[2023-06-28 10:01:32,924] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:01:32,930] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:01:32,930] [INFO] DQC Reference Directory: /var/lib/cwl/stgb24bcd98-2e8e-42c5-9930-0eed7dcebc09/dqc_reference
[2023-06-28 10:01:35,304] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:01:35,305] [INFO] Task started: Prodigal
[2023-06-28 10:01:35,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg9227529e-5cad-4a62-8853-1a20794de0c8/GCA_002708665.1_ASM270866v1_genomic.fna.gz | prodigal -d GCA_002708665.1_ASM270866v1_genomic.fna/cds.fna -a GCA_002708665.1_ASM270866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:01:38,523] [INFO] Task succeeded: Prodigal
[2023-06-28 10:01:38,524] [INFO] Task started: HMMsearch
[2023-06-28 10:01:38,524] [INFO] Running command: hmmsearch --tblout GCA_002708665.1_ASM270866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb24bcd98-2e8e-42c5-9930-0eed7dcebc09/dqc_reference/reference_markers.hmm GCA_002708665.1_ASM270866v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:01:38,750] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:01:38,752] [INFO] Found 6/6 markers.
[2023-06-28 10:01:38,774] [INFO] Query marker FASTA was written to GCA_002708665.1_ASM270866v1_genomic.fna/markers.fasta
[2023-06-28 10:01:38,774] [INFO] Task started: Blastn
[2023-06-28 10:01:38,774] [INFO] Running command: blastn -query GCA_002708665.1_ASM270866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb24bcd98-2e8e-42c5-9930-0eed7dcebc09/dqc_reference/reference_markers.fasta -out GCA_002708665.1_ASM270866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:01:39,340] [INFO] Task succeeded: Blastn
[2023-06-28 10:01:39,345] [INFO] Selected 11 target genomes.
[2023-06-28 10:01:39,345] [INFO] Target genome list was writen to GCA_002708665.1_ASM270866v1_genomic.fna/target_genomes.txt
[2023-06-28 10:01:39,350] [INFO] Task started: fastANI
[2023-06-28 10:01:39,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg9227529e-5cad-4a62-8853-1a20794de0c8/GCA_002708665.1_ASM270866v1_genomic.fna.gz --refList GCA_002708665.1_ASM270866v1_genomic.fna/target_genomes.txt --output GCA_002708665.1_ASM270866v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:01:44,473] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:44,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb24bcd98-2e8e-42c5-9930-0eed7dcebc09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:01:44,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb24bcd98-2e8e-42c5-9930-0eed7dcebc09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:01:44,476] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:01:44,476] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:01:44,477] [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
--------------------------------------------------------------------------------
[2023-06-28 10:01:44,480] [INFO] DFAST Taxonomy check result was written to GCA_002708665.1_ASM270866v1_genomic.fna/tc_result.tsv
[2023-06-28 10:01:44,481] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:01:44,481] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:01:44,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb24bcd98-2e8e-42c5-9930-0eed7dcebc09/dqc_reference/checkm_data
[2023-06-28 10:01:44,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:01:44,511] [INFO] Task started: CheckM
[2023-06-28 10:01:44,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708665.1_ASM270866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708665.1_ASM270866v1_genomic.fna/checkm_input GCA_002708665.1_ASM270866v1_genomic.fna/checkm_result
[2023-06-28 10:02:01,852] [INFO] Task succeeded: CheckM
[2023-06-28 10:02:01,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:02:01,879] [INFO] ===== Completeness check finished =====
[2023-06-28 10:02:01,880] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:02:01,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708665.1_ASM270866v1_genomic.fna/markers.fasta)
[2023-06-28 10:02:01,881] [INFO] Task started: Blastn
[2023-06-28 10:02:01,881] [INFO] Running command: blastn -query GCA_002708665.1_ASM270866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb24bcd98-2e8e-42c5-9930-0eed7dcebc09/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708665.1_ASM270866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:02:02,643] [INFO] Task succeeded: Blastn
[2023-06-28 10:02:02,648] [INFO] Selected 16 target genomes.
[2023-06-28 10:02:02,649] [INFO] Target genome list was writen to GCA_002708665.1_ASM270866v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:02:02,664] [INFO] Task started: fastANI
[2023-06-28 10:02:02,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg9227529e-5cad-4a62-8853-1a20794de0c8/GCA_002708665.1_ASM270866v1_genomic.fna.gz --refList GCA_002708665.1_ASM270866v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708665.1_ASM270866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:02:08,465] [INFO] Task succeeded: fastANI
[2023-06-28 10:02:08,472] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:02:08,472] [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_002697535.1	s__GCA-002719695 sp002697535	95.3341	430	621	d__Bacteria;p__Margulisbacteria;c__Marinamargulisbacteria;o__GCA-2716485;f__GCA-002719695;g__GCA-002719695	95.0	96.60	95.39	0.86	0.85	4	conclusive
GCA_002716725.1	s__GCA-002719695 sp002716725	81.342	245	621	d__Bacteria;p__Margulisbacteria;c__Marinamargulisbacteria;o__GCA-2716485;f__GCA-002719695;g__GCA-002719695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719695.1	s__GCA-002719695 sp002719695	80.8284	197	621	d__Bacteria;p__Margulisbacteria;c__Marinamargulisbacteria;o__GCA-2716485;f__GCA-002719695;g__GCA-002719695	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:02:08,474] [INFO] GTDB search result was written to GCA_002708665.1_ASM270866v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:02:08,475] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:02:08,477] [INFO] DFAST_QC result json was written to GCA_002708665.1_ASM270866v1_genomic.fna/dqc_result.json
[2023-06-28 10:02:08,478] [INFO] DFAST_QC completed!
[2023-06-28 10:02:08,478] [INFO] Total running time: 0h0m36s