[2023-06-29 16:26:53,761] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:26:53,763] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:26:53,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e81e326-a3d2-4ea9-b079-fc9c19c1a417/dqc_reference
[2023-06-29 16:26:54,974] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:26:54,975] [INFO] Task started: Prodigal
[2023-06-29 16:26:54,975] [INFO] Running command: gunzip -c /var/lib/cwl/stgba3223de-6bb6-4bed-aefb-d4c88b292ea3/GCA_011620135.1_ASM1162013v1_genomic.fna.gz | prodigal -d GCA_011620135.1_ASM1162013v1_genomic.fna/cds.fna -a GCA_011620135.1_ASM1162013v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:27:02,205] [INFO] Task succeeded: Prodigal
[2023-06-29 16:27:02,205] [INFO] Task started: HMMsearch
[2023-06-29 16:27:02,205] [INFO] Running command: hmmsearch --tblout GCA_011620135.1_ASM1162013v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e81e326-a3d2-4ea9-b079-fc9c19c1a417/dqc_reference/reference_markers.hmm GCA_011620135.1_ASM1162013v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:27:02,372] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:27:02,373] [INFO] Found 6/6 markers.
[2023-06-29 16:27:02,393] [INFO] Query marker FASTA was written to GCA_011620135.1_ASM1162013v1_genomic.fna/markers.fasta
[2023-06-29 16:27:02,394] [INFO] Task started: Blastn
[2023-06-29 16:27:02,394] [INFO] Running command: blastn -query GCA_011620135.1_ASM1162013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e81e326-a3d2-4ea9-b079-fc9c19c1a417/dqc_reference/reference_markers.fasta -out GCA_011620135.1_ASM1162013v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:27:03,050] [INFO] Task succeeded: Blastn
[2023-06-29 16:27:03,053] [INFO] Selected 27 target genomes.
[2023-06-29 16:27:03,054] [INFO] Target genome list was writen to GCA_011620135.1_ASM1162013v1_genomic.fna/target_genomes.txt
[2023-06-29 16:27:03,056] [INFO] Task started: fastANI
[2023-06-29 16:27:03,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgba3223de-6bb6-4bed-aefb-d4c88b292ea3/GCA_011620135.1_ASM1162013v1_genomic.fna.gz --refList GCA_011620135.1_ASM1162013v1_genomic.fna/target_genomes.txt --output GCA_011620135.1_ASM1162013v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:27:18,210] [INFO] Task succeeded: fastANI
[2023-06-29 16:27:18,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e81e326-a3d2-4ea9-b079-fc9c19c1a417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:27:18,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e81e326-a3d2-4ea9-b079-fc9c19c1a417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:27:18,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:27:18,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 16:27:18,212] [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
--------------------------------------------------------------------------------
[2023-06-29 16:27:18,214] [INFO] DFAST Taxonomy check result was written to GCA_011620135.1_ASM1162013v1_genomic.fna/tc_result.tsv
[2023-06-29 16:27:18,215] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:27:18,215] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:27:18,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e81e326-a3d2-4ea9-b079-fc9c19c1a417/dqc_reference/checkm_data
[2023-06-29 16:27:18,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:27:18,241] [INFO] Task started: CheckM
[2023-06-29 16:27:18,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011620135.1_ASM1162013v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011620135.1_ASM1162013v1_genomic.fna/checkm_input GCA_011620135.1_ASM1162013v1_genomic.fna/checkm_result
[2023-06-29 16:27:44,921] [INFO] Task succeeded: CheckM
[2023-06-29 16:27:44,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:27:44,938] [INFO] ===== Completeness check finished =====
[2023-06-29 16:27:44,938] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:27:44,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011620135.1_ASM1162013v1_genomic.fna/markers.fasta)
[2023-06-29 16:27:44,939] [INFO] Task started: Blastn
[2023-06-29 16:27:44,939] [INFO] Running command: blastn -query GCA_011620135.1_ASM1162013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e81e326-a3d2-4ea9-b079-fc9c19c1a417/dqc_reference/reference_markers_gtdb.fasta -out GCA_011620135.1_ASM1162013v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:27:45,950] [INFO] Task succeeded: Blastn
[2023-06-29 16:27:45,953] [INFO] Selected 26 target genomes.
[2023-06-29 16:27:45,953] [INFO] Target genome list was writen to GCA_011620135.1_ASM1162013v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:27:45,963] [INFO] Task started: fastANI
[2023-06-29 16:27:45,963] [INFO] Running command: fastANI --query /var/lib/cwl/stgba3223de-6bb6-4bed-aefb-d4c88b292ea3/GCA_011620135.1_ASM1162013v1_genomic.fna.gz --refList GCA_011620135.1_ASM1162013v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011620135.1_ASM1162013v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:27:58,728] [INFO] Task succeeded: fastANI
[2023-06-29 16:27:58,732] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:27:58,732] [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_011620135.1	s__WOZS01 sp011620135	100.0	660	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA2770;f__WOZS01;g__WOZS01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002862435.1	s__Macondimonas sp002862435	76.0462	52	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA5335;f__UBA5335;g__Macondimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:27:58,734] [INFO] GTDB search result was written to GCA_011620135.1_ASM1162013v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:27:58,735] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:27:58,737] [INFO] DFAST_QC result json was written to GCA_011620135.1_ASM1162013v1_genomic.fna/dqc_result.json
[2023-06-29 16:27:58,737] [INFO] DFAST_QC completed!
[2023-06-29 16:27:58,738] [INFO] Total running time: 0h1m5s