[2023-06-27 06:05:26,068] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:05:26,073] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:05:26,073] [INFO] DQC Reference Directory: /var/lib/cwl/stgb178aa50-36f6-44d6-9a29-81d1535fdba3/dqc_reference
[2023-06-27 06:05:27,599] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:05:27,600] [INFO] Task started: Prodigal
[2023-06-27 06:05:27,600] [INFO] Running command: gunzip -c /var/lib/cwl/stgddda0d09-d266-480f-a157-3648f8f8c323/GCA_026984135.1_ASM2698413v1_genomic.fna.gz | prodigal -d GCA_026984135.1_ASM2698413v1_genomic.fna/cds.fna -a GCA_026984135.1_ASM2698413v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:05:44,528] [INFO] Task succeeded: Prodigal
[2023-06-27 06:05:44,529] [INFO] Task started: HMMsearch
[2023-06-27 06:05:44,529] [INFO] Running command: hmmsearch --tblout GCA_026984135.1_ASM2698413v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb178aa50-36f6-44d6-9a29-81d1535fdba3/dqc_reference/reference_markers.hmm GCA_026984135.1_ASM2698413v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:05:44,890] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:05:44,891] [INFO] Found 6/6 markers.
[2023-06-27 06:05:44,939] [INFO] Query marker FASTA was written to GCA_026984135.1_ASM2698413v1_genomic.fna/markers.fasta
[2023-06-27 06:05:44,940] [INFO] Task started: Blastn
[2023-06-27 06:05:44,940] [INFO] Running command: blastn -query GCA_026984135.1_ASM2698413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb178aa50-36f6-44d6-9a29-81d1535fdba3/dqc_reference/reference_markers.fasta -out GCA_026984135.1_ASM2698413v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:05:45,597] [INFO] Task succeeded: Blastn
[2023-06-27 06:05:45,603] [INFO] Selected 27 target genomes.
[2023-06-27 06:05:45,603] [INFO] Target genome list was writen to GCA_026984135.1_ASM2698413v1_genomic.fna/target_genomes.txt
[2023-06-27 06:05:45,612] [INFO] Task started: fastANI
[2023-06-27 06:05:45,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgddda0d09-d266-480f-a157-3648f8f8c323/GCA_026984135.1_ASM2698413v1_genomic.fna.gz --refList GCA_026984135.1_ASM2698413v1_genomic.fna/target_genomes.txt --output GCA_026984135.1_ASM2698413v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:06:03,429] [INFO] Task succeeded: fastANI
[2023-06-27 06:06:03,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb178aa50-36f6-44d6-9a29-81d1535fdba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:06:03,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb178aa50-36f6-44d6-9a29-81d1535fdba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:06:03,432] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:06:03,432] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:06:03,432] [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 06:06:03,434] [INFO] DFAST Taxonomy check result was written to GCA_026984135.1_ASM2698413v1_genomic.fna/tc_result.tsv
[2023-06-27 06:06:03,435] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:06:03,435] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:06:03,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb178aa50-36f6-44d6-9a29-81d1535fdba3/dqc_reference/checkm_data
[2023-06-27 06:06:03,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:06:03,480] [INFO] Task started: CheckM
[2023-06-27 06:06:03,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026984135.1_ASM2698413v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026984135.1_ASM2698413v1_genomic.fna/checkm_input GCA_026984135.1_ASM2698413v1_genomic.fna/checkm_result
[2023-06-27 06:06:54,843] [INFO] Task succeeded: CheckM
[2023-06-27 06:06:54,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 2.29%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-27 06:06:54,871] [INFO] ===== Completeness check finished =====
[2023-06-27 06:06:54,872] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:06:54,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026984135.1_ASM2698413v1_genomic.fna/markers.fasta)
[2023-06-27 06:06:54,873] [INFO] Task started: Blastn
[2023-06-27 06:06:54,873] [INFO] Running command: blastn -query GCA_026984135.1_ASM2698413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb178aa50-36f6-44d6-9a29-81d1535fdba3/dqc_reference/reference_markers_gtdb.fasta -out GCA_026984135.1_ASM2698413v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:06:55,643] [INFO] Task succeeded: Blastn
[2023-06-27 06:06:55,662] [INFO] Selected 30 target genomes.
[2023-06-27 06:06:55,662] [INFO] Target genome list was writen to GCA_026984135.1_ASM2698413v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:06:55,679] [INFO] Task started: fastANI
[2023-06-27 06:06:55,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgddda0d09-d266-480f-a157-3648f8f8c323/GCA_026984135.1_ASM2698413v1_genomic.fna.gz --refList GCA_026984135.1_ASM2698413v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026984135.1_ASM2698413v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:07:12,857] [INFO] Task succeeded: fastANI
[2023-06-27 06:07:12,861] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:07:12,861] [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_013151015.1	s__JAADJA01 sp013151015	76.231	52	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__JAADJA01;g__JAADJA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:07:12,863] [INFO] GTDB search result was written to GCA_026984135.1_ASM2698413v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:07:12,864] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:07:12,866] [INFO] DFAST_QC result json was written to GCA_026984135.1_ASM2698413v1_genomic.fna/dqc_result.json
[2023-06-27 06:07:12,866] [INFO] DFAST_QC completed!
[2023-06-27 06:07:12,866] [INFO] Total running time: 0h1m47s