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:57,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:57,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:57,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8b20975-3b62-4d98-9310-de9f9662efd9/dqc_reference/checkm_data
[2024-01-24 14:19:57,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:57,414] [INFO] Task started: CheckM
[2024-01-24 14:19:57,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024623455.1_ASM2462345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024623455.1_ASM2462345v1_genomic.fna/checkm_input GCF_024623455.1_ASM2462345v1_genomic.fna/checkm_result
[2024-01-24 14:20:52,863] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:52,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:52,892] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:52,892] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:52,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024623455.1_ASM2462345v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:52,893] [INFO] Task started: Blastn
[2024-01-24 14:20:52,893] [INFO] Running command: blastn -query GCF_024623455.1_ASM2462345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8b20975-3b62-4d98-9310-de9f9662efd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_024623455.1_ASM2462345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:53,757] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:53,762] [INFO] Selected 11 target genomes.
[2024-01-24 14:20:53,762] [INFO] Target genome list was writen to GCF_024623455.1_ASM2462345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:53,788] [INFO] Task started: fastANI
[2024-01-24 14:20:53,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a80af6b-1ec0-41ba-b070-6963173f929a/GCF_024623455.1_ASM2462345v1_genomic.fna.gz --refList GCF_024623455.1_ASM2462345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024623455.1_ASM2462345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:06,824] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:06,837] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:21:06,838] [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_003583765.1	s__Paenibacillus_C nanensis	80.9045	970	2252	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	79.8152	617	2252	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_003591485.1	s__Paenibacillus_C sp003591485	79.7592	569	2252	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_003388735.1	s__Paenibacillus_C paeoniae	79.5569	488	2252	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_014705655.1	s__Paenibacillus_C sp014705655	79.505	647	2252	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	79.0716	594	2252	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	78.0646	327	2252	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_900113915.1	s__Paenibacillus_Z sp900113915	77.9782	410	2252	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
GCF_009737085.1	s__Paenibacillus_C sp009737085	77.9509	324	2252	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_009909185.1	s__Paenibacillus_Z glycinis	77.6606	401	2252	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	76.8808	255	2252	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 14:21:06,839] [INFO] GTDB search result was written to GCF_024623455.1_ASM2462345v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:06,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:06,843] [INFO] DFAST_QC result json was written to GCF_024623455.1_ASM2462345v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:06,844] [INFO] DFAST_QC completed!
[2024-01-24 14:21:06,844] [INFO] Total running time: 0h1m48s