[2023-06-08 11:32:42,309] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:32:42,313] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:32:42,313] [INFO] DQC Reference Directory: /var/lib/cwl/stge1af9954-6003-4e95-9754-5f85541bd2db/dqc_reference
[2023-06-08 11:32:43,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:32:43,641] [INFO] Task started: Prodigal
[2023-06-08 11:32:43,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg80cad0c3-790e-4d2a-8654-adea4a69279f/GCA_945889185.1_MH-21oct19-259_genomic.fna.gz | prodigal -d GCA_945889185.1_MH-21oct19-259_genomic.fna/cds.fna -a GCA_945889185.1_MH-21oct19-259_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:32:52,732] [INFO] Task succeeded: Prodigal
[2023-06-08 11:32:52,732] [INFO] Task started: HMMsearch
[2023-06-08 11:32:52,732] [INFO] Running command: hmmsearch --tblout GCA_945889185.1_MH-21oct19-259_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1af9954-6003-4e95-9754-5f85541bd2db/dqc_reference/reference_markers.hmm GCA_945889185.1_MH-21oct19-259_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:32:53,069] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:32:53,071] [INFO] Found 6/6 markers.
[2023-06-08 11:32:53,113] [INFO] Query marker FASTA was written to GCA_945889185.1_MH-21oct19-259_genomic.fna/markers.fasta
[2023-06-08 11:32:53,114] [INFO] Task started: Blastn
[2023-06-08 11:32:53,114] [INFO] Running command: blastn -query GCA_945889185.1_MH-21oct19-259_genomic.fna/markers.fasta -db /var/lib/cwl/stge1af9954-6003-4e95-9754-5f85541bd2db/dqc_reference/reference_markers.fasta -out GCA_945889185.1_MH-21oct19-259_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:32:53,696] [INFO] Task succeeded: Blastn
[2023-06-08 11:32:53,700] [INFO] Selected 15 target genomes.
[2023-06-08 11:32:53,701] [INFO] Target genome list was writen to GCA_945889185.1_MH-21oct19-259_genomic.fna/target_genomes.txt
[2023-06-08 11:32:53,702] [INFO] Task started: fastANI
[2023-06-08 11:32:53,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg80cad0c3-790e-4d2a-8654-adea4a69279f/GCA_945889185.1_MH-21oct19-259_genomic.fna.gz --refList GCA_945889185.1_MH-21oct19-259_genomic.fna/target_genomes.txt --output GCA_945889185.1_MH-21oct19-259_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:33:02,922] [INFO] Task succeeded: fastANI
[2023-06-08 11:33:02,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1af9954-6003-4e95-9754-5f85541bd2db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:33:02,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1af9954-6003-4e95-9754-5f85541bd2db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:33:02,925] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:33:02,926] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:33:02,926] [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
--------------------------------------------------------------------------------
[2023-06-08 11:33:02,927] [INFO] DFAST Taxonomy check result was written to GCA_945889185.1_MH-21oct19-259_genomic.fna/tc_result.tsv
[2023-06-08 11:33:02,928] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:33:02,929] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:33:02,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1af9954-6003-4e95-9754-5f85541bd2db/dqc_reference/checkm_data
[2023-06-08 11:33:02,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:33:02,979] [INFO] Task started: CheckM
[2023-06-08 11:33:02,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945889185.1_MH-21oct19-259_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945889185.1_MH-21oct19-259_genomic.fna/checkm_input GCA_945889185.1_MH-21oct19-259_genomic.fna/checkm_result
[2023-06-08 11:33:34,962] [INFO] Task succeeded: CheckM
[2023-06-08 11:33:34,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:33:34,984] [INFO] ===== Completeness check finished =====
[2023-06-08 11:33:34,984] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:33:34,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945889185.1_MH-21oct19-259_genomic.fna/markers.fasta)
[2023-06-08 11:33:34,985] [INFO] Task started: Blastn
[2023-06-08 11:33:34,985] [INFO] Running command: blastn -query GCA_945889185.1_MH-21oct19-259_genomic.fna/markers.fasta -db /var/lib/cwl/stge1af9954-6003-4e95-9754-5f85541bd2db/dqc_reference/reference_markers_gtdb.fasta -out GCA_945889185.1_MH-21oct19-259_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:33:35,733] [INFO] Task succeeded: Blastn
[2023-06-08 11:33:35,736] [INFO] Selected 10 target genomes.
[2023-06-08 11:33:35,737] [INFO] Target genome list was writen to GCA_945889185.1_MH-21oct19-259_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:33:35,737] [INFO] Task started: fastANI
[2023-06-08 11:33:35,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg80cad0c3-790e-4d2a-8654-adea4a69279f/GCA_945889185.1_MH-21oct19-259_genomic.fna.gz --refList GCA_945889185.1_MH-21oct19-259_genomic.fna/target_genomes_gtdb.txt --output GCA_945889185.1_MH-21oct19-259_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:33:42,764] [INFO] Task succeeded: fastANI
[2023-06-08 11:33:42,773] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:33:42,773] [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_003671255.1	s__UBA969 sp003671255	98.0981	780	1088	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	97.99	97.11	0.80	0.71	7	conclusive
GCA_002303765.1	s__UBA969 sp002303765	88.2646	857	1088	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	99.66	99.66	0.86	0.86	2	-
GCA_903960945.1	s__UBA969 sp903960945	87.7196	856	1088	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	98.76	98.01	0.87	0.84	7	-
GCA_009920765.1	s__UBA969 sp009920765	83.1134	895	1088	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	99.66	99.66	0.97	0.97	2	-
GCA_005786805.1	s__UBA969 sp005786805	77.7984	364	1088	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:33:42,776] [INFO] GTDB search result was written to GCA_945889185.1_MH-21oct19-259_genomic.fna/result_gtdb.tsv
[2023-06-08 11:33:42,776] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:33:42,780] [INFO] DFAST_QC result json was written to GCA_945889185.1_MH-21oct19-259_genomic.fna/dqc_result.json
[2023-06-08 11:33:42,780] [INFO] DFAST_QC completed!
[2023-06-08 11:33:42,780] [INFO] Total running time: 0h1m0s