[2024-01-25 18:49:50,858] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:50,859] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:50,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fb8e4f1-8899-4f54-a463-59f20a8927ef/dqc_reference
[2024-01-25 18:49:52,067] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:52,068] [INFO] Task started: Prodigal
[2024-01-25 18:49:52,068] [INFO] Running command: gunzip -c /var/lib/cwl/stg99ac8157-bb91-4e07-8615-f1c9681c75a6/GCF_003337375.1_ASM333737v1_genomic.fna.gz | prodigal -d GCF_003337375.1_ASM333737v1_genomic.fna/cds.fna -a GCF_003337375.1_ASM333737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:06,602] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:06,603] [INFO] Task started: HMMsearch
[2024-01-25 18:50:06,603] [INFO] Running command: hmmsearch --tblout GCF_003337375.1_ASM333737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fb8e4f1-8899-4f54-a463-59f20a8927ef/dqc_reference/reference_markers.hmm GCF_003337375.1_ASM333737v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:06,899] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:06,900] [INFO] Found 6/6 markers.
[2024-01-25 18:50:06,953] [INFO] Query marker FASTA was written to GCF_003337375.1_ASM333737v1_genomic.fna/markers.fasta
[2024-01-25 18:50:06,953] [INFO] Task started: Blastn
[2024-01-25 18:50:06,953] [INFO] Running command: blastn -query GCF_003337375.1_ASM333737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fb8e4f1-8899-4f54-a463-59f20a8927ef/dqc_reference/reference_markers.fasta -out GCF_003337375.1_ASM333737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:07,505] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:07,508] [INFO] Selected 15 target genomes.
[2024-01-25 18:50:07,509] [INFO] Target genome list was writen to GCF_003337375.1_ASM333737v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:07,522] [INFO] Task started: fastANI
[2024-01-25 18:50:07,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ac8157-bb91-4e07-8615-f1c9681c75a6/GCF_003337375.1_ASM333737v1_genomic.fna.gz --refList GCF_003337375.1_ASM333737v1_genomic.fna/target_genomes.txt --output GCF_003337375.1_ASM333737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:26,164] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:26,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fb8e4f1-8899-4f54-a463-59f20a8927ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:26,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fb8e4f1-8899-4f54-a463-59f20a8927ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:26,173] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:50:26,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:26,173] [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 prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	100.0	2167	2168	95	conclusive
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	82.1413	800	2168	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	81.9982	971	2168	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	80.2875	639	2168	95	below_threshold
Paenibacillus luteus	strain=R-3	GCA_006542765.1	2545753	2545753	type	True	80.124	652	2168	95	below_threshold
Paenibacillus castaneae	strain=DSM 19417	GCA_002884445.1	474957	474957	type	True	80.1119	664	2168	95	below_threshold
Paenibacillus castaneae	strain=CECT 7279	GCA_011761405.1	474957	474957	type	True	80.0729	655	2168	95	below_threshold
Paenibacillus paridis	strain=py1325	GCA_006345825.1	2583376	2583376	type	True	79.8915	618	2168	95	below_threshold
Paenibacillus sinopodophylli	strain=CCTCC AB 2016047	GCA_005930355.1	1837342	1837342	type	True	79.7576	550	2168	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	77.9418	322	2168	95	below_threshold
Paenibacillus pinihumi	strain=DSM 23905	GCA_000422505.1	669462	669462	type	True	77.0802	145	2168	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.9251	187	2168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:26,174] [INFO] DFAST Taxonomy check result was written to GCF_003337375.1_ASM333737v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:26,175] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:26,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:26,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fb8e4f1-8899-4f54-a463-59f20a8927ef/dqc_reference/checkm_data
[2024-01-25 18:50:26,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:26,237] [INFO] Task started: CheckM
[2024-01-25 18:50:26,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337375.1_ASM333737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337375.1_ASM333737v1_genomic.fna/checkm_input GCF_003337375.1_ASM333737v1_genomic.fna/checkm_result
[2024-01-25 18:51:10,098] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:10,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:10,122] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:10,122] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:10,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337375.1_ASM333737v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:10,123] [INFO] Task started: Blastn
[2024-01-25 18:51:10,123] [INFO] Running command: blastn -query GCF_003337375.1_ASM333737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fb8e4f1-8899-4f54-a463-59f20a8927ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337375.1_ASM333737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:10,959] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:10,963] [INFO] Selected 13 target genomes.
[2024-01-25 18:51:10,963] [INFO] Target genome list was writen to GCF_003337375.1_ASM333737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:10,978] [INFO] Task started: fastANI
[2024-01-25 18:51:10,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ac8157-bb91-4e07-8615-f1c9681c75a6/GCF_003337375.1_ASM333737v1_genomic.fna.gz --refList GCF_003337375.1_ASM333737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337375.1_ASM333737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:30,675] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:30,684] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:30,684] [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_003337375.1	s__Paenibacillus_C prosopidis	100.0	2167	2168	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_001428245.1	s__Paenibacillus_C sp001428245	83.3959	1171	2168	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	82.0178	967	2168	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_003217535.1	s__Paenibacillus_C sp003217535	81.9463	1025	2168	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_012935325.2	s__Paenibacillus_C sp012935325	80.8766	930	2168	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	80.8428	798	2168	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_014192395.1	s__Paenibacillus_C endophyticus	80.3069	636	2168	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	80.1371	649	2168	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_002884445.1	s__Paenibacillus_C castaneae	80.1148	664	2168	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014705655.1	s__Paenibacillus_C sp014705655	79.8406	694	2168	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_005930355.1	s__Paenibacillus_C sinopodophylli	79.777	548	2168	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_900106745.1	s__Paenibacillus_Z sp900106745	77.2302	199	2168	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_900113915.1	s__Paenibacillus_Z sp900113915	76.7045	189	2168	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:30,685] [INFO] GTDB search result was written to GCF_003337375.1_ASM333737v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:30,686] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:30,688] [INFO] DFAST_QC result json was written to GCF_003337375.1_ASM333737v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:30,689] [INFO] DFAST_QC completed!
[2024-01-25 18:51:30,689] [INFO] Total running time: 0h1m40s