[2024-01-24 11:48:21,289] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,327] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg362f2927-0154-4f5d-9f0f-9b9b86f589cf/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,567] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d9ad34f-d471-4836-90ca-6a37418e1685/GCF_014651675.1_ASM1465167v1_genomic.fna.gz | prodigal -d GCF_014651675.1_ASM1465167v1_genomic.fna/cds.fna -a GCF_014651675.1_ASM1465167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:57,095] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:57,095] [INFO] Task started: HMMsearch
[2024-01-24 11:48:57,095] [INFO] Running command: hmmsearch --tblout GCF_014651675.1_ASM1465167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg362f2927-0154-4f5d-9f0f-9b9b86f589cf/dqc_reference/reference_markers.hmm GCF_014651675.1_ASM1465167v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:57,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:57,385] [INFO] Found 6/6 markers.
[2024-01-24 11:48:57,428] [INFO] Query marker FASTA was written to GCF_014651675.1_ASM1465167v1_genomic.fna/markers.fasta
[2024-01-24 11:48:57,428] [INFO] Task started: Blastn
[2024-01-24 11:48:57,428] [INFO] Running command: blastn -query GCF_014651675.1_ASM1465167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg362f2927-0154-4f5d-9f0f-9b9b86f589cf/dqc_reference/reference_markers.fasta -out GCF_014651675.1_ASM1465167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:58,003] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:58,010] [INFO] Selected 20 target genomes.
[2024-01-24 11:48:58,010] [INFO] Target genome list was writen to GCF_014651675.1_ASM1465167v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:58,024] [INFO] Task started: fastANI
[2024-01-24 11:48:58,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d9ad34f-d471-4836-90ca-6a37418e1685/GCF_014651675.1_ASM1465167v1_genomic.fna.gz --refList GCF_014651675.1_ASM1465167v1_genomic.fna/target_genomes.txt --output GCF_014651675.1_ASM1465167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:49:13,996] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:13,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg362f2927-0154-4f5d-9f0f-9b9b86f589cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:49:13,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg362f2927-0154-4f5d-9f0f-9b9b86f589cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:49:14,006] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:49:14,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:49:14,006] [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
Roseibacillus persicicus	strain=KCTC 12988	GCA_014651675.1	454148	454148	type	True	100.0	1718	1719	95	conclusive
Roseibacillus ishigakijimensis	strain=KCTC 12986	GCA_016595415.1	454146	454146	type	True	78.0062	364	1719	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.4933	73	1719	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.1898	65	1719	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	76.1324	65	1719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:49:14,007] [INFO] DFAST Taxonomy check result was written to GCF_014651675.1_ASM1465167v1_genomic.fna/tc_result.tsv
[2024-01-24 11:49:14,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:49:14,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:49:14,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg362f2927-0154-4f5d-9f0f-9b9b86f589cf/dqc_reference/checkm_data
[2024-01-24 11:49:14,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:49:14,060] [INFO] Task started: CheckM
[2024-01-24 11:49:14,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651675.1_ASM1465167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651675.1_ASM1465167v1_genomic.fna/checkm_input GCF_014651675.1_ASM1465167v1_genomic.fna/checkm_result
[2024-01-24 11:50:42,054] [INFO] Task succeeded: CheckM
[2024-01-24 11:50:42,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:50:42,081] [INFO] ===== Completeness check finished =====
[2024-01-24 11:50:42,082] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:50:42,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651675.1_ASM1465167v1_genomic.fna/markers.fasta)
[2024-01-24 11:50:42,084] [INFO] Task started: Blastn
[2024-01-24 11:50:42,084] [INFO] Running command: blastn -query GCF_014651675.1_ASM1465167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg362f2927-0154-4f5d-9f0f-9b9b86f589cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651675.1_ASM1465167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:50:42,857] [INFO] Task succeeded: Blastn
[2024-01-24 11:50:42,862] [INFO] Selected 25 target genomes.
[2024-01-24 11:50:42,862] [INFO] Target genome list was writen to GCF_014651675.1_ASM1465167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:50:42,881] [INFO] Task started: fastANI
[2024-01-24 11:50:42,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d9ad34f-d471-4836-90ca-6a37418e1685/GCF_014651675.1_ASM1465167v1_genomic.fna.gz --refList GCF_014651675.1_ASM1465167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651675.1_ASM1465167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:00,329] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:00,342] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:00,343] [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_014651675.1	s__Roseibacillus persicicus	100.0	1718	1719	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016595415.1	s__Roseibacillus ishigakijimensis	78.0062	364	1719	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182405.1	s__SW10 sp905182405	76.8768	55	1719	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222765.1	s__SW10 sp018222765	76.6694	58	1719	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595525.1	s__Haloferula rosea	76.4933	73	1719	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478925.1	s__Luteolibacter sp905478925	76.1074	50	1719	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	97.95	97.95	0.92	0.92	2	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	75.9369	68	1719	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:00,344] [INFO] GTDB search result was written to GCF_014651675.1_ASM1465167v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:00,345] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:00,348] [INFO] DFAST_QC result json was written to GCF_014651675.1_ASM1465167v1_genomic.fna/dqc_result.json
[2024-01-24 11:51:00,349] [INFO] DFAST_QC completed!
[2024-01-24 11:51:00,349] [INFO] Total running time: 0h2m39s