[2023-06-28 14:40:11,343] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:40:11,344] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:40:11,344] [INFO] DQC Reference Directory: /var/lib/cwl/stgf94a8db9-7810-46fa-aaa5-3d1879383fd1/dqc_reference
[2023-06-28 14:40:12,444] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:40:12,445] [INFO] Task started: Prodigal
[2023-06-28 14:40:12,445] [INFO] Running command: gunzip -c /var/lib/cwl/stge9a7b424-d56e-4908-98de-7127ea6d963a/GCA_027404025.1_ASM2740402v1_genomic.fna.gz | prodigal -d GCA_027404025.1_ASM2740402v1_genomic.fna/cds.fna -a GCA_027404025.1_ASM2740402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:40:19,233] [INFO] Task succeeded: Prodigal
[2023-06-28 14:40:19,233] [INFO] Task started: HMMsearch
[2023-06-28 14:40:19,233] [INFO] Running command: hmmsearch --tblout GCA_027404025.1_ASM2740402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf94a8db9-7810-46fa-aaa5-3d1879383fd1/dqc_reference/reference_markers.hmm GCA_027404025.1_ASM2740402v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:40:19,408] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:40:19,409] [INFO] Found 6/6 markers.
[2023-06-28 14:40:19,434] [INFO] Query marker FASTA was written to GCA_027404025.1_ASM2740402v1_genomic.fna/markers.fasta
[2023-06-28 14:40:19,434] [INFO] Task started: Blastn
[2023-06-28 14:40:19,434] [INFO] Running command: blastn -query GCA_027404025.1_ASM2740402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf94a8db9-7810-46fa-aaa5-3d1879383fd1/dqc_reference/reference_markers.fasta -out GCA_027404025.1_ASM2740402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:40:20,063] [INFO] Task succeeded: Blastn
[2023-06-28 14:40:20,067] [INFO] Selected 15 target genomes.
[2023-06-28 14:40:20,067] [INFO] Target genome list was writen to GCA_027404025.1_ASM2740402v1_genomic.fna/target_genomes.txt
[2023-06-28 14:40:20,069] [INFO] Task started: fastANI
[2023-06-28 14:40:20,070] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a7b424-d56e-4908-98de-7127ea6d963a/GCA_027404025.1_ASM2740402v1_genomic.fna.gz --refList GCA_027404025.1_ASM2740402v1_genomic.fna/target_genomes.txt --output GCA_027404025.1_ASM2740402v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:40:29,396] [INFO] Task succeeded: fastANI
[2023-06-28 14:40:29,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf94a8db9-7810-46fa-aaa5-3d1879383fd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:40:29,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf94a8db9-7810-46fa-aaa5-3d1879383fd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:40:29,403] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:40:29,403] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:40:29,403] [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
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	80.0826	334	696	95	below_threshold
Oryzomonas japonica	strain=Red96	GCA_008802365.1	2603858	2603858	type	True	79.9944	319	696	95	below_threshold
Oryzomonas rubra	strain=Red88	GCA_008369015.1	2509454	2509454	type	True	79.8449	323	696	95	below_threshold
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	79.0039	250	696	95	below_threshold
Geomonas limicola	strain=Red745	GCA_014193675.1	2740186	2740186	type	True	77.8983	169	696	95	below_threshold
Geobacter soli	strain=GSS01	GCA_000816575.1	1510391	1510391	type	True	77.5161	157	696	95	below_threshold
Geobacter chapellei	strain=DSM 13688	GCA_018531195.1	44671	44671	type	True	77.0928	97	696	95	below_threshold
Desulfuromonas soudanensis	strain=WTL	GCA_001278055.1	1603606	1603606	type	True	76.7221	76	696	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:40:29,405] [INFO] DFAST Taxonomy check result was written to GCA_027404025.1_ASM2740402v1_genomic.fna/tc_result.tsv
[2023-06-28 14:40:29,406] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:40:29,406] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:40:29,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf94a8db9-7810-46fa-aaa5-3d1879383fd1/dqc_reference/checkm_data
[2023-06-28 14:40:29,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:40:29,439] [INFO] Task started: CheckM
[2023-06-28 14:40:29,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027404025.1_ASM2740402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027404025.1_ASM2740402v1_genomic.fna/checkm_input GCA_027404025.1_ASM2740402v1_genomic.fna/checkm_result
[2023-06-28 14:40:53,108] [INFO] Task succeeded: CheckM
[2023-06-28 14:40:53,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 14:40:53,130] [INFO] ===== Completeness check finished =====
[2023-06-28 14:40:53,131] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:40:53,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027404025.1_ASM2740402v1_genomic.fna/markers.fasta)
[2023-06-28 14:40:53,132] [INFO] Task started: Blastn
[2023-06-28 14:40:53,132] [INFO] Running command: blastn -query GCA_027404025.1_ASM2740402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf94a8db9-7810-46fa-aaa5-3d1879383fd1/dqc_reference/reference_markers_gtdb.fasta -out GCA_027404025.1_ASM2740402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:40:54,202] [INFO] Task succeeded: Blastn
[2023-06-28 14:40:54,205] [INFO] Selected 16 target genomes.
[2023-06-28 14:40:54,205] [INFO] Target genome list was writen to GCA_027404025.1_ASM2740402v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:40:54,212] [INFO] Task started: fastANI
[2023-06-28 14:40:54,212] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a7b424-d56e-4908-98de-7127ea6d963a/GCA_027404025.1_ASM2740402v1_genomic.fna.gz --refList GCA_027404025.1_ASM2740402v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027404025.1_ASM2740402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:41:03,515] [INFO] Task succeeded: fastANI
[2023-06-28 14:41:03,525] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 14:41:03,526] [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
GCA_015688915.1	s__JACPFJ01 sp015688915	82.5789	330	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182975.1	s__JACPFJ01 sp016182975	82.1878	291	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008330225.1	s__Oryzomonas sp008330225	80.3619	352	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802355.1	s__Oryzomonas sagensis	80.0997	333	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802365.1	s__Oryzomonas japonica	79.9788	319	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	96.07	96.07	0.87	0.87	2	-
GCA_003151775.1	s__Oryzomonas sp003151775	79.3915	253	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298925.1	s__Pelotalea sp002298925	79.0208	249	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015045.1	s__Pseudopelobacter propionicus	79.0034	250	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pseudopelobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865365.1	s__Pelotalea sp012556225	78.9905	278	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea	95.0	99.99	99.99	1.00	1.00	2	-
GCA_003574895.1	s__JACPFJ01 sp003574895	78.9116	274	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650295.1	s__CAIPTY01 sp016650295	78.5385	261	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__CAIPTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720395.1	s__CAIPTY01 sp016720395	78.3855	215	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__CAIPTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002424705.1	s__Trichlorobacter sp002424705	78.1442	110	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383415.1	s__Trichlorobacter sp002383415	78.1079	144	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380135.1	s__JACRCG01 sp014380135	78.0562	145	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026855.1	s__VEOV01 sp012026855	77.3973	72	696	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__VEOV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:41:03,527] [INFO] GTDB search result was written to GCA_027404025.1_ASM2740402v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:41:03,527] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:41:03,530] [INFO] DFAST_QC result json was written to GCA_027404025.1_ASM2740402v1_genomic.fna/dqc_result.json
[2023-06-28 14:41:03,530] [INFO] DFAST_QC completed!
[2023-06-28 14:41:03,530] [INFO] Total running time: 0h0m52s