[2023-06-27 10:50:11,505] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:50:11,707] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:50:11,707] [INFO] DQC Reference Directory: /var/lib/cwl/stgede51849-1485-426c-84ce-91e51fe3409a/dqc_reference
[2023-06-27 10:50:13,027] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:50:13,028] [INFO] Task started: Prodigal
[2023-06-27 10:50:13,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f91499f-4fb5-464a-a479-4407901c38b9/GCA_026932035.1_ASM2693203v1_genomic.fna.gz | prodigal -d GCA_026932035.1_ASM2693203v1_genomic.fna/cds.fna -a GCA_026932035.1_ASM2693203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:50:20,720] [INFO] Task succeeded: Prodigal
[2023-06-27 10:50:20,721] [INFO] Task started: HMMsearch
[2023-06-27 10:50:20,721] [INFO] Running command: hmmsearch --tblout GCA_026932035.1_ASM2693203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgede51849-1485-426c-84ce-91e51fe3409a/dqc_reference/reference_markers.hmm GCA_026932035.1_ASM2693203v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:50:20,967] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:50:20,969] [INFO] Found 6/6 markers.
[2023-06-27 10:50:21,000] [INFO] Query marker FASTA was written to GCA_026932035.1_ASM2693203v1_genomic.fna/markers.fasta
[2023-06-27 10:50:21,001] [INFO] Task started: Blastn
[2023-06-27 10:50:21,001] [INFO] Running command: blastn -query GCA_026932035.1_ASM2693203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede51849-1485-426c-84ce-91e51fe3409a/dqc_reference/reference_markers.fasta -out GCA_026932035.1_ASM2693203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:50:21,592] [INFO] Task succeeded: Blastn
[2023-06-27 10:50:21,597] [INFO] Selected 22 target genomes.
[2023-06-27 10:50:21,598] [INFO] Target genome list was writen to GCA_026932035.1_ASM2693203v1_genomic.fna/target_genomes.txt
[2023-06-27 10:50:21,604] [INFO] Task started: fastANI
[2023-06-27 10:50:21,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f91499f-4fb5-464a-a479-4407901c38b9/GCA_026932035.1_ASM2693203v1_genomic.fna.gz --refList GCA_026932035.1_ASM2693203v1_genomic.fna/target_genomes.txt --output GCA_026932035.1_ASM2693203v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:50:34,572] [INFO] Task succeeded: fastANI
[2023-06-27 10:50:34,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgede51849-1485-426c-84ce-91e51fe3409a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:50:34,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgede51849-1485-426c-84ce-91e51fe3409a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:50:34,576] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:50:34,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 10:50:34,576] [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 10:50:34,578] [INFO] DFAST Taxonomy check result was written to GCA_026932035.1_ASM2693203v1_genomic.fna/tc_result.tsv
[2023-06-27 10:50:34,579] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:50:34,579] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:50:34,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgede51849-1485-426c-84ce-91e51fe3409a/dqc_reference/checkm_data
[2023-06-27 10:50:34,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:50:34,633] [INFO] Task started: CheckM
[2023-06-27 10:50:34,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026932035.1_ASM2693203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026932035.1_ASM2693203v1_genomic.fna/checkm_input GCA_026932035.1_ASM2693203v1_genomic.fna/checkm_result
[2023-06-27 10:51:03,876] [INFO] Task succeeded: CheckM
[2023-06-27 10:51:03,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 10:51:03,915] [INFO] ===== Completeness check finished =====
[2023-06-27 10:51:03,915] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:51:03,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026932035.1_ASM2693203v1_genomic.fna/markers.fasta)
[2023-06-27 10:51:03,916] [INFO] Task started: Blastn
[2023-06-27 10:51:03,916] [INFO] Running command: blastn -query GCA_026932035.1_ASM2693203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede51849-1485-426c-84ce-91e51fe3409a/dqc_reference/reference_markers_gtdb.fasta -out GCA_026932035.1_ASM2693203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:51:04,705] [INFO] Task succeeded: Blastn
[2023-06-27 10:51:04,711] [INFO] Selected 20 target genomes.
[2023-06-27 10:51:04,711] [INFO] Target genome list was writen to GCA_026932035.1_ASM2693203v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:51:04,746] [INFO] Task started: fastANI
[2023-06-27 10:51:04,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f91499f-4fb5-464a-a479-4407901c38b9/GCA_026932035.1_ASM2693203v1_genomic.fna.gz --refList GCA_026932035.1_ASM2693203v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026932035.1_ASM2693203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:51:16,527] [INFO] Task succeeded: fastANI
[2023-06-27 10:51:16,535] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 10:51:16,535] [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_008933765.1	s__UTCHB3 sp002050155	99.9653	1079	1115	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__UTCHB3	95.0	99.95	99.91	0.99	0.99	3	conclusive
GCA_016707285.1	s__UTCHB3 sp016707285	76.7679	115	1115	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__UTCHB3	95.0	98.81	98.46	0.95	0.94	4	-
GCA_008363265.1	s__UTCHB3 sp008363265	76.1854	117	1115	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__UTCHB3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 10:51:16,538] [INFO] GTDB search result was written to GCA_026932035.1_ASM2693203v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:51:16,538] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:51:16,541] [INFO] DFAST_QC result json was written to GCA_026932035.1_ASM2693203v1_genomic.fna/dqc_result.json
[2023-06-27 10:51:16,541] [INFO] DFAST_QC completed!
[2023-06-27 10:51:16,541] [INFO] Total running time: 0h1m5s