[2024-01-24 13:17:58,777] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:58,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:58,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg480b5a18-a931-4720-9ad3-36fc626f95e2/dqc_reference
[2024-01-24 13:18:00,035] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:00,043] [INFO] Task started: Prodigal
[2024-01-24 13:18:00,043] [INFO] Running command: gunzip -c /var/lib/cwl/stge2106621-c9d3-4c32-b642-032bb79b6895/GCF_008369015.1_ASM836901v1_genomic.fna.gz | prodigal -d GCF_008369015.1_ASM836901v1_genomic.fna/cds.fna -a GCF_008369015.1_ASM836901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:12,095] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:12,096] [INFO] Task started: HMMsearch
[2024-01-24 13:18:12,097] [INFO] Running command: hmmsearch --tblout GCF_008369015.1_ASM836901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg480b5a18-a931-4720-9ad3-36fc626f95e2/dqc_reference/reference_markers.hmm GCF_008369015.1_ASM836901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:12,412] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:12,413] [INFO] Found 6/6 markers.
[2024-01-24 13:18:12,448] [INFO] Query marker FASTA was written to GCF_008369015.1_ASM836901v1_genomic.fna/markers.fasta
[2024-01-24 13:18:12,449] [INFO] Task started: Blastn
[2024-01-24 13:18:12,449] [INFO] Running command: blastn -query GCF_008369015.1_ASM836901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg480b5a18-a931-4720-9ad3-36fc626f95e2/dqc_reference/reference_markers.fasta -out GCF_008369015.1_ASM836901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:13,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:13,178] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:13,178] [INFO] Target genome list was writen to GCF_008369015.1_ASM836901v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:13,188] [INFO] Task started: fastANI
[2024-01-24 13:18:13,188] [INFO] Running command: fastANI --query /var/lib/cwl/stge2106621-c9d3-4c32-b642-032bb79b6895/GCF_008369015.1_ASM836901v1_genomic.fna.gz --refList GCF_008369015.1_ASM836901v1_genomic.fna/target_genomes.txt --output GCF_008369015.1_ASM836901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:22,702] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:22,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg480b5a18-a931-4720-9ad3-36fc626f95e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:22,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg480b5a18-a931-4720-9ad3-36fc626f95e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:22,711] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:22,712] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:18:22,712] [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 rubra	strain=Red88	GCA_008369015.1	2509454	2509454	type	True	100.0	1253	1254	95	inconclusive
Oryzomonas japonica	strain=Red96	GCA_008802365.1	2603858	2603858	type	True	96.066	1028	1254	95	inconclusive
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	95.1533	1029	1254	95	inconclusive
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	78.8747	378	1254	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	77.7913	269	1254	95	below_threshold
Geomonas agri	strain=RG53	GCA_020179605.1	2873702	2873702	type	True	77.4838	245	1254	95	below_threshold
Geomonas silvestris	strain=Red330	GCA_014193515.1	2740184	2740184	type	True	77.4562	299	1254	95	below_threshold
Trichlorobacter lovleyi	strain=SZ	GCA_000020385.1	313985	313985	type	True	77.4013	209	1254	95	below_threshold
Geobacter chapellei	strain=DSM 13688	GCA_018531195.1	44671	44671	type	True	77.1216	195	1254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:22,714] [INFO] DFAST Taxonomy check result was written to GCF_008369015.1_ASM836901v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:22,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:22,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:22,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg480b5a18-a931-4720-9ad3-36fc626f95e2/dqc_reference/checkm_data
[2024-01-24 13:18:22,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:22,764] [INFO] Task started: CheckM
[2024-01-24 13:18:22,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008369015.1_ASM836901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008369015.1_ASM836901v1_genomic.fna/checkm_input GCF_008369015.1_ASM836901v1_genomic.fna/checkm_result
[2024-01-24 13:19:00,512] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:00,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:00,530] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:00,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:00,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008369015.1_ASM836901v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:00,531] [INFO] Task started: Blastn
[2024-01-24 13:19:00,531] [INFO] Running command: blastn -query GCF_008369015.1_ASM836901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg480b5a18-a931-4720-9ad3-36fc626f95e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_008369015.1_ASM836901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:01,716] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:01,719] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:01,720] [INFO] Target genome list was writen to GCF_008369015.1_ASM836901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:01,748] [INFO] Task started: fastANI
[2024-01-24 13:19:01,748] [INFO] Running command: fastANI --query /var/lib/cwl/stge2106621-c9d3-4c32-b642-032bb79b6895/GCF_008369015.1_ASM836901v1_genomic.fna.gz --refList GCF_008369015.1_ASM836901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008369015.1_ASM836901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:10,086] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:10,095] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:19:10,095] [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_008802365.1	s__Oryzomonas japonica	96.066	1028	1254	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	96.07	96.07	0.87	0.87	2	inconclusive
GCF_008802355.1	s__Oryzomonas sagensis	95.1533	1029	1254	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_008330225.1	s__Oryzomonas sp008330225	88.9336	955	1254	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151775.1	s__Oryzomonas sp003151775	85.1383	569	1254	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182975.1	s__JACPFJ01 sp016182975	80.4407	369	1254	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015688915.1	s__JACPFJ01 sp015688915	80.3908	391	1254	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298925.1	s__Pelotalea sp002298925	79.0809	378	1254	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	78.8833	378	1254	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pseudopelobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720395.1	s__CAIPTY01 sp016720395	78.6049	329	1254	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__CAIPTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383415.1	s__Trichlorobacter sp002383415	77.87	228	1254	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:10,097] [INFO] GTDB search result was written to GCF_008369015.1_ASM836901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:10,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:10,101] [INFO] DFAST_QC result json was written to GCF_008369015.1_ASM836901v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:10,102] [INFO] DFAST_QC completed!
[2024-01-24 13:19:10,102] [INFO] Total running time: 0h1m11s