[2024-01-24 13:46:10,797] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:10,799] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:10,799] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9ba7752-ea3e-4c27-bf90-91f773c93702/dqc_reference
[2024-01-24 13:46:12,234] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:12,235] [INFO] Task started: Prodigal
[2024-01-24 13:46:12,235] [INFO] Running command: gunzip -c /var/lib/cwl/stg29545c42-109c-4cb7-b8ad-6bc96bf1d211/GCF_014212015.1_ASM1421201v1_genomic.fna.gz | prodigal -d GCF_014212015.1_ASM1421201v1_genomic.fna/cds.fna -a GCF_014212015.1_ASM1421201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:24,928] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:24,929] [INFO] Task started: HMMsearch
[2024-01-24 13:46:24,929] [INFO] Running command: hmmsearch --tblout GCF_014212015.1_ASM1421201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9ba7752-ea3e-4c27-bf90-91f773c93702/dqc_reference/reference_markers.hmm GCF_014212015.1_ASM1421201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:25,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:25,292] [INFO] Found 6/6 markers.
[2024-01-24 13:46:25,344] [INFO] Query marker FASTA was written to GCF_014212015.1_ASM1421201v1_genomic.fna/markers.fasta
[2024-01-24 13:46:25,345] [INFO] Task started: Blastn
[2024-01-24 13:46:25,345] [INFO] Running command: blastn -query GCF_014212015.1_ASM1421201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9ba7752-ea3e-4c27-bf90-91f773c93702/dqc_reference/reference_markers.fasta -out GCF_014212015.1_ASM1421201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:25,999] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:26,002] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:26,002] [INFO] Target genome list was writen to GCF_014212015.1_ASM1421201v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:26,008] [INFO] Task started: fastANI
[2024-01-24 13:46:26,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg29545c42-109c-4cb7-b8ad-6bc96bf1d211/GCF_014212015.1_ASM1421201v1_genomic.fna.gz --refList GCF_014212015.1_ASM1421201v1_genomic.fna/target_genomes.txt --output GCF_014212015.1_ASM1421201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:42,501] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:42,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9ba7752-ea3e-4c27-bf90-91f773c93702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:42,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9ba7752-ea3e-4c27-bf90-91f773c93702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:42,514] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:42,515] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:42,515] [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
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	100.0	1420	1430	95	conclusive
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	99.9901	1422	1430	95	conclusive
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	81.1409	742	1430	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	80.6608	674	1430	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	79.8533	562	1430	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	79.6044	535	1430	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	79.3006	507	1430	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.9579	311	1430	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.681	331	1430	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.3091	156	1430	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	77.2878	263	1430	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	77.1917	187	1430	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	76.9012	151	1430	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.6731	131	1430	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:42,517] [INFO] DFAST Taxonomy check result was written to GCF_014212015.1_ASM1421201v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:42,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:42,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:42,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9ba7752-ea3e-4c27-bf90-91f773c93702/dqc_reference/checkm_data
[2024-01-24 13:46:42,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:42,571] [INFO] Task started: CheckM
[2024-01-24 13:46:42,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014212015.1_ASM1421201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014212015.1_ASM1421201v1_genomic.fna/checkm_input GCF_014212015.1_ASM1421201v1_genomic.fna/checkm_result
[2024-01-24 13:47:19,882] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:19,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:19,901] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:19,901] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:19,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014212015.1_ASM1421201v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:19,902] [INFO] Task started: Blastn
[2024-01-24 13:47:19,902] [INFO] Running command: blastn -query GCF_014212015.1_ASM1421201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9ba7752-ea3e-4c27-bf90-91f773c93702/dqc_reference/reference_markers_gtdb.fasta -out GCF_014212015.1_ASM1421201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:20,798] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:20,802] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:20,803] [INFO] Target genome list was writen to GCF_014212015.1_ASM1421201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:20,814] [INFO] Task started: fastANI
[2024-01-24 13:47:20,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg29545c42-109c-4cb7-b8ad-6bc96bf1d211/GCF_014212015.1_ASM1421201v1_genomic.fna.gz --refList GCF_014212015.1_ASM1421201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014212015.1_ASM1421201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:32,407] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:32,420] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:32,420] [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_014212015.1	s__Cohnella lubricantis	100.0	1420	1430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_014212175.1	s__Cohnella xylanilytica	81.1589	740	1430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_000429825.1	s__Cohnella thermotolerans	80.664	674	1430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212055.1	s__Cohnella zeiphila	79.8441	563	1430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801405.1	s__Cohnella sp004801405	79.6138	534	1430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212125.1	s__Cohnella nanjingensis	79.3103	506	1430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990975.1	s__Cohnella sp003990975	79.2035	518	1430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208555.1	s__Cohnella sp003208555	78.4834	450	1430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008124765.1	s__Paenibacillus_Z methanolicus	77.2988	262	1430	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:32,422] [INFO] GTDB search result was written to GCF_014212015.1_ASM1421201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:32,423] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:32,427] [INFO] DFAST_QC result json was written to GCF_014212015.1_ASM1421201v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:32,427] [INFO] DFAST_QC completed!
[2024-01-24 13:47:32,428] [INFO] Total running time: 0h1m22s