[2023-06-05 18:01:55,543] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:01:55,545] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:01:55,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg80bbb803-c55b-45e9-966c-2d42ac38d313/dqc_reference
[2023-06-05 18:01:56,808] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:01:56,809] [INFO] Task started: Prodigal
[2023-06-05 18:01:56,809] [INFO] Running command: gunzip -c /var/lib/cwl/stge4776487-de81-4e2e-a196-4828292e3947/GCA_902523485.1_AG-895-F09_genomic.fna.gz | prodigal -d GCA_902523485.1_AG-895-F09_genomic.fna/cds.fna -a GCA_902523485.1_AG-895-F09_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:02:01,792] [INFO] Task succeeded: Prodigal
[2023-06-05 18:02:01,793] [INFO] Task started: HMMsearch
[2023-06-05 18:02:01,793] [INFO] Running command: hmmsearch --tblout GCA_902523485.1_AG-895-F09_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80bbb803-c55b-45e9-966c-2d42ac38d313/dqc_reference/reference_markers.hmm GCA_902523485.1_AG-895-F09_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:02:02,042] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:02:02,044] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge4776487-de81-4e2e-a196-4828292e3947/GCA_902523485.1_AG-895-F09_genomic.fna.gz]
[2023-06-05 18:02:02,075] [INFO] Query marker FASTA was written to GCA_902523485.1_AG-895-F09_genomic.fna/markers.fasta
[2023-06-05 18:02:02,076] [INFO] Task started: Blastn
[2023-06-05 18:02:02,076] [INFO] Running command: blastn -query GCA_902523485.1_AG-895-F09_genomic.fna/markers.fasta -db /var/lib/cwl/stg80bbb803-c55b-45e9-966c-2d42ac38d313/dqc_reference/reference_markers.fasta -out GCA_902523485.1_AG-895-F09_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:02,674] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:02,679] [INFO] Selected 23 target genomes.
[2023-06-05 18:02:02,679] [INFO] Target genome list was writen to GCA_902523485.1_AG-895-F09_genomic.fna/target_genomes.txt
[2023-06-05 18:02:02,688] [INFO] Task started: fastANI
[2023-06-05 18:02:02,688] [INFO] Running command: fastANI --query /var/lib/cwl/stge4776487-de81-4e2e-a196-4828292e3947/GCA_902523485.1_AG-895-F09_genomic.fna.gz --refList GCA_902523485.1_AG-895-F09_genomic.fna/target_genomes.txt --output GCA_902523485.1_AG-895-F09_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:02:18,647] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:18,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80bbb803-c55b-45e9-966c-2d42ac38d313/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:02:18,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80bbb803-c55b-45e9-966c-2d42ac38d313/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:02:18,650] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:02:18,650] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:02:18,651] [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
--------------------------------------------------------------------------------
[2023-06-05 18:02:18,653] [INFO] DFAST Taxonomy check result was written to GCA_902523485.1_AG-895-F09_genomic.fna/tc_result.tsv
[2023-06-05 18:02:18,653] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:02:18,654] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:02:18,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80bbb803-c55b-45e9-966c-2d42ac38d313/dqc_reference/checkm_data
[2023-06-05 18:02:18,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:02:18,679] [INFO] Task started: CheckM
[2023-06-05 18:02:18,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902523485.1_AG-895-F09_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902523485.1_AG-895-F09_genomic.fna/checkm_input GCA_902523485.1_AG-895-F09_genomic.fna/checkm_result
[2023-06-05 18:02:40,399] [INFO] Task succeeded: CheckM
[2023-06-05 18:02:40,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:02:40,421] [INFO] ===== Completeness check finished =====
[2023-06-05 18:02:40,422] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:02:40,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902523485.1_AG-895-F09_genomic.fna/markers.fasta)
[2023-06-05 18:02:40,422] [INFO] Task started: Blastn
[2023-06-05 18:02:40,423] [INFO] Running command: blastn -query GCA_902523485.1_AG-895-F09_genomic.fna/markers.fasta -db /var/lib/cwl/stg80bbb803-c55b-45e9-966c-2d42ac38d313/dqc_reference/reference_markers_gtdb.fasta -out GCA_902523485.1_AG-895-F09_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:41,332] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:41,336] [INFO] Selected 16 target genomes.
[2023-06-05 18:02:41,336] [INFO] Target genome list was writen to GCA_902523485.1_AG-895-F09_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:02:41,354] [INFO] Task started: fastANI
[2023-06-05 18:02:41,354] [INFO] Running command: fastANI --query /var/lib/cwl/stge4776487-de81-4e2e-a196-4828292e3947/GCA_902523485.1_AG-895-F09_genomic.fna.gz --refList GCA_902523485.1_AG-895-F09_genomic.fna/target_genomes_gtdb.txt --output GCA_902523485.1_AG-895-F09_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:02:49,765] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:49,775] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:02:49,776] [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_016780765.1	s__UBA8309 sp016780765	97.5627	315	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	conclusive
GCA_002683535.1	s__UBA8309 sp002683535	87.9782	208	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	79.8942	75	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	78.6763	149	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_011522725.1	s__UBA8309 sp001627655	78.2451	128	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_009920665.1	s__UBA8309 sp009920665	77.7366	152	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	77.7121	136	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731315.1	s__UBA8309 sp002731315	77.486	71	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524735.1	s__UBA8309 sp011524735	77.1535	77	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936825.1	s__UBA8309 sp009936825	77.1235	64	490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:02:49,778] [INFO] GTDB search result was written to GCA_902523485.1_AG-895-F09_genomic.fna/result_gtdb.tsv
[2023-06-05 18:02:49,779] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:02:49,784] [INFO] DFAST_QC result json was written to GCA_902523485.1_AG-895-F09_genomic.fna/dqc_result.json
[2023-06-05 18:02:49,785] [INFO] DFAST_QC completed!
[2023-06-05 18:02:49,785] [INFO] Total running time: 0h0m54s