[2024-01-24 13:40:34,992] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,994] [INFO] DQC Reference Directory: /var/lib/cwl/stg787e655b-7aa0-48a8-8896-951946b8ba9c/dqc_reference
[2024-01-24 13:40:36,337] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,345] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,346] [INFO] Running command: gunzip -c /var/lib/cwl/stg81f3380e-8df3-4743-bb78-12f05c090a20/GCF_006542765.1_ASM654276v1_genomic.fna.gz | prodigal -d GCF_006542765.1_ASM654276v1_genomic.fna/cds.fna -a GCF_006542765.1_ASM654276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:59,173] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:59,174] [INFO] Task started: HMMsearch
[2024-01-24 13:40:59,174] [INFO] Running command: hmmsearch --tblout GCF_006542765.1_ASM654276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg787e655b-7aa0-48a8-8896-951946b8ba9c/dqc_reference/reference_markers.hmm GCF_006542765.1_ASM654276v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:59,670] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:59,671] [INFO] Found 6/6 markers.
[2024-01-24 13:40:59,747] [INFO] Query marker FASTA was written to GCF_006542765.1_ASM654276v1_genomic.fna/markers.fasta
[2024-01-24 13:40:59,748] [INFO] Task started: Blastn
[2024-01-24 13:40:59,748] [INFO] Running command: blastn -query GCF_006542765.1_ASM654276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg787e655b-7aa0-48a8-8896-951946b8ba9c/dqc_reference/reference_markers.fasta -out GCF_006542765.1_ASM654276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:00,358] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:00,362] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:00,363] [INFO] Target genome list was writen to GCF_006542765.1_ASM654276v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:00,368] [INFO] Task started: fastANI
[2024-01-24 13:41:00,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg81f3380e-8df3-4743-bb78-12f05c090a20/GCF_006542765.1_ASM654276v1_genomic.fna.gz --refList GCF_006542765.1_ASM654276v1_genomic.fna/target_genomes.txt --output GCF_006542765.1_ASM654276v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg787e655b-7aa0-48a8-8896-951946b8ba9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg787e655b-7aa0-48a8-8896-951946b8ba9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,733] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:13,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:13,734] [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 luteus	strain=R-3	GCA_006542765.1	2545753	2545753	type	True	100.0	2789	2794	95	conclusive
Paenibacillus paridis	strain=py1325	GCA_006345825.1	2583376	2583376	type	True	93.6293	2179	2794	95	below_threshold
Paenibacillus sinopodophylli	strain=CCTCC AB 2016047	GCA_005930355.1	1837342	1837342	type	True	82.3008	1124	2794	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	81.7815	1048	2794	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	80.1093	586	2794	95	below_threshold
Paenibacillus castaneae	strain=DSM 19417	GCA_002884445.1	474957	474957	type	True	80.1023	684	2794	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	80.0414	671	2794	95	below_threshold
Paenibacillus castaneae	strain=CECT 7279	GCA_011761405.1	474957	474957	type	True	79.9694	687	2794	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	76.5278	66	2794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,735] [INFO] DFAST Taxonomy check result was written to GCF_006542765.1_ASM654276v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,736] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg787e655b-7aa0-48a8-8896-951946b8ba9c/dqc_reference/checkm_data
[2024-01-24 13:41:13,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,814] [INFO] Task started: CheckM
[2024-01-24 13:41:13,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006542765.1_ASM654276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006542765.1_ASM654276v1_genomic.fna/checkm_input GCF_006542765.1_ASM654276v1_genomic.fna/checkm_result
[2024-01-24 13:42:21,062] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:21,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:21,088] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:21,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:21,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006542765.1_ASM654276v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:21,090] [INFO] Task started: Blastn
[2024-01-24 13:42:21,090] [INFO] Running command: blastn -query GCF_006542765.1_ASM654276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg787e655b-7aa0-48a8-8896-951946b8ba9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006542765.1_ASM654276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:21,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:21,886] [INFO] Selected 10 target genomes.
[2024-01-24 13:42:21,886] [INFO] Target genome list was writen to GCF_006542765.1_ASM654276v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:21,913] [INFO] Task started: fastANI
[2024-01-24 13:42:21,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg81f3380e-8df3-4743-bb78-12f05c090a20/GCF_006542765.1_ASM654276v1_genomic.fna.gz --refList GCF_006542765.1_ASM654276v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006542765.1_ASM654276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:38,048] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:38,065] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:38,066] [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_006542765.1	s__Paenibacillus_C luteus	100.0	2789	2794	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_006345825.1	s__Paenibacillus_C paridis	93.6215	2180	2794	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	82.289	1126	2794	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	81.7965	1048	2794	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_001428245.1	s__Paenibacillus_C sp001428245	81.5356	792	2794	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_001956095.1	s__Paenibacillus_C sp001956095	81.5334	1112	2794	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	81.5317	1073	2794	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	81.4552	1071	2794	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	81.2788	874	2794	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	81.0061	976	2794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:38,068] [INFO] GTDB search result was written to GCF_006542765.1_ASM654276v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:38,068] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:38,072] [INFO] DFAST_QC result json was written to GCF_006542765.1_ASM654276v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:38,072] [INFO] DFAST_QC completed!
[2024-01-24 13:42:38,072] [INFO] Total running time: 0h2m3s