[2023-06-19 08:52:50,661] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:52:50,664] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:52:50,664] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbc38ae5-397e-4d4c-bd87-5f21527f30ba/dqc_reference
[2023-06-19 08:52:51,978] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:52:51,979] [INFO] Task started: Prodigal
[2023-06-19 08:52:51,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg5029ba0d-142f-4568-b5c4-2b7471e1d251/GCA_018677255.1_ASM1867725v1_genomic.fna.gz | prodigal -d GCA_018677255.1_ASM1867725v1_genomic.fna/cds.fna -a GCA_018677255.1_ASM1867725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:52:58,456] [INFO] Task succeeded: Prodigal
[2023-06-19 08:52:58,456] [INFO] Task started: HMMsearch
[2023-06-19 08:52:58,456] [INFO] Running command: hmmsearch --tblout GCA_018677255.1_ASM1867725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbc38ae5-397e-4d4c-bd87-5f21527f30ba/dqc_reference/reference_markers.hmm GCA_018677255.1_ASM1867725v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:52:58,710] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:52:58,712] [INFO] Found 6/6 markers.
[2023-06-19 08:52:58,748] [INFO] Query marker FASTA was written to GCA_018677255.1_ASM1867725v1_genomic.fna/markers.fasta
[2023-06-19 08:52:58,748] [INFO] Task started: Blastn
[2023-06-19 08:52:58,749] [INFO] Running command: blastn -query GCA_018677255.1_ASM1867725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbc38ae5-397e-4d4c-bd87-5f21527f30ba/dqc_reference/reference_markers.fasta -out GCA_018677255.1_ASM1867725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:52:59,462] [INFO] Task succeeded: Blastn
[2023-06-19 08:52:59,468] [INFO] Selected 34 target genomes.
[2023-06-19 08:52:59,468] [INFO] Target genome list was writen to GCA_018677255.1_ASM1867725v1_genomic.fna/target_genomes.txt
[2023-06-19 08:52:59,470] [INFO] Task started: fastANI
[2023-06-19 08:52:59,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg5029ba0d-142f-4568-b5c4-2b7471e1d251/GCA_018677255.1_ASM1867725v1_genomic.fna.gz --refList GCA_018677255.1_ASM1867725v1_genomic.fna/target_genomes.txt --output GCA_018677255.1_ASM1867725v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:53:23,523] [INFO] Task succeeded: fastANI
[2023-06-19 08:53:23,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbc38ae5-397e-4d4c-bd87-5f21527f30ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:53:23,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbc38ae5-397e-4d4c-bd87-5f21527f30ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:53:23,526] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:53:23,527] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:53:23,527] [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
--------------------------------------------------------------------------------
[2023-06-19 08:53:23,529] [INFO] DFAST Taxonomy check result was written to GCA_018677255.1_ASM1867725v1_genomic.fna/tc_result.tsv
[2023-06-19 08:53:23,529] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:53:23,529] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:53:23,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbc38ae5-397e-4d4c-bd87-5f21527f30ba/dqc_reference/checkm_data
[2023-06-19 08:53:23,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:53:23,565] [INFO] Task started: CheckM
[2023-06-19 08:53:23,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018677255.1_ASM1867725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018677255.1_ASM1867725v1_genomic.fna/checkm_input GCA_018677255.1_ASM1867725v1_genomic.fna/checkm_result
[2023-06-19 08:53:48,718] [INFO] Task succeeded: CheckM
[2023-06-19 08:53:48,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.94%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 08:53:48,747] [INFO] ===== Completeness check finished =====
[2023-06-19 08:53:48,747] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:53:48,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018677255.1_ASM1867725v1_genomic.fna/markers.fasta)
[2023-06-19 08:53:48,748] [INFO] Task started: Blastn
[2023-06-19 08:53:48,748] [INFO] Running command: blastn -query GCA_018677255.1_ASM1867725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbc38ae5-397e-4d4c-bd87-5f21527f30ba/dqc_reference/reference_markers_gtdb.fasta -out GCA_018677255.1_ASM1867725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:53:49,908] [INFO] Task succeeded: Blastn
[2023-06-19 08:53:49,914] [INFO] Selected 29 target genomes.
[2023-06-19 08:53:49,914] [INFO] Target genome list was writen to GCA_018677255.1_ASM1867725v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:53:49,916] [INFO] Task started: fastANI
[2023-06-19 08:53:49,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg5029ba0d-142f-4568-b5c4-2b7471e1d251/GCA_018677255.1_ASM1867725v1_genomic.fna.gz --refList GCA_018677255.1_ASM1867725v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018677255.1_ASM1867725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:54:06,767] [INFO] Task succeeded: fastANI
[2023-06-19 08:54:06,772] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:54:06,773] [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_013043705.1	s__UBA7434 sp004283095	99.6545	578	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.65	99.50	0.89	0.87	6	conclusive
--------------------------------------------------------------------------------
[2023-06-19 08:54:06,779] [INFO] GTDB search result was written to GCA_018677255.1_ASM1867725v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:54:06,779] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:54:06,781] [INFO] DFAST_QC result json was written to GCA_018677255.1_ASM1867725v1_genomic.fna/dqc_result.json
[2023-06-19 08:54:06,782] [INFO] DFAST_QC completed!
[2023-06-19 08:54:06,782] [INFO] Total running time: 0h1m16s