[2023-06-28 03:49:36,734] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:49:36,737] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:49:36,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg43f5ec81-d0b9-4421-a427-d39e6cb92417/dqc_reference
[2023-06-28 03:49:38,213] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:49:38,214] [INFO] Task started: Prodigal
[2023-06-28 03:49:38,214] [INFO] Running command: gunzip -c /var/lib/cwl/stg80e1e968-4229-46b4-93f4-081bbdde5f5b/GCA_017421065.1_ASM1742106v1_genomic.fna.gz | prodigal -d GCA_017421065.1_ASM1742106v1_genomic.fna/cds.fna -a GCA_017421065.1_ASM1742106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:49:44,412] [INFO] Task succeeded: Prodigal
[2023-06-28 03:49:44,413] [INFO] Task started: HMMsearch
[2023-06-28 03:49:44,413] [INFO] Running command: hmmsearch --tblout GCA_017421065.1_ASM1742106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43f5ec81-d0b9-4421-a427-d39e6cb92417/dqc_reference/reference_markers.hmm GCA_017421065.1_ASM1742106v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:49:44,734] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:49:44,735] [INFO] Found 6/6 markers.
[2023-06-28 03:49:44,761] [INFO] Query marker FASTA was written to GCA_017421065.1_ASM1742106v1_genomic.fna/markers.fasta
[2023-06-28 03:49:44,761] [INFO] Task started: Blastn
[2023-06-28 03:49:44,761] [INFO] Running command: blastn -query GCA_017421065.1_ASM1742106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f5ec81-d0b9-4421-a427-d39e6cb92417/dqc_reference/reference_markers.fasta -out GCA_017421065.1_ASM1742106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:49:45,532] [INFO] Task succeeded: Blastn
[2023-06-28 03:49:45,536] [INFO] Selected 24 target genomes.
[2023-06-28 03:49:45,536] [INFO] Target genome list was writen to GCA_017421065.1_ASM1742106v1_genomic.fna/target_genomes.txt
[2023-06-28 03:49:45,540] [INFO] Task started: fastANI
[2023-06-28 03:49:45,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg80e1e968-4229-46b4-93f4-081bbdde5f5b/GCA_017421065.1_ASM1742106v1_genomic.fna.gz --refList GCA_017421065.1_ASM1742106v1_genomic.fna/target_genomes.txt --output GCA_017421065.1_ASM1742106v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:50:00,964] [INFO] Task succeeded: fastANI
[2023-06-28 03:50:00,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43f5ec81-d0b9-4421-a427-d39e6cb92417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:50:00,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43f5ec81-d0b9-4421-a427-d39e6cb92417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:50:00,967] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:50:00,967] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 03:50:00,967] [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 03:50:00,969] [INFO] DFAST Taxonomy check result was written to GCA_017421065.1_ASM1742106v1_genomic.fna/tc_result.tsv
[2023-06-28 03:50:00,970] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:50:00,970] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:50:00,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43f5ec81-d0b9-4421-a427-d39e6cb92417/dqc_reference/checkm_data
[2023-06-28 03:50:00,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:50:01,006] [INFO] Task started: CheckM
[2023-06-28 03:50:01,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017421065.1_ASM1742106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017421065.1_ASM1742106v1_genomic.fna/checkm_input GCA_017421065.1_ASM1742106v1_genomic.fna/checkm_result
[2023-06-28 03:50:26,178] [INFO] Task succeeded: CheckM
[2023-06-28 03:50:26,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.36%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 03:50:26,206] [INFO] ===== Completeness check finished =====
[2023-06-28 03:50:26,207] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:50:26,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017421065.1_ASM1742106v1_genomic.fna/markers.fasta)
[2023-06-28 03:50:26,208] [INFO] Task started: Blastn
[2023-06-28 03:50:26,208] [INFO] Running command: blastn -query GCA_017421065.1_ASM1742106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f5ec81-d0b9-4421-a427-d39e6cb92417/dqc_reference/reference_markers_gtdb.fasta -out GCA_017421065.1_ASM1742106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:50:27,355] [INFO] Task succeeded: Blastn
[2023-06-28 03:50:27,359] [INFO] Selected 22 target genomes.
[2023-06-28 03:50:27,359] [INFO] Target genome list was writen to GCA_017421065.1_ASM1742106v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:50:27,387] [INFO] Task started: fastANI
[2023-06-28 03:50:27,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg80e1e968-4229-46b4-93f4-081bbdde5f5b/GCA_017421065.1_ASM1742106v1_genomic.fna.gz --refList GCA_017421065.1_ASM1742106v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017421065.1_ASM1742106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:50:35,752] [INFO] Task succeeded: fastANI
[2023-06-28 03:50:35,771] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 03:50:35,771] [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_015063645.1	s__SIG701 sp015063645	79.4726	251	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__SIG701	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017468385.1	s__SIG701 sp017468385	77.8947	157	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__SIG701	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063805.1	s__SIG693 sp015063805	76.9902	59	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__SIG693	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015064285.1	s__UMGS1696 sp015064285	76.8759	69	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017466375.1	s__SIG701 sp017466375	76.8209	88	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__SIG701	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063745.1	s__UMGS1696 sp015063745	76.5879	58	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017560565.1	s__UMGS1696 sp017560565	76.5497	65	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288155.1	s__SIG701 sp016288155	76.4823	78	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__SIG701	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015065385.1	s__UMGS1696 sp015065385	76.146	57	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017415325.1	s__UMGS1696 sp017415325	76.054	74	705	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 03:50:35,774] [INFO] GTDB search result was written to GCA_017421065.1_ASM1742106v1_genomic.fna/result_gtdb.tsv
[2023-06-28 03:50:35,775] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:50:35,779] [INFO] DFAST_QC result json was written to GCA_017421065.1_ASM1742106v1_genomic.fna/dqc_result.json
[2023-06-28 03:50:35,779] [INFO] DFAST_QC completed!
[2023-06-28 03:50:35,779] [INFO] Total running time: 0h0m59s