[2024-01-24 13:58:25,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,670] [INFO] DQC Reference Directory: /var/lib/cwl/stga0fa3b42-43cd-443d-a800-7c30fe77483a/dqc_reference
[2024-01-24 13:58:27,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:27,026] [INFO] Task started: Prodigal
[2024-01-24 13:58:27,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e2ea633-c43e-458d-9cd6-25fdaf2706b7/GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/cds.fna -a GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:46,548] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:46,548] [INFO] Task started: HMMsearch
[2024-01-24 13:58:46,549] [INFO] Running command: hmmsearch --tblout GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0fa3b42-43cd-443d-a800-7c30fe77483a/dqc_reference/reference_markers.hmm GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:46,908] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:46,909] [INFO] Found 6/6 markers.
[2024-01-24 13:58:46,972] [INFO] Query marker FASTA was written to GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:58:46,973] [INFO] Task started: Blastn
[2024-01-24 13:58:46,973] [INFO] Running command: blastn -query GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga0fa3b42-43cd-443d-a800-7c30fe77483a/dqc_reference/reference_markers.fasta -out GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:47,593] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:47,596] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:47,597] [INFO] Target genome list was writen to GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:47,608] [INFO] Task started: fastANI
[2024-01-24 13:58:47,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e2ea633-c43e-458d-9cd6-25fdaf2706b7/GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna.gz --refList GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:13,863] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:13,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0fa3b42-43cd-443d-a800-7c30fe77483a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:13,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0fa3b42-43cd-443d-a800-7c30fe77483a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:13,884] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:59:13,885] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:13,885] [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 algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	100.0	2446	2451	95	conclusive
Paenibacillus algorifonticola	strain=XJ259	GCA_000971975.1	684063	684063	type	True	99.9829	2404	2451	95	conclusive
Paenibacillus luteus	strain=R-3	GCA_006542765.1	2545753	2545753	type	True	78.3261	420	2451	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	78.245	380	2451	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	78.187	376	2451	95	below_threshold
Paenibacillus lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	78.1008	300	2451	95	below_threshold
Paenibacillus catalpae	strain=CGMCC 1.10784	GCA_900112695.1	1045775	1045775	type	True	78.0858	332	2451	95	below_threshold
Paenibacillus paridis	strain=py1325	GCA_006345825.1	2583376	2583376	type	True	78.047	386	2451	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.978	378	2451	95	below_threshold
Paenibacillus sinopodophylli	strain=CCTCC AB 2016047	GCA_005930355.1	1837342	1837342	type	True	77.9539	365	2451	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	77.8779	343	2451	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	77.7966	324	2451	95	below_threshold
Paenibacillus pinihumi	strain=DSM 23905	GCA_000422505.1	669462	669462	type	True	77.269	195	2451	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	77.2297	200	2451	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.2149	107	2451	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.2098	179	2451	95	below_threshold
Paenibacillus oryzae	strain=1DrF-4	GCA_001675045.1	1844972	1844972	type	True	77.126	239	2451	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.0465	186	2451	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	76.8315	207	2451	95	below_threshold
Paenibacillus xylaniclasticus	strain=NBRC 106381	GCA_004001065.1	588083	588083	type	True	76.826	152	2451	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.6403	127	2451	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.0618	93	2451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:13,887] [INFO] DFAST Taxonomy check result was written to GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:59:13,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:13,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:13,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0fa3b42-43cd-443d-a800-7c30fe77483a/dqc_reference/checkm_data
[2024-01-24 13:59:13,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:13,965] [INFO] Task started: CheckM
[2024-01-24 13:59:13,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/checkm_input GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:00:09,912] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:09,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:09,934] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:09,934] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:09,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:00:09,935] [INFO] Task started: Blastn
[2024-01-24 14:00:09,935] [INFO] Running command: blastn -query GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga0fa3b42-43cd-443d-a800-7c30fe77483a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:10,752] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:10,756] [INFO] Selected 22 target genomes.
[2024-01-24 14:00:10,757] [INFO] Target genome list was writen to GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:10,780] [INFO] Task started: fastANI
[2024-01-24 14:00:10,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e2ea633-c43e-458d-9cd6-25fdaf2706b7/GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna.gz --refList GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:37,201] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:37,224] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:37,224] [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_000971975.1	s__Paenibacillus_C algorifonticola	99.9829	2404	2451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_002741035.1	s__Paenibacillus_C sp002741035	91.148	1881	2451	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_012935325.2	s__Paenibacillus_C sp012935325	78.8373	409	2451	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_006542765.1	s__Paenibacillus_C luteus	78.3675	416	2451	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_014641555.1	s__Paenibacillus_C radicis	78.245	380	2451	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_011761355.1	s__Paenibacillus_C lupini	78.0889	301	2451	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_006345825.1	s__Paenibacillus_C paridis	78.0776	382	2451	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_001682865.1	s__Paenibacillus_C sp001682865	78.0361	401	2451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.12	99.12	0.94	0.94	2	-
GCF_003217535.1	s__Paenibacillus_C sp003217535	77.9939	368	2451	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_000513275.1	s__Paenibacillus_C gorillae	77.9875	377	2451	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_009737085.1	s__Paenibacillus_C sp009737085	77.9053	370	2451	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_001956295.1	s__Paenibacillus_C sp001956295	77.8931	337	2451	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_000422465.1	s__Paenibacillus_C harenae	77.8621	344	2451	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	77.7239	349	2451	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_001956095.1	s__Paenibacillus_C sp001956095	77.7061	350	2451	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_014640295.1	s__Paenibacillus_D abyssi	77.2362	177	2451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705655.1	s__Paenibacillus_C sp014705655	77.2342	317	2451	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_003991425.1	s__Paenibacillus_A lutimineralis	77.1819	102	2451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001675045.1	s__Paenibacillus_C oryzae	77.1287	239	2451	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	76.8765	191	2451	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_008124765.1	s__Paenibacillus_Z methanolicus	76.8517	207	2451	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_004001065.1	s__Paenibacillus_T xylaniclasticus	76.8393	152	2451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:37,226] [INFO] GTDB search result was written to GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:37,226] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:37,230] [INFO] DFAST_QC result json was written to GCF_900112925.1_IMG-taxon_2617270911_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:00:37,230] [INFO] DFAST_QC completed!
[2024-01-24 14:00:37,230] [INFO] Total running time: 0h2m12s