[2024-01-25 19:47:20,421] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,422] [INFO] DQC Reference Directory: /var/lib/cwl/stg690e95f4-993f-41ee-9fb8-1163982bfd90/dqc_reference
[2024-01-25 19:47:21,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,639] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg03c6f535-5d31-44b1-aca6-70417a5c2826/GCF_009856625.1_ASM985662v1_genomic.fna.gz | prodigal -d GCF_009856625.1_ASM985662v1_genomic.fna/cds.fna -a GCF_009856625.1_ASM985662v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:35,087] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:35,087] [INFO] Task started: HMMsearch
[2024-01-25 19:47:35,087] [INFO] Running command: hmmsearch --tblout GCF_009856625.1_ASM985662v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg690e95f4-993f-41ee-9fb8-1163982bfd90/dqc_reference/reference_markers.hmm GCF_009856625.1_ASM985662v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:35,367] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:35,369] [INFO] Found 6/6 markers.
[2024-01-25 19:47:35,415] [INFO] Query marker FASTA was written to GCF_009856625.1_ASM985662v1_genomic.fna/markers.fasta
[2024-01-25 19:47:35,416] [INFO] Task started: Blastn
[2024-01-25 19:47:35,416] [INFO] Running command: blastn -query GCF_009856625.1_ASM985662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg690e95f4-993f-41ee-9fb8-1163982bfd90/dqc_reference/reference_markers.fasta -out GCF_009856625.1_ASM985662v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:36,297] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:36,299] [INFO] Selected 12 target genomes.
[2024-01-25 19:47:36,300] [INFO] Target genome list was writen to GCF_009856625.1_ASM985662v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:36,307] [INFO] Task started: fastANI
[2024-01-25 19:47:36,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg03c6f535-5d31-44b1-aca6-70417a5c2826/GCF_009856625.1_ASM985662v1_genomic.fna.gz --refList GCF_009856625.1_ASM985662v1_genomic.fna/target_genomes.txt --output GCF_009856625.1_ASM985662v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:47,116] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:47,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg690e95f4-993f-41ee-9fb8-1163982bfd90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:47,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg690e95f4-993f-41ee-9fb8-1163982bfd90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:47,125] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:47,125] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:47,125] [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
Aquitalea denitrificans	strain=5YN1-3	GCA_009856625.1	519081	519081	type	True	100.0	1497	1500	95	conclusive
Aquitalea pelogenes	strain=CCM 7557	GCA_001515305.1	1293573	1293573	type	True	89.1472	1173	1500	95	below_threshold
Aquitalea magnusonii	strain=DSM 25134	GCA_003202035.1	332411	332411	suspected-type	True	87.3105	1133	1500	95	below_threshold
Aquitalea aquatilis	strain=THG-DN7.12	GCA_005155025.1	1537400	1537400	type	True	86.7173	1126	1500	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	80.4813	592	1500	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	80.4806	571	1500	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	80.475	625	1500	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	80.3332	582	1500	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	80.3114	589	1500	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	80.2899	567	1500	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	79.7184	533	1500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:47,126] [INFO] DFAST Taxonomy check result was written to GCF_009856625.1_ASM985662v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:47,127] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:47,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:47,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg690e95f4-993f-41ee-9fb8-1163982bfd90/dqc_reference/checkm_data
[2024-01-25 19:47:47,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:47,169] [INFO] Task started: CheckM
[2024-01-25 19:47:47,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009856625.1_ASM985662v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009856625.1_ASM985662v1_genomic.fna/checkm_input GCF_009856625.1_ASM985662v1_genomic.fna/checkm_result
[2024-01-25 19:48:29,759] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:29,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:29,777] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:29,777] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:29,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009856625.1_ASM985662v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:29,778] [INFO] Task started: Blastn
[2024-01-25 19:48:29,778] [INFO] Running command: blastn -query GCF_009856625.1_ASM985662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg690e95f4-993f-41ee-9fb8-1163982bfd90/dqc_reference/reference_markers_gtdb.fasta -out GCF_009856625.1_ASM985662v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:31,437] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:31,440] [INFO] Selected 8 target genomes.
[2024-01-25 19:48:31,440] [INFO] Target genome list was writen to GCF_009856625.1_ASM985662v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:31,447] [INFO] Task started: fastANI
[2024-01-25 19:48:31,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg03c6f535-5d31-44b1-aca6-70417a5c2826/GCF_009856625.1_ASM985662v1_genomic.fna.gz --refList GCF_009856625.1_ASM985662v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009856625.1_ASM985662v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:40,784] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:40,790] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:40,791] [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_009856625.1	s__Aquitalea denitrificans	100.0	1497	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002217795.2	s__Aquitalea magnusonii_B	90.6337	1267	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001515305.1	s__Aquitalea pelogenes	89.1472	1173	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	97.38	96.32	0.89	0.86	4	-
GCF_013391415.1	s__Aquitalea sp013391415	88.1709	1185	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202035.1	s__Aquitalea magnusonii	87.3122	1133	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	99.21	98.53	0.95	0.91	3	-
GCF_005155025.1	s__Aquitalea aquatilis	86.7014	1127	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	99.19	99.19	0.95	0.95	2	-
GCF_003693445.1	s__Aquitalea sp003693445	86.6829	1046	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013911085.1	s__Aquitalea magnusonii_C	86.5924	1108	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:40,792] [INFO] GTDB search result was written to GCF_009856625.1_ASM985662v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:40,792] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:40,795] [INFO] DFAST_QC result json was written to GCF_009856625.1_ASM985662v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:40,795] [INFO] DFAST_QC completed!
[2024-01-25 19:48:40,795] [INFO] Total running time: 0h1m20s