[2023-06-27 06:05:41,424] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:05:41,438] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:05:41,438] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8a9becd-5b11-4473-8394-bbb6b7e15198/dqc_reference
[2023-06-27 06:05:42,924] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:05:42,926] [INFO] Task started: Prodigal
[2023-06-27 06:05:42,929] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9a43676-5aa2-4d61-95ab-ad62cf6cb7bf/GCA_026393295.1_ASM2639329v1_genomic.fna.gz | prodigal -d GCA_026393295.1_ASM2639329v1_genomic.fna/cds.fna -a GCA_026393295.1_ASM2639329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:05:45,034] [INFO] Task succeeded: Prodigal
[2023-06-27 06:05:45,034] [INFO] Task started: HMMsearch
[2023-06-27 06:05:45,035] [INFO] Running command: hmmsearch --tblout GCA_026393295.1_ASM2639329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8a9becd-5b11-4473-8394-bbb6b7e15198/dqc_reference/reference_markers.hmm GCA_026393295.1_ASM2639329v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:05:45,287] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:05:45,288] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf9a43676-5aa2-4d61-95ab-ad62cf6cb7bf/GCA_026393295.1_ASM2639329v1_genomic.fna.gz]
[2023-06-27 06:05:45,304] [INFO] Query marker FASTA was written to GCA_026393295.1_ASM2639329v1_genomic.fna/markers.fasta
[2023-06-27 06:05:45,305] [INFO] Task started: Blastn
[2023-06-27 06:05:45,305] [INFO] Running command: blastn -query GCA_026393295.1_ASM2639329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8a9becd-5b11-4473-8394-bbb6b7e15198/dqc_reference/reference_markers.fasta -out GCA_026393295.1_ASM2639329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:05:45,911] [INFO] Task succeeded: Blastn
[2023-06-27 06:05:45,916] [INFO] Selected 21 target genomes.
[2023-06-27 06:05:45,917] [INFO] Target genome list was writen to GCA_026393295.1_ASM2639329v1_genomic.fna/target_genomes.txt
[2023-06-27 06:05:45,925] [INFO] Task started: fastANI
[2023-06-27 06:05:45,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9a43676-5aa2-4d61-95ab-ad62cf6cb7bf/GCA_026393295.1_ASM2639329v1_genomic.fna.gz --refList GCA_026393295.1_ASM2639329v1_genomic.fna/target_genomes.txt --output GCA_026393295.1_ASM2639329v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:05:58,366] [INFO] Task succeeded: fastANI
[2023-06-27 06:05:58,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8a9becd-5b11-4473-8394-bbb6b7e15198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:05:58,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8a9becd-5b11-4473-8394-bbb6b7e15198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:05:58,369] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:05:58,370] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:05:58,370] [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
--------------------------------------------------------------------------------
[2023-06-27 06:05:58,373] [INFO] DFAST Taxonomy check result was written to GCA_026393295.1_ASM2639329v1_genomic.fna/tc_result.tsv
[2023-06-27 06:05:58,374] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:05:58,374] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:05:58,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8a9becd-5b11-4473-8394-bbb6b7e15198/dqc_reference/checkm_data
[2023-06-27 06:05:58,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:05:58,403] [INFO] Task started: CheckM
[2023-06-27 06:05:58,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026393295.1_ASM2639329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026393295.1_ASM2639329v1_genomic.fna/checkm_input GCA_026393295.1_ASM2639329v1_genomic.fna/checkm_result
[2023-06-27 06:06:13,493] [INFO] Task succeeded: CheckM
[2023-06-27 06:06:13,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:06:13,530] [INFO] ===== Completeness check finished =====
[2023-06-27 06:06:13,530] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:06:13,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026393295.1_ASM2639329v1_genomic.fna/markers.fasta)
[2023-06-27 06:06:13,531] [INFO] Task started: Blastn
[2023-06-27 06:06:13,531] [INFO] Running command: blastn -query GCA_026393295.1_ASM2639329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8a9becd-5b11-4473-8394-bbb6b7e15198/dqc_reference/reference_markers_gtdb.fasta -out GCA_026393295.1_ASM2639329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:06:14,433] [INFO] Task succeeded: Blastn
[2023-06-27 06:06:14,438] [INFO] Selected 18 target genomes.
[2023-06-27 06:06:14,438] [INFO] Target genome list was writen to GCA_026393295.1_ASM2639329v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:06:14,448] [INFO] Task started: fastANI
[2023-06-27 06:06:14,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9a43676-5aa2-4d61-95ab-ad62cf6cb7bf/GCA_026393295.1_ASM2639329v1_genomic.fna.gz --refList GCA_026393295.1_ASM2639329v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026393295.1_ASM2639329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:06:18,057] [INFO] Task succeeded: fastANI
[2023-06-27 06:06:18,066] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:06:18,067] [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_009703635.1	s__Rhodoluna sp009703635	89.2741	80	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702645.1	s__Rhodoluna sp009702645	82.5353	93	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703455.1	s__Rhodoluna sp009703455	79.6988	92	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704605.1	s__Rhodoluna sp009704605	78.6683	52	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.13	98.01	0.83	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-27 06:06:18,087] [INFO] GTDB search result was written to GCA_026393295.1_ASM2639329v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:06:18,088] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:06:18,095] [INFO] DFAST_QC result json was written to GCA_026393295.1_ASM2639329v1_genomic.fna/dqc_result.json
[2023-06-27 06:06:18,095] [INFO] DFAST_QC completed!
[2023-06-27 06:06:18,095] [INFO] Total running time: 0h0m37s