[2024-01-24 12:14:33,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg38b7b596-79cb-4006-9a77-7d07499f8f1a/dqc_reference
[2024-01-24 12:14:35,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,135] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,135] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2dc77f2-2137-4319-a37b-fe61508daf20/GCF_004135365.1_ASM413536v1_genomic.fna.gz | prodigal -d GCF_004135365.1_ASM413536v1_genomic.fna/cds.fna -a GCF_004135365.1_ASM413536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:45,670] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:45,671] [INFO] Task started: HMMsearch
[2024-01-24 12:14:45,671] [INFO] Running command: hmmsearch --tblout GCF_004135365.1_ASM413536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38b7b596-79cb-4006-9a77-7d07499f8f1a/dqc_reference/reference_markers.hmm GCF_004135365.1_ASM413536v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:45,902] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:45,903] [INFO] Found 6/6 markers.
[2024-01-24 12:14:45,936] [INFO] Query marker FASTA was written to GCF_004135365.1_ASM413536v1_genomic.fna/markers.fasta
[2024-01-24 12:14:45,936] [INFO] Task started: Blastn
[2024-01-24 12:14:45,937] [INFO] Running command: blastn -query GCF_004135365.1_ASM413536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38b7b596-79cb-4006-9a77-7d07499f8f1a/dqc_reference/reference_markers.fasta -out GCF_004135365.1_ASM413536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:46,499] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:46,643] [INFO] Selected 26 target genomes.
[2024-01-24 12:14:46,643] [INFO] Target genome list was writen to GCF_004135365.1_ASM413536v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:46,652] [INFO] Task started: fastANI
[2024-01-24 12:14:46,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2dc77f2-2137-4319-a37b-fe61508daf20/GCF_004135365.1_ASM413536v1_genomic.fna.gz --refList GCF_004135365.1_ASM413536v1_genomic.fna/target_genomes.txt --output GCF_004135365.1_ASM413536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:15,443] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:15,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38b7b596-79cb-4006-9a77-7d07499f8f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:15,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38b7b596-79cb-4006-9a77-7d07499f8f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:15,458] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:15,459] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:15,459] [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 protaetiae	strain=FW100M-2	GCA_004135365.1	2509456	2509456	type	True	100.0	1409	1409	95	conclusive
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	78.4642	248	1409	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	78.4528	240	1409	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	78.0038	115	1409	95	below_threshold
Paenibacillus castaneae	strain=DSM 19417	GCA_002884445.1	474957	474957	type	True	77.9065	182	1409	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	77.8843	345	1409	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	77.859	300	1409	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	77.8086	327	1409	95	below_threshold
Paenibacillus catalpae	strain=CGMCC 1.10784	GCA_900112695.1	1045775	1045775	type	True	77.7903	307	1409	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	77.7573	235	1409	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	77.7521	274	1409	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.75	295	1409	95	below_threshold
Paenibacillus lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	77.7081	245	1409	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	77.6902	232	1409	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	77.5825	258	1409	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	77.4526	200	1409	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	77.2665	221	1409	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	77.2428	237	1409	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.0455	154	1409	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.0069	191	1409	95	below_threshold
Paenibacillus cisolokensis	strain=LC2-13A	GCA_018403665.1	1658519	1658519	type	True	76.8609	191	1409	95	below_threshold
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	76.8012	126	1409	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	76.6492	151	1409	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.4315	129	1409	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.2782	90	1409	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	76.2776	167	1409	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:15,460] [INFO] DFAST Taxonomy check result was written to GCF_004135365.1_ASM413536v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:15,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:15,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:15,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38b7b596-79cb-4006-9a77-7d07499f8f1a/dqc_reference/checkm_data
[2024-01-24 12:15:15,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:15,501] [INFO] Task started: CheckM
[2024-01-24 12:15:15,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004135365.1_ASM413536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004135365.1_ASM413536v1_genomic.fna/checkm_input GCF_004135365.1_ASM413536v1_genomic.fna/checkm_result
[2024-01-24 12:15:48,172] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:48,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:48,188] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:48,189] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:48,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004135365.1_ASM413536v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:48,189] [INFO] Task started: Blastn
[2024-01-24 12:15:48,189] [INFO] Running command: blastn -query GCF_004135365.1_ASM413536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38b7b596-79cb-4006-9a77-7d07499f8f1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004135365.1_ASM413536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:48,953] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:48,957] [INFO] Selected 22 target genomes.
[2024-01-24 12:15:48,957] [INFO] Target genome list was writen to GCF_004135365.1_ASM413536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:48,969] [INFO] Task started: fastANI
[2024-01-24 12:15:48,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2dc77f2-2137-4319-a37b-fe61508daf20/GCF_004135365.1_ASM413536v1_genomic.fna.gz --refList GCF_004135365.1_ASM413536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004135365.1_ASM413536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:15,920] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:15,933] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:15,934] [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_004135365.1	s__Paenibacillus_C protaetiae	100.0	1409	1409	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_000023585.1	s__Paenibacillus_C sp000023585	78.6961	331	1409	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_000961095.1	s__Paenibacillus_O beijingensis	78.5432	239	1409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009737085.1	s__Paenibacillus_C sp009737085	78.0534	302	1409	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_003952225.1	s__Paenibacillus_Z albus	77.9908	198	1409	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_014641555.1	s__Paenibacillus_C radicis	77.8524	302	1409	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_004000805.1	s__Paenibacillus_C glycanilyticus	77.8102	328	1409	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_900112695.1	s__Paenibacillus_C catalpae	77.8031	308	1409	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	77.7573	235	1409	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	77.7496	295	1409	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	77.7087	245	1409	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_003337375.1	s__Paenibacillus_C prosopidis	77.7043	231	1409	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	77.6904	348	1409	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_003583765.1	s__Paenibacillus_C nanensis	77.5825	258	1409	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	77.5422	308	1409	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	77.4517	201	1409	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_014192395.1	s__Paenibacillus_C endophyticus	77.2665	221	1409	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	77.2485	201	1409	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_003386535.1	s__Paenibacillus_Z taihuensis	77.0083	190	1409	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_018403665.1	s__Paenibacillus_AH cisolokensis	76.848	192	1409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_AH	95.0	98.86	98.86	0.88	0.88	2	-
GCF_004000785.1	s__Paenibacillus_G ehimensis	76.6492	151	1409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
GCF_000429825.1	s__Cohnella thermotolerans	76.3365	169	1409	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:15,936] [INFO] GTDB search result was written to GCF_004135365.1_ASM413536v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:15,936] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:15,940] [INFO] DFAST_QC result json was written to GCF_004135365.1_ASM413536v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:15,940] [INFO] DFAST_QC completed!
[2024-01-24 12:16:15,940] [INFO] Total running time: 0h1m42s