[2024-01-24 13:46:03,735] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg69be7f8f-6966-432a-941e-15e9f42f0f05/dqc_reference
[2024-01-24 13:46:05,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:05,119] [INFO] Task started: Prodigal
[2024-01-24 13:46:05,119] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fbb7c50-d957-4361-b93e-a7c2d35768e9/GCF_014841135.1_ASM1484113v1_genomic.fna.gz | prodigal -d GCF_014841135.1_ASM1484113v1_genomic.fna/cds.fna -a GCF_014841135.1_ASM1484113v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:20,469] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:20,469] [INFO] Task started: HMMsearch
[2024-01-24 13:46:20,469] [INFO] Running command: hmmsearch --tblout GCF_014841135.1_ASM1484113v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69be7f8f-6966-432a-941e-15e9f42f0f05/dqc_reference/reference_markers.hmm GCF_014841135.1_ASM1484113v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:20,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:20,762] [INFO] Found 6/6 markers.
[2024-01-24 13:46:20,816] [INFO] Query marker FASTA was written to GCF_014841135.1_ASM1484113v1_genomic.fna/markers.fasta
[2024-01-24 13:46:20,817] [INFO] Task started: Blastn
[2024-01-24 13:46:20,817] [INFO] Running command: blastn -query GCF_014841135.1_ASM1484113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69be7f8f-6966-432a-941e-15e9f42f0f05/dqc_reference/reference_markers.fasta -out GCF_014841135.1_ASM1484113v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:21,479] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:21,483] [INFO] Selected 23 target genomes.
[2024-01-24 13:46:21,483] [INFO] Target genome list was writen to GCF_014841135.1_ASM1484113v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:21,494] [INFO] Task started: fastANI
[2024-01-24 13:46:21,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fbb7c50-d957-4361-b93e-a7c2d35768e9/GCF_014841135.1_ASM1484113v1_genomic.fna.gz --refList GCF_014841135.1_ASM1484113v1_genomic.fna/target_genomes.txt --output GCF_014841135.1_ASM1484113v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:42,154] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:42,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69be7f8f-6966-432a-941e-15e9f42f0f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:42,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69be7f8f-6966-432a-941e-15e9f42f0f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:42,168] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:42,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:42,169] [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 arenosi	strain=CAU 1523	GCA_014841135.1	2774142	2774142	type	True	100.0	1735	1740	95	conclusive
Paenibacillus assamensis	strain=DSM 18201	GCA_000422445.1	311244	311244	type	True	93.4063	1473	1740	95	below_threshold
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_007066085.1	49283	49283	type	True	78.7843	133	1740	95	below_threshold
Paenibacillus aquistagni	strain=11	GCA_900177815.1	1852522	1852522	type	True	78.6399	190	1740	95	below_threshold
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_002161855.1	49283	49283	type	True	78.4811	130	1740	95	below_threshold
Paenibacillus taiwanensis	strain=DSM 18679	GCA_000425125.1	401638	401638	type	True	78.0728	204	1740	95	below_threshold
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	77.3734	72	1740	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	77.1619	76	1740	95	below_threshold
Paenibacillus catalpae	strain=CGMCC 1.10784	GCA_900112695.1	1045775	1045775	type	True	77.0867	53	1740	95	below_threshold
Paenibacillus hunanensis	strain=CGMCC 1.8907	GCA_014645615.1	539262	539262	type	True	77.0634	54	1740	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	76.7714	69	1740	95	below_threshold
Paenibacillus castaneae	strain=DSM 19417	GCA_002884445.1	474957	474957	type	True	76.7264	62	1740	95	below_threshold
Paenibacillus ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	76.6356	62	1740	95	below_threshold
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	76.6355	70	1740	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	76.5153	84	1740	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:42,173] [INFO] DFAST Taxonomy check result was written to GCF_014841135.1_ASM1484113v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:42,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:42,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:42,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69be7f8f-6966-432a-941e-15e9f42f0f05/dqc_reference/checkm_data
[2024-01-24 13:46:42,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:42,233] [INFO] Task started: CheckM
[2024-01-24 13:46:42,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014841135.1_ASM1484113v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014841135.1_ASM1484113v1_genomic.fna/checkm_input GCF_014841135.1_ASM1484113v1_genomic.fna/checkm_result
[2024-01-24 13:47:29,987] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:29,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:30,011] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:30,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:30,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014841135.1_ASM1484113v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:30,012] [INFO] Task started: Blastn
[2024-01-24 13:47:30,012] [INFO] Running command: blastn -query GCF_014841135.1_ASM1484113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69be7f8f-6966-432a-941e-15e9f42f0f05/dqc_reference/reference_markers_gtdb.fasta -out GCF_014841135.1_ASM1484113v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:30,761] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:30,764] [INFO] Selected 16 target genomes.
[2024-01-24 13:47:30,764] [INFO] Target genome list was writen to GCF_014841135.1_ASM1484113v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:30,778] [INFO] Task started: fastANI
[2024-01-24 13:47:30,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fbb7c50-d957-4361-b93e-a7c2d35768e9/GCF_014841135.1_ASM1484113v1_genomic.fna.gz --refList GCF_014841135.1_ASM1484113v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014841135.1_ASM1484113v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:46,423] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:46,435] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:46,435] [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_014841135.1	s__Paenibacillus_B sp014841135	100.0	1735	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000422445.1	s__Paenibacillus_B assamensis	93.4009	1474	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007786455.1	s__Paenibacillus_B sp007786455	88.6457	1472	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000245555.1	s__Paenibacillus_B dendritiformis_A	78.1954	112	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	97.57	96.94	0.92	0.90	3	-
GCF_000425125.1	s__Paenibacillus_B taiwanensis	78.0847	202	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894745.1	s__Paenibacillus_B sp001894745	77.9816	182	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	96.43	95.29	0.89	0.85	9	-
GCF_000283315.1	s__Paenibacillus_B sp000283315	77.7105	166	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758585.1	s__Paenibacillus sp000758585	77.5125	68	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.21	98.21	0.91	0.91	2	-
GCF_018403285.1	s__Paenibacillus sp018403285	77.4264	53	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758725.1	s__Paenibacillus odorifer	77.3714	74	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.05	97.01	0.93	0.91	32	-
GCF_000758545.1	s__Paenibacillus sp000758545	77.2628	70	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.87	97.65	0.91	0.90	4	-
GCF_003952225.1	s__Paenibacillus_Z albus	77.1637	75	1740	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_900112695.1	s__Paenibacillus_C catalpae	77.0867	53	1740	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_009870785.1	s__Paenibacillus sp009870785	76.518	55	1740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:46,437] [INFO] GTDB search result was written to GCF_014841135.1_ASM1484113v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:46,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:46,442] [INFO] DFAST_QC result json was written to GCF_014841135.1_ASM1484113v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:46,442] [INFO] DFAST_QC completed!
[2024-01-24 13:47:46,442] [INFO] Total running time: 0h1m43s