[2024-01-24 15:03:29,339] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:29,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:29,341] [INFO] DQC Reference Directory: /var/lib/cwl/stge7ebd4d3-ca81-4a57-885a-c95a4cc88ef7/dqc_reference
[2024-01-24 15:03:32,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:32,683] [INFO] Task started: Prodigal
[2024-01-24 15:03:32,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg70d1fa47-f2f7-4a01-9e7c-36491a703bb8/GCF_002884445.1_ASM288444v1_genomic.fna.gz | prodigal -d GCF_002884445.1_ASM288444v1_genomic.fna/cds.fna -a GCF_002884445.1_ASM288444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:46,336] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:46,336] [INFO] Task started: HMMsearch
[2024-01-24 15:03:46,336] [INFO] Running command: hmmsearch --tblout GCF_002884445.1_ASM288444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7ebd4d3-ca81-4a57-885a-c95a4cc88ef7/dqc_reference/reference_markers.hmm GCF_002884445.1_ASM288444v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:46,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:46,610] [INFO] Found 6/6 markers.
[2024-01-24 15:03:46,655] [INFO] Query marker FASTA was written to GCF_002884445.1_ASM288444v1_genomic.fna/markers.fasta
[2024-01-24 15:03:46,655] [INFO] Task started: Blastn
[2024-01-24 15:03:46,655] [INFO] Running command: blastn -query GCF_002884445.1_ASM288444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7ebd4d3-ca81-4a57-885a-c95a4cc88ef7/dqc_reference/reference_markers.fasta -out GCF_002884445.1_ASM288444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:47,201] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:47,203] [INFO] Selected 15 target genomes.
[2024-01-24 15:03:47,203] [INFO] Target genome list was writen to GCF_002884445.1_ASM288444v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:47,212] [INFO] Task started: fastANI
[2024-01-24 15:03:47,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg70d1fa47-f2f7-4a01-9e7c-36491a703bb8/GCF_002884445.1_ASM288444v1_genomic.fna.gz --refList GCF_002884445.1_ASM288444v1_genomic.fna/target_genomes.txt --output GCF_002884445.1_ASM288444v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:04,322] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:04,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7ebd4d3-ca81-4a57-885a-c95a4cc88ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:04,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7ebd4d3-ca81-4a57-885a-c95a4cc88ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:04,330] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:04:04,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:04:04,331] [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 castaneae	strain=DSM 19417	GCA_002884445.1	474957	474957	type	True	99.9995	2097	2099	95	conclusive
Paenibacillus castaneae	strain=CECT 7279	GCA_011761405.1	474957	474957	type	True	99.9897	2049	2099	95	conclusive
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	80.0994	653	2099	95	below_threshold
Paenibacillus luteus	strain=R-3	GCA_006542765.1	2545753	2545753	type	True	80.0689	701	2099	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	79.9369	598	2099	95	below_threshold
Paenibacillus paridis	strain=py1325	GCA_006345825.1	2583376	2583376	type	True	79.9067	643	2099	95	below_threshold
Paenibacillus sinopodophylli	strain=CCTCC AB 2016047	GCA_005930355.1	1837342	1837342	type	True	79.7872	548	2099	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	79.7075	649	2099	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	79.1719	546	2099	95	below_threshold
Paenibacillus glucanolyticus	strain=NBRC 15330	GCA_004000885.1	59843	59843	type	True	76.7503	88	2099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:04,332] [INFO] DFAST Taxonomy check result was written to GCF_002884445.1_ASM288444v1_genomic.fna/tc_result.tsv
[2024-01-24 15:04:04,333] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:04,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:04,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7ebd4d3-ca81-4a57-885a-c95a4cc88ef7/dqc_reference/checkm_data
[2024-01-24 15:04:04,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:04,393] [INFO] Task started: CheckM
[2024-01-24 15:04:04,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002884445.1_ASM288444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002884445.1_ASM288444v1_genomic.fna/checkm_input GCF_002884445.1_ASM288444v1_genomic.fna/checkm_result
[2024-01-24 15:04:45,258] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:45,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:45,274] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:45,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:45,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002884445.1_ASM288444v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:45,274] [INFO] Task started: Blastn
[2024-01-24 15:04:45,274] [INFO] Running command: blastn -query GCF_002884445.1_ASM288444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7ebd4d3-ca81-4a57-885a-c95a4cc88ef7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002884445.1_ASM288444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:46,032] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:46,034] [INFO] Selected 16 target genomes.
[2024-01-24 15:04:46,034] [INFO] Target genome list was writen to GCF_002884445.1_ASM288444v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:46,043] [INFO] Task started: fastANI
[2024-01-24 15:04:46,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg70d1fa47-f2f7-4a01-9e7c-36491a703bb8/GCF_002884445.1_ASM288444v1_genomic.fna.gz --refList GCF_002884445.1_ASM288444v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002884445.1_ASM288444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:06,361] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:06,371] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:06,371] [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_002884445.1	s__Paenibacillus_C castaneae	99.9995	2096	2099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001280845.1	s__Paenibacillus_C sp001280845	80.7112	807	2099	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	80.5048	800	2099	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	80.4138	790	2099	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_001428245.1	s__Paenibacillus_C sp001428245	80.4018	688	2099	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	80.3493	807	2099	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	80.292	689	2099	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	80.1004	654	2099	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	80.0793	699	2099	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	79.9151	642	2099	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	79.8117	545	2099	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	79.6972	649	2099	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	79.1665	546	2099	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	78.0028	259	2099	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_009789195.1	s__Paenibacillus_T sp009789195	76.8614	162	2099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000885.1	s__Paenibacillus glucanolyticus	76.7781	87	2099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.37	98.87	0.95	0.92	9	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:06,372] [INFO] GTDB search result was written to GCF_002884445.1_ASM288444v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:06,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:06,375] [INFO] DFAST_QC result json was written to GCF_002884445.1_ASM288444v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:06,376] [INFO] DFAST_QC completed!
[2024-01-24 15:05:06,376] [INFO] Total running time: 0h1m37s