[2023-06-28 00:28:10,841] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:28:10,845] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:28:10,845] [INFO] DQC Reference Directory: /var/lib/cwl/stga346a8ba-b179-4c6b-a5c5-65b1963a4529/dqc_reference
[2023-06-28 00:28:12,183] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:28:12,184] [INFO] Task started: Prodigal
[2023-06-28 00:28:12,184] [INFO] Running command: gunzip -c /var/lib/cwl/stga4d61abf-2deb-47fd-bc93-ccff461500b2/GCA_017556945.1_ASM1755694v1_genomic.fna.gz | prodigal -d GCA_017556945.1_ASM1755694v1_genomic.fna/cds.fna -a GCA_017556945.1_ASM1755694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:28:15,018] [INFO] Task succeeded: Prodigal
[2023-06-28 00:28:15,018] [INFO] Task started: HMMsearch
[2023-06-28 00:28:15,019] [INFO] Running command: hmmsearch --tblout GCA_017556945.1_ASM1755694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga346a8ba-b179-4c6b-a5c5-65b1963a4529/dqc_reference/reference_markers.hmm GCA_017556945.1_ASM1755694v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:28:15,224] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:28:15,225] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga4d61abf-2deb-47fd-bc93-ccff461500b2/GCA_017556945.1_ASM1755694v1_genomic.fna.gz]
[2023-06-28 00:28:15,245] [INFO] Query marker FASTA was written to GCA_017556945.1_ASM1755694v1_genomic.fna/markers.fasta
[2023-06-28 00:28:15,246] [INFO] Task started: Blastn
[2023-06-28 00:28:15,246] [INFO] Running command: blastn -query GCA_017556945.1_ASM1755694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga346a8ba-b179-4c6b-a5c5-65b1963a4529/dqc_reference/reference_markers.fasta -out GCA_017556945.1_ASM1755694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:28:15,908] [INFO] Task succeeded: Blastn
[2023-06-28 00:28:15,912] [INFO] Selected 15 target genomes.
[2023-06-28 00:28:15,912] [INFO] Target genome list was writen to GCA_017556945.1_ASM1755694v1_genomic.fna/target_genomes.txt
[2023-06-28 00:28:15,913] [INFO] Task started: fastANI
[2023-06-28 00:28:15,913] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d61abf-2deb-47fd-bc93-ccff461500b2/GCA_017556945.1_ASM1755694v1_genomic.fna.gz --refList GCA_017556945.1_ASM1755694v1_genomic.fna/target_genomes.txt --output GCA_017556945.1_ASM1755694v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:28:24,032] [INFO] Task succeeded: fastANI
[2023-06-28 00:28:24,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga346a8ba-b179-4c6b-a5c5-65b1963a4529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:28:24,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga346a8ba-b179-4c6b-a5c5-65b1963a4529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:28:24,034] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:28:24,034] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:28:24,034] [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 00:28:24,036] [INFO] DFAST Taxonomy check result was written to GCA_017556945.1_ASM1755694v1_genomic.fna/tc_result.tsv
[2023-06-28 00:28:24,037] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:28:24,037] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:28:24,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga346a8ba-b179-4c6b-a5c5-65b1963a4529/dqc_reference/checkm_data
[2023-06-28 00:28:24,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:28:24,056] [INFO] Task started: CheckM
[2023-06-28 00:28:24,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017556945.1_ASM1755694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017556945.1_ASM1755694v1_genomic.fna/checkm_input GCA_017556945.1_ASM1755694v1_genomic.fna/checkm_result
[2023-06-28 00:28:41,265] [INFO] Task succeeded: CheckM
[2023-06-28 00:28:41,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.09%
Contamintation: 4.17%
Strain heterogeneity: 62.50%
--------------------------------------------------------------------------------
[2023-06-28 00:28:41,301] [INFO] ===== Completeness check finished =====
[2023-06-28 00:28:41,301] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:28:41,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017556945.1_ASM1755694v1_genomic.fna/markers.fasta)
[2023-06-28 00:28:41,302] [INFO] Task started: Blastn
[2023-06-28 00:28:41,302] [INFO] Running command: blastn -query GCA_017556945.1_ASM1755694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga346a8ba-b179-4c6b-a5c5-65b1963a4529/dqc_reference/reference_markers_gtdb.fasta -out GCA_017556945.1_ASM1755694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:28:42,283] [INFO] Task succeeded: Blastn
[2023-06-28 00:28:42,305] [INFO] Selected 8 target genomes.
[2023-06-28 00:28:42,306] [INFO] Target genome list was writen to GCA_017556945.1_ASM1755694v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:28:42,309] [INFO] Task started: fastANI
[2023-06-28 00:28:42,310] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d61abf-2deb-47fd-bc93-ccff461500b2/GCA_017556945.1_ASM1755694v1_genomic.fna.gz --refList GCA_017556945.1_ASM1755694v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017556945.1_ASM1755694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:28:45,166] [INFO] Task succeeded: fastANI
[2023-06-28 00:28:45,178] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:28:45,179] [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_015067145.1	s__RGIG3102 sp015067145	85.9212	234	307	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435045.1	s__RGIG3102 sp017435045	84.8238	226	307	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017505635.1	s__RGIG3102 sp017505635	84.771	227	307	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436765.1	s__RGIG3102 sp017436765	84.5021	225	307	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017442085.1	s__RGIG3102 sp017442085	84.0247	219	307	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067245.1	s__RGIG3102 sp015067245	82.8743	191	307	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018109965.1	s__RGIG3102 sp018109965	82.1367	161	307	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067215.1	s__RGIG3102 sp015067215	81.0835	177	307	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:28:45,181] [INFO] GTDB search result was written to GCA_017556945.1_ASM1755694v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:28:45,182] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:28:45,184] [INFO] DFAST_QC result json was written to GCA_017556945.1_ASM1755694v1_genomic.fna/dqc_result.json
[2023-06-28 00:28:45,184] [INFO] DFAST_QC completed!
[2023-06-28 00:28:45,184] [INFO] Total running time: 0h0m34s