[2023-06-19 14:07:08,598] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:07:08,603] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:07:08,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg235cc35a-61ae-4b7d-be3f-922095527b9e/dqc_reference
[2023-06-19 14:07:09,960] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:07:09,961] [INFO] Task started: Prodigal
[2023-06-19 14:07:09,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e279b35-0433-46fc-82ee-9f5a1c9bacd3/GCA_018676495.1_ASM1867649v1_genomic.fna.gz | prodigal -d GCA_018676495.1_ASM1867649v1_genomic.fna/cds.fna -a GCA_018676495.1_ASM1867649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:07:12,803] [INFO] Task succeeded: Prodigal
[2023-06-19 14:07:12,803] [INFO] Task started: HMMsearch
[2023-06-19 14:07:12,804] [INFO] Running command: hmmsearch --tblout GCA_018676495.1_ASM1867649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg235cc35a-61ae-4b7d-be3f-922095527b9e/dqc_reference/reference_markers.hmm GCA_018676495.1_ASM1867649v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:07:13,057] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:07:13,058] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2e279b35-0433-46fc-82ee-9f5a1c9bacd3/GCA_018676495.1_ASM1867649v1_genomic.fna.gz]
[2023-06-19 14:07:13,087] [INFO] Query marker FASTA was written to GCA_018676495.1_ASM1867649v1_genomic.fna/markers.fasta
[2023-06-19 14:07:13,088] [INFO] Task started: Blastn
[2023-06-19 14:07:13,088] [INFO] Running command: blastn -query GCA_018676495.1_ASM1867649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg235cc35a-61ae-4b7d-be3f-922095527b9e/dqc_reference/reference_markers.fasta -out GCA_018676495.1_ASM1867649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:13,691] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:13,695] [INFO] Selected 24 target genomes.
[2023-06-19 14:07:13,696] [INFO] Target genome list was writen to GCA_018676495.1_ASM1867649v1_genomic.fna/target_genomes.txt
[2023-06-19 14:07:13,703] [INFO] Task started: fastANI
[2023-06-19 14:07:13,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e279b35-0433-46fc-82ee-9f5a1c9bacd3/GCA_018676495.1_ASM1867649v1_genomic.fna.gz --refList GCA_018676495.1_ASM1867649v1_genomic.fna/target_genomes.txt --output GCA_018676495.1_ASM1867649v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:07:25,242] [INFO] Task succeeded: fastANI
[2023-06-19 14:07:25,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg235cc35a-61ae-4b7d-be3f-922095527b9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:07:25,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg235cc35a-61ae-4b7d-be3f-922095527b9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:07:25,246] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:07:25,246] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 14:07:25,247] [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 14:07:25,249] [INFO] DFAST Taxonomy check result was written to GCA_018676495.1_ASM1867649v1_genomic.fna/tc_result.tsv
[2023-06-19 14:07:25,251] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:07:25,251] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:07:25,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg235cc35a-61ae-4b7d-be3f-922095527b9e/dqc_reference/checkm_data
[2023-06-19 14:07:25,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:07:25,282] [INFO] Task started: CheckM
[2023-06-19 14:07:25,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018676495.1_ASM1867649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018676495.1_ASM1867649v1_genomic.fna/checkm_input GCA_018676495.1_ASM1867649v1_genomic.fna/checkm_result
[2023-06-19 14:07:42,289] [INFO] Task succeeded: CheckM
[2023-06-19 14:07:42,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:07:42,317] [INFO] ===== Completeness check finished =====
[2023-06-19 14:07:42,318] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:07:42,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018676495.1_ASM1867649v1_genomic.fna/markers.fasta)
[2023-06-19 14:07:42,318] [INFO] Task started: Blastn
[2023-06-19 14:07:42,319] [INFO] Running command: blastn -query GCA_018676495.1_ASM1867649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg235cc35a-61ae-4b7d-be3f-922095527b9e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018676495.1_ASM1867649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:43,235] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:43,242] [INFO] Selected 16 target genomes.
[2023-06-19 14:07:43,242] [INFO] Target genome list was writen to GCA_018676495.1_ASM1867649v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:07:43,302] [INFO] Task started: fastANI
[2023-06-19 14:07:43,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e279b35-0433-46fc-82ee-9f5a1c9bacd3/GCA_018676495.1_ASM1867649v1_genomic.fna.gz --refList GCA_018676495.1_ASM1867649v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018676495.1_ASM1867649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:07:50,492] [INFO] Task succeeded: fastANI
[2023-06-19 14:07:50,500] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:07:50,500] [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_001901525.1	s__OPU3-GD-OMZ sp001901525	98.9204	309	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__OPU3-GD-OMZ	95.0	98.79	96.80	0.86	0.78	19	conclusive
GCA_012965425.1	s__OPU3-GD-OMZ sp012965425	91.1075	330	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__OPU3-GD-OMZ	95.0	99.81	99.76	0.91	0.86	6	-
GCA_012959905.1	s__OPU3-GD-OMZ sp012959905	83.6518	244	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__OPU3-GD-OMZ	95.0	99.80	99.80	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-19 14:07:50,502] [INFO] GTDB search result was written to GCA_018676495.1_ASM1867649v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:07:50,503] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:07:50,506] [INFO] DFAST_QC result json was written to GCA_018676495.1_ASM1867649v1_genomic.fna/dqc_result.json
[2023-06-19 14:07:50,512] [INFO] DFAST_QC completed!
[2023-06-19 14:07:50,512] [INFO] Total running time: 0h0m42s