[2023-06-27 08:15:38,071] [INFO] DFAST_QC pipeline started.
[2023-06-27 08:15:38,073] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 08:15:38,073] [INFO] DQC Reference Directory: /var/lib/cwl/stg755e75d4-bb4f-4a31-a2a2-380cd905755b/dqc_reference
[2023-06-27 08:15:39,516] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 08:15:39,517] [INFO] Task started: Prodigal
[2023-06-27 08:15:39,518] [INFO] Running command: gunzip -c /var/lib/cwl/stg881f7673-99b9-4d63-803d-0127606ec1b5/GCA_002310415.1_ASM231041v1_genomic.fna.gz | prodigal -d GCA_002310415.1_ASM231041v1_genomic.fna/cds.fna -a GCA_002310415.1_ASM231041v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 08:15:41,979] [INFO] Task succeeded: Prodigal
[2023-06-27 08:15:41,980] [INFO] Task started: HMMsearch
[2023-06-27 08:15:41,980] [INFO] Running command: hmmsearch --tblout GCA_002310415.1_ASM231041v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg755e75d4-bb4f-4a31-a2a2-380cd905755b/dqc_reference/reference_markers.hmm GCA_002310415.1_ASM231041v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 08:15:42,192] [INFO] Task succeeded: HMMsearch
[2023-06-27 08:15:42,193] [INFO] Found 6/6 markers.
[2023-06-27 08:15:42,212] [INFO] Query marker FASTA was written to GCA_002310415.1_ASM231041v1_genomic.fna/markers.fasta
[2023-06-27 08:15:42,212] [INFO] Task started: Blastn
[2023-06-27 08:15:42,212] [INFO] Running command: blastn -query GCA_002310415.1_ASM231041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg755e75d4-bb4f-4a31-a2a2-380cd905755b/dqc_reference/reference_markers.fasta -out GCA_002310415.1_ASM231041v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:15:42,894] [INFO] Task succeeded: Blastn
[2023-06-27 08:15:42,898] [INFO] Selected 24 target genomes.
[2023-06-27 08:15:42,899] [INFO] Target genome list was writen to GCA_002310415.1_ASM231041v1_genomic.fna/target_genomes.txt
[2023-06-27 08:15:42,959] [INFO] Task started: fastANI
[2023-06-27 08:15:42,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg881f7673-99b9-4d63-803d-0127606ec1b5/GCA_002310415.1_ASM231041v1_genomic.fna.gz --refList GCA_002310415.1_ASM231041v1_genomic.fna/target_genomes.txt --output GCA_002310415.1_ASM231041v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 08:15:53,639] [INFO] Task succeeded: fastANI
[2023-06-27 08:15:53,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg755e75d4-bb4f-4a31-a2a2-380cd905755b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 08:15:53,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg755e75d4-bb4f-4a31-a2a2-380cd905755b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 08:15:53,641] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 08:15:53,641] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 08:15:53,641] [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
--------------------------------------------------------------------------------
[2023-06-27 08:15:53,643] [INFO] DFAST Taxonomy check result was written to GCA_002310415.1_ASM231041v1_genomic.fna/tc_result.tsv
[2023-06-27 08:15:53,644] [INFO] ===== Taxonomy check completed =====
[2023-06-27 08:15:53,644] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 08:15:53,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg755e75d4-bb4f-4a31-a2a2-380cd905755b/dqc_reference/checkm_data
[2023-06-27 08:15:53,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 08:15:53,707] [INFO] Task started: CheckM
[2023-06-27 08:15:53,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310415.1_ASM231041v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310415.1_ASM231041v1_genomic.fna/checkm_input GCA_002310415.1_ASM231041v1_genomic.fna/checkm_result
[2023-06-27 08:16:09,228] [INFO] Task succeeded: CheckM
[2023-06-27 08:16:09,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 08:16:09,250] [INFO] ===== Completeness check finished =====
[2023-06-27 08:16:09,250] [INFO] ===== Start GTDB Search =====
[2023-06-27 08:16:09,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310415.1_ASM231041v1_genomic.fna/markers.fasta)
[2023-06-27 08:16:09,251] [INFO] Task started: Blastn
[2023-06-27 08:16:09,251] [INFO] Running command: blastn -query GCA_002310415.1_ASM231041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg755e75d4-bb4f-4a31-a2a2-380cd905755b/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310415.1_ASM231041v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:16:10,336] [INFO] Task succeeded: Blastn
[2023-06-27 08:16:10,341] [INFO] Selected 13 target genomes.
[2023-06-27 08:16:10,341] [INFO] Target genome list was writen to GCA_002310415.1_ASM231041v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 08:16:10,347] [INFO] Task started: fastANI
[2023-06-27 08:16:10,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg881f7673-99b9-4d63-803d-0127606ec1b5/GCA_002310415.1_ASM231041v1_genomic.fna.gz --refList GCA_002310415.1_ASM231041v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310415.1_ASM231041v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 08:16:13,070] [INFO] Task succeeded: fastANI
[2023-06-27 08:16:13,084] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 08:16:13,084] [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_002310415.1	s__Enterousia sp002310415	100.0	279	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002309215.1	s__Enterousia sp002309215	81.2864	167	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236005.1	s__Enterousia sp905236005	81.2446	185	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427715.1	s__Enterousia sp017427715	80.7602	176	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798205.1	s__Enterousia sp902798205	79.9017	136	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017528045.1	s__Enterousia sp017528045	79.4694	147	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781465.1	s__Enterousia sp902781465	79.1365	131	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313285.1	s__Enterousia sp900313285	79.0983	134	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900321105.1	s__Enterousia sp900321105	78.9307	137	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018065345.1	s__Enterousia sp018065345	78.8979	81	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642585.1	s__Enterousia sp017642585	78.8921	135	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902771095.1	s__Enterousia sp902771095	78.8066	126	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642565.1	s__Enterousia sp017642565	78.316	95	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 08:16:13,087] [INFO] GTDB search result was written to GCA_002310415.1_ASM231041v1_genomic.fna/result_gtdb.tsv
[2023-06-27 08:16:13,087] [INFO] ===== GTDB Search completed =====
[2023-06-27 08:16:13,112] [INFO] DFAST_QC result json was written to GCA_002310415.1_ASM231041v1_genomic.fna/dqc_result.json
[2023-06-27 08:16:13,113] [INFO] DFAST_QC completed!
[2023-06-27 08:16:13,113] [INFO] Total running time: 0h0m35s