[2023-06-30 00:56:25,757] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:56:25,760] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:56:25,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d9e2fa4-d40d-4d33-9a21-8896113133db/dqc_reference
[2023-06-30 00:56:26,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:56:26,976] [INFO] Task started: Prodigal
[2023-06-30 00:56:26,976] [INFO] Running command: gunzip -c /var/lib/cwl/stg0beac565-6802-48e0-a76e-577a576f26c7/GCA_024643525.1_ASM2464352v1_genomic.fna.gz | prodigal -d GCA_024643525.1_ASM2464352v1_genomic.fna/cds.fna -a GCA_024643525.1_ASM2464352v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:56:39,602] [INFO] Task succeeded: Prodigal
[2023-06-30 00:56:39,603] [INFO] Task started: HMMsearch
[2023-06-30 00:56:39,603] [INFO] Running command: hmmsearch --tblout GCA_024643525.1_ASM2464352v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d9e2fa4-d40d-4d33-9a21-8896113133db/dqc_reference/reference_markers.hmm GCA_024643525.1_ASM2464352v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:56:39,865] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:56:39,866] [INFO] Found 6/6 markers.
[2023-06-30 00:56:39,901] [INFO] Query marker FASTA was written to GCA_024643525.1_ASM2464352v1_genomic.fna/markers.fasta
[2023-06-30 00:56:39,902] [INFO] Task started: Blastn
[2023-06-30 00:56:39,902] [INFO] Running command: blastn -query GCA_024643525.1_ASM2464352v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d9e2fa4-d40d-4d33-9a21-8896113133db/dqc_reference/reference_markers.fasta -out GCA_024643525.1_ASM2464352v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:40,479] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:40,484] [INFO] Selected 24 target genomes.
[2023-06-30 00:56:40,484] [INFO] Target genome list was writen to GCA_024643525.1_ASM2464352v1_genomic.fna/target_genomes.txt
[2023-06-30 00:56:40,487] [INFO] Task started: fastANI
[2023-06-30 00:56:40,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg0beac565-6802-48e0-a76e-577a576f26c7/GCA_024643525.1_ASM2464352v1_genomic.fna.gz --refList GCA_024643525.1_ASM2464352v1_genomic.fna/target_genomes.txt --output GCA_024643525.1_ASM2464352v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:56:56,889] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:56,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d9e2fa4-d40d-4d33-9a21-8896113133db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:56:56,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d9e2fa4-d40d-4d33-9a21-8896113133db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:56:56,892] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:56:56,892] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:56:56,893] [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
--------------------------------------------------------------------------------
[2023-06-30 00:56:56,895] [INFO] DFAST Taxonomy check result was written to GCA_024643525.1_ASM2464352v1_genomic.fna/tc_result.tsv
[2023-06-30 00:56:56,896] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:56:56,896] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:56:56,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d9e2fa4-d40d-4d33-9a21-8896113133db/dqc_reference/checkm_data
[2023-06-30 00:56:56,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:56:56,938] [INFO] Task started: CheckM
[2023-06-30 00:56:56,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024643525.1_ASM2464352v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024643525.1_ASM2464352v1_genomic.fna/checkm_input GCA_024643525.1_ASM2464352v1_genomic.fna/checkm_result
[2023-06-30 00:57:38,798] [INFO] Task succeeded: CheckM
[2023-06-30 00:57:38,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 20.83%
Strain heterogeneity: 42.11%
--------------------------------------------------------------------------------
[2023-06-30 00:57:38,829] [INFO] ===== Completeness check finished =====
[2023-06-30 00:57:38,829] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:57:38,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024643525.1_ASM2464352v1_genomic.fna/markers.fasta)
[2023-06-30 00:57:38,830] [INFO] Task started: Blastn
[2023-06-30 00:57:38,830] [INFO] Running command: blastn -query GCA_024643525.1_ASM2464352v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d9e2fa4-d40d-4d33-9a21-8896113133db/dqc_reference/reference_markers_gtdb.fasta -out GCA_024643525.1_ASM2464352v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:57:39,629] [INFO] Task succeeded: Blastn
[2023-06-30 00:57:39,634] [INFO] Selected 25 target genomes.
[2023-06-30 00:57:39,634] [INFO] Target genome list was writen to GCA_024643525.1_ASM2464352v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:57:39,677] [INFO] Task started: fastANI
[2023-06-30 00:57:39,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg0beac565-6802-48e0-a76e-577a576f26c7/GCA_024643525.1_ASM2464352v1_genomic.fna.gz --refList GCA_024643525.1_ASM2464352v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024643525.1_ASM2464352v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:57:57,761] [INFO] Task succeeded: fastANI
[2023-06-30 00:57:57,768] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:57:57,768] [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_016709845.1	s__ELB16-189 sp016709845	76.3909	50	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344065.1	s__UBA2336 sp002344065	75.7776	50	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA2336	95.0	99.89	99.67	0.98	0.95	4	-
GCA_016787565.1	s__JAEUUG01 sp016787565	75.5397	58	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__JAEUUG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:57:57,771] [INFO] GTDB search result was written to GCA_024643525.1_ASM2464352v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:57:57,771] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:57:57,774] [INFO] DFAST_QC result json was written to GCA_024643525.1_ASM2464352v1_genomic.fna/dqc_result.json
[2023-06-30 00:57:57,774] [INFO] DFAST_QC completed!
[2023-06-30 00:57:57,775] [INFO] Total running time: 0h1m32s