[2024-01-24 12:15:04,015] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,019] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg6693cd56-41d8-47db-beac-633dcaa8b4f7/dqc_reference
[2024-01-24 12:15:05,334] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,335] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,335] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfddf631-bb47-4f28-96b1-984383341481/GCF_016458235.1_ASM1645823v1_genomic.fna.gz | prodigal -d GCF_016458235.1_ASM1645823v1_genomic.fna/cds.fna -a GCF_016458235.1_ASM1645823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:19,780] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:19,780] [INFO] Task started: HMMsearch
[2024-01-24 12:15:19,780] [INFO] Running command: hmmsearch --tblout GCF_016458235.1_ASM1645823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6693cd56-41d8-47db-beac-633dcaa8b4f7/dqc_reference/reference_markers.hmm GCF_016458235.1_ASM1645823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:20,072] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:20,074] [INFO] Found 6/6 markers.
[2024-01-24 12:15:20,116] [INFO] Query marker FASTA was written to GCF_016458235.1_ASM1645823v1_genomic.fna/markers.fasta
[2024-01-24 12:15:20,116] [INFO] Task started: Blastn
[2024-01-24 12:15:20,116] [INFO] Running command: blastn -query GCF_016458235.1_ASM1645823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6693cd56-41d8-47db-beac-633dcaa8b4f7/dqc_reference/reference_markers.fasta -out GCF_016458235.1_ASM1645823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:20,774] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:20,778] [INFO] Selected 5 target genomes.
[2024-01-24 12:15:20,778] [INFO] Target genome list was writen to GCF_016458235.1_ASM1645823v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:20,781] [INFO] Task started: fastANI
[2024-01-24 12:15:20,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfddf631-bb47-4f28-96b1-984383341481/GCF_016458235.1_ASM1645823v1_genomic.fna.gz --refList GCF_016458235.1_ASM1645823v1_genomic.fna/target_genomes.txt --output GCF_016458235.1_ASM1645823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:28,543] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:28,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6693cd56-41d8-47db-beac-633dcaa8b4f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:28,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6693cd56-41d8-47db-beac-633dcaa8b4f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:28,550] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:28,550] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:28,551] [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
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	100.0	1643	1646	95	conclusive
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	89.059	1321	1646	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	89.0504	1293	1646	95	below_threshold
Geomonas agri	strain=RG53	GCA_020179605.1	2873702	2873702	type	True	88.7366	1269	1646	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	88.7048	1317	1646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,552] [INFO] DFAST Taxonomy check result was written to GCF_016458235.1_ASM1645823v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:28,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:28,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:28,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6693cd56-41d8-47db-beac-633dcaa8b4f7/dqc_reference/checkm_data
[2024-01-24 12:15:28,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:28,605] [INFO] Task started: CheckM
[2024-01-24 12:15:28,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016458235.1_ASM1645823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016458235.1_ASM1645823v1_genomic.fna/checkm_input GCF_016458235.1_ASM1645823v1_genomic.fna/checkm_result
[2024-01-24 12:16:10,694] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:10,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:10,716] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:10,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:10,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016458235.1_ASM1645823v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:10,717] [INFO] Task started: Blastn
[2024-01-24 12:16:10,717] [INFO] Running command: blastn -query GCF_016458235.1_ASM1645823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6693cd56-41d8-47db-beac-633dcaa8b4f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_016458235.1_ASM1645823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:11,692] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:11,696] [INFO] Selected 6 target genomes.
[2024-01-24 12:16:11,696] [INFO] Target genome list was writen to GCF_016458235.1_ASM1645823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:11,700] [INFO] Task started: fastANI
[2024-01-24 12:16:11,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfddf631-bb47-4f28-96b1-984383341481/GCF_016458235.1_ASM1645823v1_genomic.fna.gz --refList GCF_016458235.1_ASM1645823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016458235.1_ASM1645823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:20,014] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:20,020] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:20,020] [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_016458235.1	s__Geomonas propionica	100.0	1643	1646	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018919395.1	s__Geomonas sp018919395	89.0479	1322	1646	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193585.1	s__Geomonas paludis	89.0397	1294	1646	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016458305.1	s__Geomonas anaerohicana	88.6941	1318	1646	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018986935.1	s__Geomonas sp018986935	88.0143	1257	1646	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.24	99.10	0.94	0.94	3	-
GCF_018986915.1	s__Geomonas sp018986915	87.8679	1280	1646	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:20,022] [INFO] GTDB search result was written to GCF_016458235.1_ASM1645823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:20,022] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:20,025] [INFO] DFAST_QC result json was written to GCF_016458235.1_ASM1645823v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:20,025] [INFO] DFAST_QC completed!
[2024-01-24 12:16:20,025] [INFO] Total running time: 0h1m16s