[2023-06-13 03:34:34,954] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:34:34,957] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:34:34,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg1860d7d8-411d-4f9f-809c-0084b8528613/dqc_reference
[2023-06-13 03:34:36,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:34:36,379] [INFO] Task started: Prodigal
[2023-06-13 03:34:36,379] [INFO] Running command: gunzip -c /var/lib/cwl/stg93edca74-4773-4040-b257-96f365cb2b20/GCA_022796765.1_ASM2279676v1_genomic.fna.gz | prodigal -d GCA_022796765.1_ASM2279676v1_genomic.fna/cds.fna -a GCA_022796765.1_ASM2279676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:34:39,632] [INFO] Task succeeded: Prodigal
[2023-06-13 03:34:39,633] [INFO] Task started: HMMsearch
[2023-06-13 03:34:39,633] [INFO] Running command: hmmsearch --tblout GCA_022796765.1_ASM2279676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1860d7d8-411d-4f9f-809c-0084b8528613/dqc_reference/reference_markers.hmm GCA_022796765.1_ASM2279676v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:34:39,873] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:34:39,875] [INFO] Found 6/6 markers.
[2023-06-13 03:34:39,901] [INFO] Query marker FASTA was written to GCA_022796765.1_ASM2279676v1_genomic.fna/markers.fasta
[2023-06-13 03:34:39,901] [INFO] Task started: Blastn
[2023-06-13 03:34:39,901] [INFO] Running command: blastn -query GCA_022796765.1_ASM2279676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1860d7d8-411d-4f9f-809c-0084b8528613/dqc_reference/reference_markers.fasta -out GCA_022796765.1_ASM2279676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:34:40,493] [INFO] Task succeeded: Blastn
[2023-06-13 03:34:40,497] [INFO] Selected 24 target genomes.
[2023-06-13 03:34:40,497] [INFO] Target genome list was writen to GCA_022796765.1_ASM2279676v1_genomic.fna/target_genomes.txt
[2023-06-13 03:34:40,502] [INFO] Task started: fastANI
[2023-06-13 03:34:40,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg93edca74-4773-4040-b257-96f365cb2b20/GCA_022796765.1_ASM2279676v1_genomic.fna.gz --refList GCA_022796765.1_ASM2279676v1_genomic.fna/target_genomes.txt --output GCA_022796765.1_ASM2279676v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:34:54,552] [INFO] Task succeeded: fastANI
[2023-06-13 03:34:54,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1860d7d8-411d-4f9f-809c-0084b8528613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:34:54,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1860d7d8-411d-4f9f-809c-0084b8528613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:34:54,555] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:34:54,555] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 03:34:54,555] [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
--------------------------------------------------------------------------------
[2023-06-13 03:34:54,557] [INFO] DFAST Taxonomy check result was written to GCA_022796765.1_ASM2279676v1_genomic.fna/tc_result.tsv
[2023-06-13 03:34:54,557] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:34:54,557] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:34:54,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1860d7d8-411d-4f9f-809c-0084b8528613/dqc_reference/checkm_data
[2023-06-13 03:34:54,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:34:54,582] [INFO] Task started: CheckM
[2023-06-13 03:34:54,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022796765.1_ASM2279676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022796765.1_ASM2279676v1_genomic.fna/checkm_input GCA_022796765.1_ASM2279676v1_genomic.fna/checkm_result
[2023-06-13 03:35:12,781] [INFO] Task succeeded: CheckM
[2023-06-13 03:35:12,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:35:12,803] [INFO] ===== Completeness check finished =====
[2023-06-13 03:35:12,803] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:35:12,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022796765.1_ASM2279676v1_genomic.fna/markers.fasta)
[2023-06-13 03:35:12,804] [INFO] Task started: Blastn
[2023-06-13 03:35:12,804] [INFO] Running command: blastn -query GCA_022796765.1_ASM2279676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1860d7d8-411d-4f9f-809c-0084b8528613/dqc_reference/reference_markers_gtdb.fasta -out GCA_022796765.1_ASM2279676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:35:13,636] [INFO] Task succeeded: Blastn
[2023-06-13 03:35:13,640] [INFO] Selected 18 target genomes.
[2023-06-13 03:35:13,641] [INFO] Target genome list was writen to GCA_022796765.1_ASM2279676v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:35:13,647] [INFO] Task started: fastANI
[2023-06-13 03:35:13,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg93edca74-4773-4040-b257-96f365cb2b20/GCA_022796765.1_ASM2279676v1_genomic.fna.gz --refList GCA_022796765.1_ASM2279676v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022796765.1_ASM2279676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:35:20,889] [INFO] Task succeeded: fastANI
[2023-06-13 03:35:20,899] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:35:20,899] [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_010206265.1	s__CAG-41 sp010206265	98.2933	444	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	97.79	97.79	0.83	0.83	2	conclusive
GCA_910579415.1	s__CAG-41 sp910579415	82.4911	301	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585795.1	s__CAG-41 sp910585795	79.7829	167	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585485.1	s__CAG-41 sp910585485	78.7991	172	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001941225.1	s__CAG-41 sp001941225	78.022	128	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003460745.1	s__CAG-41 sp900066215	77.8371	170	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	97.67	97.16	0.82	0.77	17	-
--------------------------------------------------------------------------------
[2023-06-13 03:35:20,901] [INFO] GTDB search result was written to GCA_022796765.1_ASM2279676v1_genomic.fna/result_gtdb.tsv
[2023-06-13 03:35:20,902] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:35:20,904] [INFO] DFAST_QC result json was written to GCA_022796765.1_ASM2279676v1_genomic.fna/dqc_result.json
[2023-06-13 03:35:20,905] [INFO] DFAST_QC completed!
[2023-06-13 03:35:20,905] [INFO] Total running time: 0h0m46s