[2023-06-30 13:05:25,334] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:05:25,337] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:05:25,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg80e7969b-e661-40fa-9089-5bfb6e363566/dqc_reference
[2023-06-30 13:05:26,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:05:26,752] [INFO] Task started: Prodigal
[2023-06-30 13:05:26,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg031d0837-d42c-4fd4-a821-d65d5bc72097/GCA_025606285.1_ASM2560628v1_genomic.fna.gz | prodigal -d GCA_025606285.1_ASM2560628v1_genomic.fna/cds.fna -a GCA_025606285.1_ASM2560628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:05:29,340] [INFO] Task succeeded: Prodigal
[2023-06-30 13:05:29,340] [INFO] Task started: HMMsearch
[2023-06-30 13:05:29,340] [INFO] Running command: hmmsearch --tblout GCA_025606285.1_ASM2560628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80e7969b-e661-40fa-9089-5bfb6e363566/dqc_reference/reference_markers.hmm GCA_025606285.1_ASM2560628v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:05:29,617] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:05:29,619] [INFO] Found 6/6 markers.
[2023-06-30 13:05:29,641] [INFO] Query marker FASTA was written to GCA_025606285.1_ASM2560628v1_genomic.fna/markers.fasta
[2023-06-30 13:05:29,641] [INFO] Task started: Blastn
[2023-06-30 13:05:29,641] [INFO] Running command: blastn -query GCA_025606285.1_ASM2560628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e7969b-e661-40fa-9089-5bfb6e363566/dqc_reference/reference_markers.fasta -out GCA_025606285.1_ASM2560628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:05:30,326] [INFO] Task succeeded: Blastn
[2023-06-30 13:05:30,330] [INFO] Selected 22 target genomes.
[2023-06-30 13:05:30,330] [INFO] Target genome list was writen to GCA_025606285.1_ASM2560628v1_genomic.fna/target_genomes.txt
[2023-06-30 13:05:30,332] [INFO] Task started: fastANI
[2023-06-30 13:05:30,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg031d0837-d42c-4fd4-a821-d65d5bc72097/GCA_025606285.1_ASM2560628v1_genomic.fna.gz --refList GCA_025606285.1_ASM2560628v1_genomic.fna/target_genomes.txt --output GCA_025606285.1_ASM2560628v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:05:39,036] [INFO] Task succeeded: fastANI
[2023-06-30 13:05:39,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80e7969b-e661-40fa-9089-5bfb6e363566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:05:39,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80e7969b-e661-40fa-9089-5bfb6e363566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:05:39,041] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 13:05:39,041] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 13:05:39,041] [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
Candidatus Liberibacter asiaticus	strain=A4	GCA_000590865.3	34021	34021	reftype	True	99.8546	404	409	95	conclusive
--------------------------------------------------------------------------------
[2023-06-30 13:05:39,043] [INFO] DFAST Taxonomy check result was written to GCA_025606285.1_ASM2560628v1_genomic.fna/tc_result.tsv
[2023-06-30 13:05:39,044] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:05:39,044] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:05:39,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80e7969b-e661-40fa-9089-5bfb6e363566/dqc_reference/checkm_data
[2023-06-30 13:05:39,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:05:39,061] [INFO] Task started: CheckM
[2023-06-30 13:05:39,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025606285.1_ASM2560628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025606285.1_ASM2560628v1_genomic.fna/checkm_input GCA_025606285.1_ASM2560628v1_genomic.fna/checkm_result
[2023-06-30 13:05:55,601] [INFO] Task succeeded: CheckM
[2023-06-30 13:05:55,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:05:55,632] [INFO] ===== Completeness check finished =====
[2023-06-30 13:05:55,633] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:05:55,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025606285.1_ASM2560628v1_genomic.fna/markers.fasta)
[2023-06-30 13:05:55,634] [INFO] Task started: Blastn
[2023-06-30 13:05:55,634] [INFO] Running command: blastn -query GCA_025606285.1_ASM2560628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e7969b-e661-40fa-9089-5bfb6e363566/dqc_reference/reference_markers_gtdb.fasta -out GCA_025606285.1_ASM2560628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:05:56,718] [INFO] Task succeeded: Blastn
[2023-06-30 13:05:56,722] [INFO] Selected 13 target genomes.
[2023-06-30 13:05:56,722] [INFO] Target genome list was writen to GCA_025606285.1_ASM2560628v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:05:56,730] [INFO] Task started: fastANI
[2023-06-30 13:05:56,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg031d0837-d42c-4fd4-a821-d65d5bc72097/GCA_025606285.1_ASM2560628v1_genomic.fna.gz --refList GCA_025606285.1_ASM2560628v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025606285.1_ASM2560628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:06:00,312] [INFO] Task succeeded: fastANI
[2023-06-30 13:06:00,322] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:06:00,322] [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_000590865.3	s__Liberibacter asiaticus	99.8546	404	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Liberibacter	95.0	99.90	99.77	0.99	0.91	34	conclusive
GCF_001021085.1	s__Liberibacter africanus	80.9145	301	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Liberibacter	95.0	99.89	99.89	1.00	1.00	2	-
GCF_000183665.1	s__Liberibacter solanacearum	79.6235	254	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Liberibacter	95.0	97.50	97.27	0.94	0.91	8	-
GCA_003045065.1	s__Liberibacter europaeus	77.6013	113	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Liberibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016808295.1	s__Liberibacter ctenarytainae	76.8818	131	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Liberibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014048425.1	s__Liberibacter sp014048425	76.3208	80	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Liberibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:06:00,324] [INFO] GTDB search result was written to GCA_025606285.1_ASM2560628v1_genomic.fna/result_gtdb.tsv
[2023-06-30 13:06:00,325] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:06:00,327] [INFO] DFAST_QC result json was written to GCA_025606285.1_ASM2560628v1_genomic.fna/dqc_result.json
[2023-06-30 13:06:00,328] [INFO] DFAST_QC completed!
[2023-06-30 13:06:00,328] [INFO] Total running time: 0h0m35s