[2024-01-24 13:37:40,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:40,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:40,060] [INFO] DQC Reference Directory: /var/lib/cwl/stge8e07bb6-fa3e-46cf-a663-bb035b303cf9/dqc_reference
[2024-01-24 13:37:41,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:41,201] [INFO] Task started: Prodigal
[2024-01-24 13:37:41,201] [INFO] Running command: gunzip -c /var/lib/cwl/stg12bca03f-2951-4389-be05-6fa62e4d3056/GCF_014212175.1_ASM1421217v1_genomic.fna.gz | prodigal -d GCF_014212175.1_ASM1421217v1_genomic.fna/cds.fna -a GCF_014212175.1_ASM1421217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:57,138] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:57,138] [INFO] Task started: HMMsearch
[2024-01-24 13:37:57,138] [INFO] Running command: hmmsearch --tblout GCF_014212175.1_ASM1421217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8e07bb6-fa3e-46cf-a663-bb035b303cf9/dqc_reference/reference_markers.hmm GCF_014212175.1_ASM1421217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:57,468] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:57,469] [INFO] Found 6/6 markers.
[2024-01-24 13:37:57,523] [INFO] Query marker FASTA was written to GCF_014212175.1_ASM1421217v1_genomic.fna/markers.fasta
[2024-01-24 13:37:57,523] [INFO] Task started: Blastn
[2024-01-24 13:37:57,524] [INFO] Running command: blastn -query GCF_014212175.1_ASM1421217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8e07bb6-fa3e-46cf-a663-bb035b303cf9/dqc_reference/reference_markers.fasta -out GCF_014212175.1_ASM1421217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:58,188] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:58,190] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:58,191] [INFO] Target genome list was writen to GCF_014212175.1_ASM1421217v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:58,195] [INFO] Task started: fastANI
[2024-01-24 13:37:58,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg12bca03f-2951-4389-be05-6fa62e4d3056/GCF_014212175.1_ASM1421217v1_genomic.fna.gz --refList GCF_014212175.1_ASM1421217v1_genomic.fna/target_genomes.txt --output GCF_014212175.1_ASM1421217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:15,451] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:15,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8e07bb6-fa3e-46cf-a663-bb035b303cf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:15,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8e07bb6-fa3e-46cf-a663-bb035b303cf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:15,461] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:15,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:15,461] [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 xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	100.0	2345	2356	95	conclusive
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	82.0995	964	2356	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	80.9826	748	2356	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	80.9419	771	2356	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	80.57	880	2356	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	79.9465	874	2356	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	79.7732	778	2356	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	78.1402	472	2356	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	78.1241	491	2356	95	below_threshold
Paenibacillus pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	78.1174	486	2356	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.8166	552	2356	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.3925	197	2356	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.3436	131	2356	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.1909	138	2356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:15,466] [INFO] DFAST Taxonomy check result was written to GCF_014212175.1_ASM1421217v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:15,467] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:15,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:15,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8e07bb6-fa3e-46cf-a663-bb035b303cf9/dqc_reference/checkm_data
[2024-01-24 13:38:15,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:15,536] [INFO] Task started: CheckM
[2024-01-24 13:38:15,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014212175.1_ASM1421217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014212175.1_ASM1421217v1_genomic.fna/checkm_input GCF_014212175.1_ASM1421217v1_genomic.fna/checkm_result
[2024-01-24 13:38:58,919] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:58,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:58,937] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:58,937] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:58,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014212175.1_ASM1421217v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:58,937] [INFO] Task started: Blastn
[2024-01-24 13:38:58,937] [INFO] Running command: blastn -query GCF_014212175.1_ASM1421217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8e07bb6-fa3e-46cf-a663-bb035b303cf9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014212175.1_ASM1421217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:59,909] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:59,912] [INFO] Selected 10 target genomes.
[2024-01-24 13:38:59,912] [INFO] Target genome list was writen to GCF_014212175.1_ASM1421217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:59,918] [INFO] Task started: fastANI
[2024-01-24 13:38:59,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg12bca03f-2951-4389-be05-6fa62e4d3056/GCF_014212175.1_ASM1421217v1_genomic.fna.gz --refList GCF_014212175.1_ASM1421217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014212175.1_ASM1421217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:14,335] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:14,342] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:14,342] [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_014212175.1	s__Cohnella xylanilytica	100.0	2345	2356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	conclusive
GCF_000429825.1	s__Cohnella thermotolerans	82.1267	960	2356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212015.1	s__Cohnella lubricantis	80.9828	748	2356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014212135.1	s__Cohnella thailandensis	80.6135	908	2356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014212055.1	s__Cohnella zeiphila	80.5643	881	2356	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	79.9365	876	2356	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	79.8292	769	2356	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	79.773	778	2356	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	79.2271	717	2356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003851045.1	s__Paenibacillus_D sp003851045	77.167	320	2356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:14,343] [INFO] GTDB search result was written to GCF_014212175.1_ASM1421217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:14,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:14,346] [INFO] DFAST_QC result json was written to GCF_014212175.1_ASM1421217v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:14,347] [INFO] DFAST_QC completed!
[2024-01-24 13:39:14,347] [INFO] Total running time: 0h1m34s