[2023-06-17 01:17:02,082] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:17:02,085] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:17:02,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg99ec5f8a-cb0a-4d01-b464-a0950032070e/dqc_reference
[2023-06-17 01:17:03,393] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:17:03,394] [INFO] Task started: Prodigal
[2023-06-17 01:17:03,394] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ccd6aa4-bf58-40b2-aa9f-e9e94fbd03c8/GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna.gz | prodigal -d GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/cds.fna -a GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:17:08,598] [INFO] Task succeeded: Prodigal
[2023-06-17 01:17:08,598] [INFO] Task started: HMMsearch
[2023-06-17 01:17:08,598] [INFO] Running command: hmmsearch --tblout GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99ec5f8a-cb0a-4d01-b464-a0950032070e/dqc_reference/reference_markers.hmm GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:17:08,838] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:17:08,839] [INFO] Found 6/6 markers.
[2023-06-17 01:17:08,869] [INFO] Query marker FASTA was written to GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/markers.fasta
[2023-06-17 01:17:08,870] [INFO] Task started: Blastn
[2023-06-17 01:17:08,870] [INFO] Running command: blastn -query GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/markers.fasta -db /var/lib/cwl/stg99ec5f8a-cb0a-4d01-b464-a0950032070e/dqc_reference/reference_markers.fasta -out GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:17:09,530] [INFO] Task succeeded: Blastn
[2023-06-17 01:17:09,534] [INFO] Selected 10 target genomes.
[2023-06-17 01:17:09,535] [INFO] Target genome list was writen to GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/target_genomes.txt
[2023-06-17 01:17:09,537] [INFO] Task started: fastANI
[2023-06-17 01:17:09,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ccd6aa4-bf58-40b2-aa9f-e9e94fbd03c8/GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna.gz --refList GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/target_genomes.txt --output GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:17:13,911] [INFO] Task succeeded: fastANI
[2023-06-17 01:17:13,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99ec5f8a-cb0a-4d01-b464-a0950032070e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:17:13,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99ec5f8a-cb0a-4d01-b464-a0950032070e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:17:13,913] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:17:13,913] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 01:17:13,913] [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
--------------------------------------------------------------------------------
[2023-06-17 01:17:13,915] [INFO] DFAST Taxonomy check result was written to GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/tc_result.tsv
[2023-06-17 01:17:13,915] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:17:13,915] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:17:13,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99ec5f8a-cb0a-4d01-b464-a0950032070e/dqc_reference/checkm_data
[2023-06-17 01:17:13,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:17:13,950] [INFO] Task started: CheckM
[2023-06-17 01:17:13,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/checkm_input GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/checkm_result
[2023-06-17 01:17:37,977] [INFO] Task succeeded: CheckM
[2023-06-17 01:17:37,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.29%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-17 01:17:38,003] [INFO] ===== Completeness check finished =====
[2023-06-17 01:17:38,003] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:17:38,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/markers.fasta)
[2023-06-17 01:17:38,004] [INFO] Task started: Blastn
[2023-06-17 01:17:38,004] [INFO] Running command: blastn -query GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/markers.fasta -db /var/lib/cwl/stg99ec5f8a-cb0a-4d01-b464-a0950032070e/dqc_reference/reference_markers_gtdb.fasta -out GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:17:38,953] [INFO] Task succeeded: Blastn
[2023-06-17 01:17:38,959] [INFO] Selected 16 target genomes.
[2023-06-17 01:17:38,959] [INFO] Target genome list was writen to GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:17:38,972] [INFO] Task started: fastANI
[2023-06-17 01:17:38,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ccd6aa4-bf58-40b2-aa9f-e9e94fbd03c8/GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna.gz --refList GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/target_genomes_gtdb.txt --output GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:17:45,177] [INFO] Task succeeded: fastANI
[2023-06-17 01:17:45,184] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:17:45,185] [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_905477545.1	s__UBA9040 sp905477545	100.0	699	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA9040	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002731665.1	s__UBA9040 sp002731665	91.2975	403	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA9040	95.0	99.68	99.68	0.65	0.65	2	-
GCA_905182565.1	s__UBA9040 sp905182565	88.2005	640	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA9040	95.0	99.80	99.80	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-17 01:17:45,187] [INFO] GTDB search result was written to GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/result_gtdb.tsv
[2023-06-17 01:17:45,187] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:17:45,190] [INFO] DFAST_QC result json was written to GCA_905477545.1_0.2_20180319_Bin_108_genomic.fna/dqc_result.json
[2023-06-17 01:17:45,190] [INFO] DFAST_QC completed!
[2023-06-17 01:17:45,190] [INFO] Total running time: 0h0m43s