[2023-06-28 18:52:32,837] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:52:32,845] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:52:32,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg15127096-e124-4c82-acb7-eaf02c1c9166/dqc_reference
[2023-06-28 18:52:35,140] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:52:35,141] [INFO] Task started: Prodigal
[2023-06-28 18:52:35,141] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d09a28f-c9ea-4b9e-87dd-ab7fe59cc7c6/GCA_017466595.1_ASM1746659v1_genomic.fna.gz | prodigal -d GCA_017466595.1_ASM1746659v1_genomic.fna/cds.fna -a GCA_017466595.1_ASM1746659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:52:39,359] [INFO] Task succeeded: Prodigal
[2023-06-28 18:52:39,360] [INFO] Task started: HMMsearch
[2023-06-28 18:52:39,360] [INFO] Running command: hmmsearch --tblout GCA_017466595.1_ASM1746659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15127096-e124-4c82-acb7-eaf02c1c9166/dqc_reference/reference_markers.hmm GCA_017466595.1_ASM1746659v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:52:39,573] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:52:39,575] [INFO] Found 6/6 markers.
[2023-06-28 18:52:39,605] [INFO] Query marker FASTA was written to GCA_017466595.1_ASM1746659v1_genomic.fna/markers.fasta
[2023-06-28 18:52:39,606] [INFO] Task started: Blastn
[2023-06-28 18:52:39,606] [INFO] Running command: blastn -query GCA_017466595.1_ASM1746659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15127096-e124-4c82-acb7-eaf02c1c9166/dqc_reference/reference_markers.fasta -out GCA_017466595.1_ASM1746659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:52:40,165] [INFO] Task succeeded: Blastn
[2023-06-28 18:52:40,170] [INFO] Selected 23 target genomes.
[2023-06-28 18:52:40,171] [INFO] Target genome list was writen to GCA_017466595.1_ASM1746659v1_genomic.fna/target_genomes.txt
[2023-06-28 18:52:40,175] [INFO] Task started: fastANI
[2023-06-28 18:52:40,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d09a28f-c9ea-4b9e-87dd-ab7fe59cc7c6/GCA_017466595.1_ASM1746659v1_genomic.fna.gz --refList GCA_017466595.1_ASM1746659v1_genomic.fna/target_genomes.txt --output GCA_017466595.1_ASM1746659v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:52:51,634] [INFO] Task succeeded: fastANI
[2023-06-28 18:52:51,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15127096-e124-4c82-acb7-eaf02c1c9166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:52:51,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15127096-e124-4c82-acb7-eaf02c1c9166/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:52:51,637] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:52:51,638] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:52:51,638] [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 18:52:51,640] [INFO] DFAST Taxonomy check result was written to GCA_017466595.1_ASM1746659v1_genomic.fna/tc_result.tsv
[2023-06-28 18:52:51,641] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:52:51,642] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:52:51,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15127096-e124-4c82-acb7-eaf02c1c9166/dqc_reference/checkm_data
[2023-06-28 18:52:51,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:52:51,670] [INFO] Task started: CheckM
[2023-06-28 18:52:51,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017466595.1_ASM1746659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017466595.1_ASM1746659v1_genomic.fna/checkm_input GCA_017466595.1_ASM1746659v1_genomic.fna/checkm_result
[2023-06-28 18:53:11,122] [INFO] Task succeeded: CheckM
[2023-06-28 18:53:11,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 18:53:11,148] [INFO] ===== Completeness check finished =====
[2023-06-28 18:53:11,148] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:53:11,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017466595.1_ASM1746659v1_genomic.fna/markers.fasta)
[2023-06-28 18:53:11,149] [INFO] Task started: Blastn
[2023-06-28 18:53:11,149] [INFO] Running command: blastn -query GCA_017466595.1_ASM1746659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15127096-e124-4c82-acb7-eaf02c1c9166/dqc_reference/reference_markers_gtdb.fasta -out GCA_017466595.1_ASM1746659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:53:11,956] [INFO] Task succeeded: Blastn
[2023-06-28 18:53:11,961] [INFO] Selected 28 target genomes.
[2023-06-28 18:53:11,961] [INFO] Target genome list was writen to GCA_017466595.1_ASM1746659v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:53:11,969] [INFO] Task started: fastANI
[2023-06-28 18:53:11,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d09a28f-c9ea-4b9e-87dd-ab7fe59cc7c6/GCA_017466595.1_ASM1746659v1_genomic.fna.gz --refList GCA_017466595.1_ASM1746659v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017466595.1_ASM1746659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:53:22,756] [INFO] Task succeeded: fastANI
[2023-06-28 18:53:22,766] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:53:22,766] [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_017558545.1	s__RGIG7114 sp017558545	80.4109	157	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG7114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068425.1	s__RGIG7114 sp015068425	79.6532	195	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG7114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067465.1	s__RGIG7114 sp015067465	77.2961	71	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG7114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068365.1	s__RGIG7114 sp015068365	76.9831	99	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG7114	95.0	98.05	98.05	0.85	0.85	2	-
GCA_900316205.1	s__Limivicinus sp900316205	76.6985	62	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.11	98.31	0.88	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-28 18:53:22,768] [INFO] GTDB search result was written to GCA_017466595.1_ASM1746659v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:53:22,768] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:53:22,771] [INFO] DFAST_QC result json was written to GCA_017466595.1_ASM1746659v1_genomic.fna/dqc_result.json
[2023-06-28 18:53:22,771] [INFO] DFAST_QC completed!
[2023-06-28 18:53:22,771] [INFO] Total running time: 0h0m50s