[2023-06-29 15:40:05,383] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:40:05,389] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:40:05,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg57e793a4-668f-46da-87e1-d6b42a37c51b/dqc_reference
[2023-06-29 15:40:07,125] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:40:07,126] [INFO] Task started: Prodigal
[2023-06-29 15:40:07,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg423ccdd1-ac40-43db-acca-15cb29ea66e3/GCA_021621925.1_ASM2162192v1_genomic.fna.gz | prodigal -d GCA_021621925.1_ASM2162192v1_genomic.fna/cds.fna -a GCA_021621925.1_ASM2162192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:40:14,680] [INFO] Task succeeded: Prodigal
[2023-06-29 15:40:14,681] [INFO] Task started: HMMsearch
[2023-06-29 15:40:14,681] [INFO] Running command: hmmsearch --tblout GCA_021621925.1_ASM2162192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57e793a4-668f-46da-87e1-d6b42a37c51b/dqc_reference/reference_markers.hmm GCA_021621925.1_ASM2162192v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:40:14,930] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:40:14,931] [INFO] Found 6/6 markers.
[2023-06-29 15:40:14,972] [INFO] Query marker FASTA was written to GCA_021621925.1_ASM2162192v1_genomic.fna/markers.fasta
[2023-06-29 15:40:14,972] [INFO] Task started: Blastn
[2023-06-29 15:40:14,972] [INFO] Running command: blastn -query GCA_021621925.1_ASM2162192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e793a4-668f-46da-87e1-d6b42a37c51b/dqc_reference/reference_markers.fasta -out GCA_021621925.1_ASM2162192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:40:15,624] [INFO] Task succeeded: Blastn
[2023-06-29 15:40:15,628] [INFO] Selected 26 target genomes.
[2023-06-29 15:40:15,628] [INFO] Target genome list was writen to GCA_021621925.1_ASM2162192v1_genomic.fna/target_genomes.txt
[2023-06-29 15:40:15,632] [INFO] Task started: fastANI
[2023-06-29 15:40:15,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg423ccdd1-ac40-43db-acca-15cb29ea66e3/GCA_021621925.1_ASM2162192v1_genomic.fna.gz --refList GCA_021621925.1_ASM2162192v1_genomic.fna/target_genomes.txt --output GCA_021621925.1_ASM2162192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:40:33,502] [INFO] Task succeeded: fastANI
[2023-06-29 15:40:33,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57e793a4-668f-46da-87e1-d6b42a37c51b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:40:33,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57e793a4-668f-46da-87e1-d6b42a37c51b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:40:33,504] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:40:33,505] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 15:40:33,505] [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
--------------------------------------------------------------------------------
[2023-06-29 15:40:33,507] [INFO] DFAST Taxonomy check result was written to GCA_021621925.1_ASM2162192v1_genomic.fna/tc_result.tsv
[2023-06-29 15:40:33,508] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:40:33,508] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:40:33,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57e793a4-668f-46da-87e1-d6b42a37c51b/dqc_reference/checkm_data
[2023-06-29 15:40:33,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:40:33,546] [INFO] Task started: CheckM
[2023-06-29 15:40:33,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021621925.1_ASM2162192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021621925.1_ASM2162192v1_genomic.fna/checkm_input GCA_021621925.1_ASM2162192v1_genomic.fna/checkm_result
[2023-06-29 15:41:00,812] [INFO] Task succeeded: CheckM
[2023-06-29 15:41:00,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:41:00,838] [INFO] ===== Completeness check finished =====
[2023-06-29 15:41:00,838] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:41:00,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021621925.1_ASM2162192v1_genomic.fna/markers.fasta)
[2023-06-29 15:41:00,839] [INFO] Task started: Blastn
[2023-06-29 15:41:00,839] [INFO] Running command: blastn -query GCA_021621925.1_ASM2162192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e793a4-668f-46da-87e1-d6b42a37c51b/dqc_reference/reference_markers_gtdb.fasta -out GCA_021621925.1_ASM2162192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:41:01,703] [INFO] Task succeeded: Blastn
[2023-06-29 15:41:01,708] [INFO] Selected 14 target genomes.
[2023-06-29 15:41:01,708] [INFO] Target genome list was writen to GCA_021621925.1_ASM2162192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:41:01,712] [INFO] Task started: fastANI
[2023-06-29 15:41:01,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg423ccdd1-ac40-43db-acca-15cb29ea66e3/GCA_021621925.1_ASM2162192v1_genomic.fna.gz --refList GCA_021621925.1_ASM2162192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021621925.1_ASM2162192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:41:09,472] [INFO] Task succeeded: fastANI
[2023-06-29 15:41:09,495] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:41:09,496] [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_000437595.1	s__UBA11524 sp000437595	97.1543	655	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	97.36	96.94	0.88	0.81	39	conclusive
GCA_900769075.1	s__UBA11524 sp900769075	78.6514	206	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465155.1	s__UBA11524 sp017465155	78.2403	163	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481825.1	s__UBA11524 sp017481825	78.1048	194	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410455.1	s__UBA11524 sp017410455	78.0256	200	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056085.1	s__UBA11524 sp015056085	77.9987	131	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017397765.1	s__UBA11524 sp017397765	77.9809	169	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056155.1	s__UBA11524 sp015056155	77.9697	196	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399225.1	s__UBA11524 sp017399225	77.8472	193	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017513475.1	s__UBA11524 sp017513475	77.784	161	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463245.1	s__UBA11524 sp017463245	77.6894	163	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056415.1	s__UBA11524 sp015056415	77.2996	121	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017516305.1	s__UBA11524 sp017516305	77.164	176	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:41:09,498] [INFO] GTDB search result was written to GCA_021621925.1_ASM2162192v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:41:09,498] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:41:09,502] [INFO] DFAST_QC result json was written to GCA_021621925.1_ASM2162192v1_genomic.fna/dqc_result.json
[2023-06-29 15:41:09,502] [INFO] DFAST_QC completed!
[2023-06-29 15:41:09,502] [INFO] Total running time: 0h1m4s