[2023-06-04 21:08:44,694] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:08:44,699] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:08:44,699] [INFO] DQC Reference Directory: /var/lib/cwl/stgd08f7f30-cf72-422d-bc57-f7b585bb37b7/dqc_reference
[2023-06-04 21:08:45,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:08:45,945] [INFO] Task started: Prodigal
[2023-06-04 21:08:45,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cc1a114-2dee-40a2-885b-c2d915a672b7/GCA_001898705.1_ASM189870v1_genomic.fna.gz | prodigal -d GCA_001898705.1_ASM189870v1_genomic.fna/cds.fna -a GCA_001898705.1_ASM189870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:08:49,770] [INFO] Task succeeded: Prodigal
[2023-06-04 21:08:49,771] [INFO] Task started: HMMsearch
[2023-06-04 21:08:49,771] [INFO] Running command: hmmsearch --tblout GCA_001898705.1_ASM189870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd08f7f30-cf72-422d-bc57-f7b585bb37b7/dqc_reference/reference_markers.hmm GCA_001898705.1_ASM189870v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:08:50,099] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:08:50,101] [INFO] Found 6/6 markers.
[2023-06-04 21:08:50,134] [INFO] Query marker FASTA was written to GCA_001898705.1_ASM189870v1_genomic.fna/markers.fasta
[2023-06-04 21:08:50,134] [INFO] Task started: Blastn
[2023-06-04 21:08:50,135] [INFO] Running command: blastn -query GCA_001898705.1_ASM189870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd08f7f30-cf72-422d-bc57-f7b585bb37b7/dqc_reference/reference_markers.fasta -out GCA_001898705.1_ASM189870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:08:50,783] [INFO] Task succeeded: Blastn
[2023-06-04 21:08:50,787] [INFO] Selected 30 target genomes.
[2023-06-04 21:08:50,788] [INFO] Target genome list was writen to GCA_001898705.1_ASM189870v1_genomic.fna/target_genomes.txt
[2023-06-04 21:08:50,888] [INFO] Task started: fastANI
[2023-06-04 21:08:50,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc1a114-2dee-40a2-885b-c2d915a672b7/GCA_001898705.1_ASM189870v1_genomic.fna.gz --refList GCA_001898705.1_ASM189870v1_genomic.fna/target_genomes.txt --output GCA_001898705.1_ASM189870v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:09:04,944] [INFO] Task succeeded: fastANI
[2023-06-04 21:09:04,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd08f7f30-cf72-422d-bc57-f7b585bb37b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:09:04,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd08f7f30-cf72-422d-bc57-f7b585bb37b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:09:04,948] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:09:04,948] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 21:09:04,948] [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
--------------------------------------------------------------------------------
[2023-06-04 21:09:04,950] [INFO] DFAST Taxonomy check result was written to GCA_001898705.1_ASM189870v1_genomic.fna/tc_result.tsv
[2023-06-04 21:09:04,951] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:09:04,951] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:09:04,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd08f7f30-cf72-422d-bc57-f7b585bb37b7/dqc_reference/checkm_data
[2023-06-04 21:09:04,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:09:04,986] [INFO] Task started: CheckM
[2023-06-04 21:09:04,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001898705.1_ASM189870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001898705.1_ASM189870v1_genomic.fna/checkm_input GCA_001898705.1_ASM189870v1_genomic.fna/checkm_result
[2023-06-04 21:09:24,935] [INFO] Task succeeded: CheckM
[2023-06-04 21:09:24,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:09:24,966] [INFO] ===== Completeness check finished =====
[2023-06-04 21:09:24,967] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:09:24,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001898705.1_ASM189870v1_genomic.fna/markers.fasta)
[2023-06-04 21:09:24,968] [INFO] Task started: Blastn
[2023-06-04 21:09:24,968] [INFO] Running command: blastn -query GCA_001898705.1_ASM189870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd08f7f30-cf72-422d-bc57-f7b585bb37b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_001898705.1_ASM189870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:09:25,737] [INFO] Task succeeded: Blastn
[2023-06-04 21:09:25,741] [INFO] Selected 17 target genomes.
[2023-06-04 21:09:25,741] [INFO] Target genome list was writen to GCA_001898705.1_ASM189870v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:09:25,987] [INFO] Task started: fastANI
[2023-06-04 21:09:25,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc1a114-2dee-40a2-885b-c2d915a672b7/GCA_001898705.1_ASM189870v1_genomic.fna.gz --refList GCA_001898705.1_ASM189870v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001898705.1_ASM189870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:09:31,599] [INFO] Task succeeded: fastANI
[2023-06-04 21:09:31,609] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:09:31,609] [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_001898705.1	s__Paracaedimonas sp001898705	100.0	613	617	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caedimonadales;f__Caedimonadaceae;g__Paracaedimonas	95.0	99.93	99.93	0.96	0.96	2	conclusive
GCA_000743035.1	s__Paracaedimonas acanthamoebae	85.5683	444	617	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caedimonadales;f__Caedimonadaceae;g__Paracaedimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307065.1	s__Paracaedimonas acanthamoebae_A	81.6309	359	617	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caedimonadales;f__Caedimonadaceae;g__Paracaedimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898725.1	s__Paracaedimonas sp001898725	78.7461	249	617	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caedimonadales;f__Caedimonadaceae;g__Paracaedimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 21:09:31,611] [INFO] GTDB search result was written to GCA_001898705.1_ASM189870v1_genomic.fna/result_gtdb.tsv
[2023-06-04 21:09:31,612] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:09:31,617] [INFO] DFAST_QC result json was written to GCA_001898705.1_ASM189870v1_genomic.fna/dqc_result.json
[2023-06-04 21:09:31,617] [INFO] DFAST_QC completed!
[2023-06-04 21:09:31,617] [INFO] Total running time: 0h0m47s