[2023-06-28 23:57:39,326] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:57:39,328] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:57:39,328] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb0371a7-4034-4803-a76c-86c05b13597a/dqc_reference
[2023-06-28 23:57:40,697] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:57:40,698] [INFO] Task started: Prodigal
[2023-06-28 23:57:40,698] [INFO] Running command: gunzip -c /var/lib/cwl/stgeddfef61-83e5-4467-b935-1e1a1320e0f3/GCA_017501745.1_ASM1750174v1_genomic.fna.gz | prodigal -d GCA_017501745.1_ASM1750174v1_genomic.fna/cds.fna -a GCA_017501745.1_ASM1750174v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:57:45,034] [INFO] Task succeeded: Prodigal
[2023-06-28 23:57:45,035] [INFO] Task started: HMMsearch
[2023-06-28 23:57:45,035] [INFO] Running command: hmmsearch --tblout GCA_017501745.1_ASM1750174v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb0371a7-4034-4803-a76c-86c05b13597a/dqc_reference/reference_markers.hmm GCA_017501745.1_ASM1750174v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:57:45,298] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:57:45,300] [INFO] Found 6/6 markers.
[2023-06-28 23:57:45,324] [INFO] Query marker FASTA was written to GCA_017501745.1_ASM1750174v1_genomic.fna/markers.fasta
[2023-06-28 23:57:45,325] [INFO] Task started: Blastn
[2023-06-28 23:57:45,325] [INFO] Running command: blastn -query GCA_017501745.1_ASM1750174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb0371a7-4034-4803-a76c-86c05b13597a/dqc_reference/reference_markers.fasta -out GCA_017501745.1_ASM1750174v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:57:45,947] [INFO] Task succeeded: Blastn
[2023-06-28 23:57:45,951] [INFO] Selected 16 target genomes.
[2023-06-28 23:57:45,952] [INFO] Target genome list was writen to GCA_017501745.1_ASM1750174v1_genomic.fna/target_genomes.txt
[2023-06-28 23:57:45,957] [INFO] Task started: fastANI
[2023-06-28 23:57:45,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgeddfef61-83e5-4467-b935-1e1a1320e0f3/GCA_017501745.1_ASM1750174v1_genomic.fna.gz --refList GCA_017501745.1_ASM1750174v1_genomic.fna/target_genomes.txt --output GCA_017501745.1_ASM1750174v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:57:52,786] [INFO] Task succeeded: fastANI
[2023-06-28 23:57:52,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb0371a7-4034-4803-a76c-86c05b13597a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:57:52,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb0371a7-4034-4803-a76c-86c05b13597a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:57:52,789] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:57:52,790] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:57:52,790] [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 23:57:52,792] [INFO] DFAST Taxonomy check result was written to GCA_017501745.1_ASM1750174v1_genomic.fna/tc_result.tsv
[2023-06-28 23:57:52,793] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:57:52,793] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:57:52,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb0371a7-4034-4803-a76c-86c05b13597a/dqc_reference/checkm_data
[2023-06-28 23:57:52,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:57:52,823] [INFO] Task started: CheckM
[2023-06-28 23:57:52,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017501745.1_ASM1750174v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017501745.1_ASM1750174v1_genomic.fna/checkm_input GCA_017501745.1_ASM1750174v1_genomic.fna/checkm_result
[2023-06-28 23:58:12,893] [INFO] Task succeeded: CheckM
[2023-06-28 23:58:12,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 23:58:12,918] [INFO] ===== Completeness check finished =====
[2023-06-28 23:58:12,918] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:58:12,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017501745.1_ASM1750174v1_genomic.fna/markers.fasta)
[2023-06-28 23:58:12,919] [INFO] Task started: Blastn
[2023-06-28 23:58:12,919] [INFO] Running command: blastn -query GCA_017501745.1_ASM1750174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb0371a7-4034-4803-a76c-86c05b13597a/dqc_reference/reference_markers_gtdb.fasta -out GCA_017501745.1_ASM1750174v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:58:13,916] [INFO] Task succeeded: Blastn
[2023-06-28 23:58:13,921] [INFO] Selected 7 target genomes.
[2023-06-28 23:58:13,921] [INFO] Target genome list was writen to GCA_017501745.1_ASM1750174v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:58:13,928] [INFO] Task started: fastANI
[2023-06-28 23:58:13,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgeddfef61-83e5-4467-b935-1e1a1320e0f3/GCA_017501745.1_ASM1750174v1_genomic.fna.gz --refList GCA_017501745.1_ASM1750174v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017501745.1_ASM1750174v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:58:17,304] [INFO] Task succeeded: fastANI
[2023-06-28 23:58:17,312] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:58:17,312] [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_017399965.1	s__SFLA01 sp017399965	97.8917	530	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__SFLA01	95.0	97.88	97.87	0.91	0.90	3	conclusive
GCA_017381715.1	s__SFLA01 sp017381715	89.6761	456	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__SFLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017646185.1	s__SFLA01 sp017646185	88.4601	313	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__SFLA01	95.0	98.44	98.20	0.80	0.78	4	-
GCA_017537345.1	s__SFLA01 sp017537345	88.4506	498	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__SFLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625615.1	s__SFLA01 sp017625615	81.6821	378	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__SFLA01	95.0	97.58	97.58	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-28 23:58:17,314] [INFO] GTDB search result was written to GCA_017501745.1_ASM1750174v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:58:17,315] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:58:17,317] [INFO] DFAST_QC result json was written to GCA_017501745.1_ASM1750174v1_genomic.fna/dqc_result.json
[2023-06-28 23:58:17,318] [INFO] DFAST_QC completed!
[2023-06-28 23:58:17,318] [INFO] Total running time: 0h0m38s