[2023-06-18 22:57:18,938] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:57:18,940] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:57:18,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e3c9d8a-9f5f-410b-8ded-471c4e7cd67a/dqc_reference
[2023-06-18 22:57:20,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:57:20,227] [INFO] Task started: Prodigal
[2023-06-18 22:57:20,228] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fba5ed9-3fe8-4004-8cd6-615c5185ce94/GCA_018693125.1_ASM1869312v1_genomic.fna.gz | prodigal -d GCA_018693125.1_ASM1869312v1_genomic.fna/cds.fna -a GCA_018693125.1_ASM1869312v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:57:22,165] [INFO] Task succeeded: Prodigal
[2023-06-18 22:57:22,166] [INFO] Task started: HMMsearch
[2023-06-18 22:57:22,166] [INFO] Running command: hmmsearch --tblout GCA_018693125.1_ASM1869312v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e3c9d8a-9f5f-410b-8ded-471c4e7cd67a/dqc_reference/reference_markers.hmm GCA_018693125.1_ASM1869312v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:57:22,402] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:57:22,404] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8fba5ed9-3fe8-4004-8cd6-615c5185ce94/GCA_018693125.1_ASM1869312v1_genomic.fna.gz]
[2023-06-18 22:57:22,437] [INFO] Query marker FASTA was written to GCA_018693125.1_ASM1869312v1_genomic.fna/markers.fasta
[2023-06-18 22:57:22,437] [INFO] Task started: Blastn
[2023-06-18 22:57:22,437] [INFO] Running command: blastn -query GCA_018693125.1_ASM1869312v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e3c9d8a-9f5f-410b-8ded-471c4e7cd67a/dqc_reference/reference_markers.fasta -out GCA_018693125.1_ASM1869312v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:23,052] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:23,056] [INFO] Selected 21 target genomes.
[2023-06-18 22:57:23,056] [INFO] Target genome list was writen to GCA_018693125.1_ASM1869312v1_genomic.fna/target_genomes.txt
[2023-06-18 22:57:23,060] [INFO] Task started: fastANI
[2023-06-18 22:57:23,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fba5ed9-3fe8-4004-8cd6-615c5185ce94/GCA_018693125.1_ASM1869312v1_genomic.fna.gz --refList GCA_018693125.1_ASM1869312v1_genomic.fna/target_genomes.txt --output GCA_018693125.1_ASM1869312v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:57:32,579] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:32,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e3c9d8a-9f5f-410b-8ded-471c4e7cd67a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:57:32,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e3c9d8a-9f5f-410b-8ded-471c4e7cd67a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:57:32,583] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:57:32,583] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 22:57:32,583] [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
--------------------------------------------------------------------------------
[2023-06-18 22:57:32,585] [INFO] DFAST Taxonomy check result was written to GCA_018693125.1_ASM1869312v1_genomic.fna/tc_result.tsv
[2023-06-18 22:57:32,586] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:57:32,587] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:57:32,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e3c9d8a-9f5f-410b-8ded-471c4e7cd67a/dqc_reference/checkm_data
[2023-06-18 22:57:32,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:57:32,610] [INFO] Task started: CheckM
[2023-06-18 22:57:32,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018693125.1_ASM1869312v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018693125.1_ASM1869312v1_genomic.fna/checkm_input GCA_018693125.1_ASM1869312v1_genomic.fna/checkm_result
[2023-06-18 22:57:47,205] [INFO] Task succeeded: CheckM
[2023-06-18 22:57:47,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 12.50%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-18 22:57:47,234] [INFO] ===== Completeness check finished =====
[2023-06-18 22:57:47,234] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:57:47,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018693125.1_ASM1869312v1_genomic.fna/markers.fasta)
[2023-06-18 22:57:47,235] [INFO] Task started: Blastn
[2023-06-18 22:57:47,235] [INFO] Running command: blastn -query GCA_018693125.1_ASM1869312v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e3c9d8a-9f5f-410b-8ded-471c4e7cd67a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018693125.1_ASM1869312v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:48,229] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:48,234] [INFO] Selected 24 target genomes.
[2023-06-18 22:57:48,235] [INFO] Target genome list was writen to GCA_018693125.1_ASM1869312v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:57:48,300] [INFO] Task started: fastANI
[2023-06-18 22:57:48,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fba5ed9-3fe8-4004-8cd6-615c5185ce94/GCA_018693125.1_ASM1869312v1_genomic.fna.gz --refList GCA_018693125.1_ASM1869312v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018693125.1_ASM1869312v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:57:54,588] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:54,600] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 22:57:54,601] [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_015660425.1	s__TMED109 sp015660425	84.158	124	277	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684605.1	s__TMED109 sp002684605	83.3915	198	277	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171375.1	s__TMED109 sp002171375	77.8274	117	277	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	98.96	97.53	0.84	0.73	4	-
GCA_002720535.1	s__TMED109 sp002720535	77.5988	121	277	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	95.89	95.27	0.82	0.81	3	-
GCA_002937655.1	s__TMED109 sp002937655	77.2176	108	277	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	99.81	99.81	0.91	0.91	2	-
GCA_002715265.1	s__GCA-002727615 sp002715265	76.5156	75	277	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__GCA-002727615	95.0	98.23	98.23	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-18 22:57:54,603] [INFO] GTDB search result was written to GCA_018693125.1_ASM1869312v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:57:54,603] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:57:54,606] [INFO] DFAST_QC result json was written to GCA_018693125.1_ASM1869312v1_genomic.fna/dqc_result.json
[2023-06-18 22:57:54,606] [INFO] DFAST_QC completed!
[2023-06-18 22:57:54,606] [INFO] Total running time: 0h0m36s