[2023-06-17 11:08:17,580] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:08:17,584] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:08:17,584] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb3c0579-1a7c-4466-aa6f-f85dc32dfbc7/dqc_reference
[2023-06-17 11:08:18,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:08:18,963] [INFO] Task started: Prodigal
[2023-06-17 11:08:18,963] [INFO] Running command: gunzip -c /var/lib/cwl/stg29274408-8bd6-473a-aca5-3ded1cd83183/GCA_028705135.1_ASM2870513v1_genomic.fna.gz | prodigal -d GCA_028705135.1_ASM2870513v1_genomic.fna/cds.fna -a GCA_028705135.1_ASM2870513v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:08:30,136] [INFO] Task succeeded: Prodigal
[2023-06-17 11:08:30,137] [INFO] Task started: HMMsearch
[2023-06-17 11:08:30,137] [INFO] Running command: hmmsearch --tblout GCA_028705135.1_ASM2870513v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb3c0579-1a7c-4466-aa6f-f85dc32dfbc7/dqc_reference/reference_markers.hmm GCA_028705135.1_ASM2870513v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:08:30,398] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:08:30,400] [INFO] Found 6/6 markers.
[2023-06-17 11:08:30,424] [INFO] Query marker FASTA was written to GCA_028705135.1_ASM2870513v1_genomic.fna/markers.fasta
[2023-06-17 11:08:30,425] [INFO] Task started: Blastn
[2023-06-17 11:08:30,425] [INFO] Running command: blastn -query GCA_028705135.1_ASM2870513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb3c0579-1a7c-4466-aa6f-f85dc32dfbc7/dqc_reference/reference_markers.fasta -out GCA_028705135.1_ASM2870513v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:08:31,010] [INFO] Task succeeded: Blastn
[2023-06-17 11:08:31,015] [INFO] Selected 24 target genomes.
[2023-06-17 11:08:31,016] [INFO] Target genome list was writen to GCA_028705135.1_ASM2870513v1_genomic.fna/target_genomes.txt
[2023-06-17 11:08:31,022] [INFO] Task started: fastANI
[2023-06-17 11:08:31,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg29274408-8bd6-473a-aca5-3ded1cd83183/GCA_028705135.1_ASM2870513v1_genomic.fna.gz --refList GCA_028705135.1_ASM2870513v1_genomic.fna/target_genomes.txt --output GCA_028705135.1_ASM2870513v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:08:46,355] [INFO] Task succeeded: fastANI
[2023-06-17 11:08:46,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb3c0579-1a7c-4466-aa6f-f85dc32dfbc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:08:46,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb3c0579-1a7c-4466-aa6f-f85dc32dfbc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:08:46,357] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:08:46,358] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 11:08:46,358] [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
--------------------------------------------------------------------------------
[2023-06-17 11:08:46,360] [INFO] DFAST Taxonomy check result was written to GCA_028705135.1_ASM2870513v1_genomic.fna/tc_result.tsv
[2023-06-17 11:08:46,361] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:08:46,361] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:08:46,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb3c0579-1a7c-4466-aa6f-f85dc32dfbc7/dqc_reference/checkm_data
[2023-06-17 11:08:46,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:08:46,395] [INFO] Task started: CheckM
[2023-06-17 11:08:46,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028705135.1_ASM2870513v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028705135.1_ASM2870513v1_genomic.fna/checkm_input GCA_028705135.1_ASM2870513v1_genomic.fna/checkm_result
[2023-06-17 11:09:22,824] [INFO] Task succeeded: CheckM
[2023-06-17 11:09:22,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:09:22,846] [INFO] ===== Completeness check finished =====
[2023-06-17 11:09:22,846] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:09:22,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028705135.1_ASM2870513v1_genomic.fna/markers.fasta)
[2023-06-17 11:09:22,847] [INFO] Task started: Blastn
[2023-06-17 11:09:22,847] [INFO] Running command: blastn -query GCA_028705135.1_ASM2870513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb3c0579-1a7c-4466-aa6f-f85dc32dfbc7/dqc_reference/reference_markers_gtdb.fasta -out GCA_028705135.1_ASM2870513v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:09:23,616] [INFO] Task succeeded: Blastn
[2023-06-17 11:09:23,620] [INFO] Selected 9 target genomes.
[2023-06-17 11:09:23,620] [INFO] Target genome list was writen to GCA_028705135.1_ASM2870513v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:09:23,626] [INFO] Task started: fastANI
[2023-06-17 11:09:23,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg29274408-8bd6-473a-aca5-3ded1cd83183/GCA_028705135.1_ASM2870513v1_genomic.fna.gz --refList GCA_028705135.1_ASM2870513v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028705135.1_ASM2870513v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:09:27,619] [INFO] Task succeeded: fastANI
[2023-06-17 11:09:27,629] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:09:27,630] [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_002070565.1	s__DMER64 sp002070565	96.4712	534	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.14	99.14	0.85	0.85	2	conclusive
GCA_002305545.1	s__DMER64 sp002305545	87.6281	549	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.79	99.75	0.96	0.96	3	-
GCA_002409325.1	s__DMER64 sp002409325	86.7625	550	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002071385.1	s__DMER64 sp002071385	83.8807	517	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.62	99.43	0.93	0.90	7	-
GCA_001603455.1	s__DMER64 sp001603455	78.8754	262	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.83	99.68	0.89	0.76	4	-
GCA_001512865.1	s__DMER64 sp001512865	78.2269	246	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.73	99.73	0.89	0.89	2	-
GCA_002071175.1	s__DMER64 sp002071175	78.1465	163	649	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:09:27,632] [INFO] GTDB search result was written to GCA_028705135.1_ASM2870513v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:09:27,632] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:09:27,635] [INFO] DFAST_QC result json was written to GCA_028705135.1_ASM2870513v1_genomic.fna/dqc_result.json
[2023-06-17 11:09:27,635] [INFO] DFAST_QC completed!
[2023-06-17 11:09:27,635] [INFO] Total running time: 0h1m10s