[2023-06-28 00:20:37,326] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:20:37,328] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:20:37,328] [INFO] DQC Reference Directory: /var/lib/cwl/stga12cf609-e03d-4c91-a4f0-04fc1ff901b0/dqc_reference
[2023-06-28 00:20:38,617] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:20:38,618] [INFO] Task started: Prodigal
[2023-06-28 00:20:38,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg11ef5121-389b-4400-9eb2-393627b22968/GCA_017559015.1_ASM1755901v1_genomic.fna.gz | prodigal -d GCA_017559015.1_ASM1755901v1_genomic.fna/cds.fna -a GCA_017559015.1_ASM1755901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:20:40,592] [INFO] Task succeeded: Prodigal
[2023-06-28 00:20:40,593] [INFO] Task started: HMMsearch
[2023-06-28 00:20:40,593] [INFO] Running command: hmmsearch --tblout GCA_017559015.1_ASM1755901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga12cf609-e03d-4c91-a4f0-04fc1ff901b0/dqc_reference/reference_markers.hmm GCA_017559015.1_ASM1755901v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:20:40,805] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:20:40,807] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg11ef5121-389b-4400-9eb2-393627b22968/GCA_017559015.1_ASM1755901v1_genomic.fna.gz]
[2023-06-28 00:20:40,829] [INFO] Query marker FASTA was written to GCA_017559015.1_ASM1755901v1_genomic.fna/markers.fasta
[2023-06-28 00:20:40,829] [INFO] Task started: Blastn
[2023-06-28 00:20:40,830] [INFO] Running command: blastn -query GCA_017559015.1_ASM1755901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga12cf609-e03d-4c91-a4f0-04fc1ff901b0/dqc_reference/reference_markers.fasta -out GCA_017559015.1_ASM1755901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:20:41,405] [INFO] Task succeeded: Blastn
[2023-06-28 00:20:41,410] [INFO] Selected 14 target genomes.
[2023-06-28 00:20:41,410] [INFO] Target genome list was writen to GCA_017559015.1_ASM1755901v1_genomic.fna/target_genomes.txt
[2023-06-28 00:20:41,416] [INFO] Task started: fastANI
[2023-06-28 00:20:41,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg11ef5121-389b-4400-9eb2-393627b22968/GCA_017559015.1_ASM1755901v1_genomic.fna.gz --refList GCA_017559015.1_ASM1755901v1_genomic.fna/target_genomes.txt --output GCA_017559015.1_ASM1755901v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:20:50,332] [INFO] Task succeeded: fastANI
[2023-06-28 00:20:50,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga12cf609-e03d-4c91-a4f0-04fc1ff901b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:20:50,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga12cf609-e03d-4c91-a4f0-04fc1ff901b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:20:50,334] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:20:50,334] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:20:50,334] [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 00:20:50,336] [INFO] DFAST Taxonomy check result was written to GCA_017559015.1_ASM1755901v1_genomic.fna/tc_result.tsv
[2023-06-28 00:20:50,337] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:20:50,337] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:20:50,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga12cf609-e03d-4c91-a4f0-04fc1ff901b0/dqc_reference/checkm_data
[2023-06-28 00:20:50,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:20:50,361] [INFO] Task started: CheckM
[2023-06-28 00:20:50,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017559015.1_ASM1755901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017559015.1_ASM1755901v1_genomic.fna/checkm_input GCA_017559015.1_ASM1755901v1_genomic.fna/checkm_result
[2023-06-28 00:21:04,803] [INFO] Task succeeded: CheckM
[2023-06-28 00:21:04,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.64%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:21:04,829] [INFO] ===== Completeness check finished =====
[2023-06-28 00:21:04,830] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:21:04,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017559015.1_ASM1755901v1_genomic.fna/markers.fasta)
[2023-06-28 00:21:04,830] [INFO] Task started: Blastn
[2023-06-28 00:21:04,831] [INFO] Running command: blastn -query GCA_017559015.1_ASM1755901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga12cf609-e03d-4c91-a4f0-04fc1ff901b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_017559015.1_ASM1755901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:21:05,669] [INFO] Task succeeded: Blastn
[2023-06-28 00:21:05,672] [INFO] Selected 12 target genomes.
[2023-06-28 00:21:05,673] [INFO] Target genome list was writen to GCA_017559015.1_ASM1755901v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:21:05,713] [INFO] Task started: fastANI
[2023-06-28 00:21:05,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg11ef5121-389b-4400-9eb2-393627b22968/GCA_017559015.1_ASM1755901v1_genomic.fna.gz --refList GCA_017559015.1_ASM1755901v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017559015.1_ASM1755901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:21:10,060] [INFO] Task succeeded: fastANI
[2023-06-28 00:21:10,070] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:21:10,070] [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_017379935.1	s__CAG-488 sp017379935	86.1321	203	218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017415025.1	s__CAG-488 sp017415025	84.5205	201	218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	97.47	97.27	0.84	0.82	3	-
GCA_017481575.1	s__CAG-488 sp017481575	82.4973	172	218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017522225.1	s__CAG-488 sp017522225	82.4459	154	218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017380575.1	s__CAG-488 sp017380575	80.8876	158	218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625835.1	s__CAG-488 sp017625835	80.6428	135	218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936645.1	s__CAG-488 sp017936645	79.1557	113	218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:21:10,073] [INFO] GTDB search result was written to GCA_017559015.1_ASM1755901v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:21:10,074] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:21:10,077] [INFO] DFAST_QC result json was written to GCA_017559015.1_ASM1755901v1_genomic.fna/dqc_result.json
[2023-06-28 00:21:10,078] [INFO] DFAST_QC completed!
[2023-06-28 00:21:10,078] [INFO] Total running time: 0h0m33s