[2023-06-07 20:07:45,638] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:07:45,641] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:07:45,641] [INFO] DQC Reference Directory: /var/lib/cwl/stgb24205b8-5da7-4cec-ac17-e45b0f63beea/dqc_reference
[2023-06-07 20:07:47,331] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:07:47,332] [INFO] Task started: Prodigal
[2023-06-07 20:07:47,332] [INFO] Running command: gunzip -c /var/lib/cwl/stg038f5287-a386-47af-8cea-e047bc5fc515/GCA_945903285.1_TrH-03may19-99_genomic.fna.gz | prodigal -d GCA_945903285.1_TrH-03may19-99_genomic.fna/cds.fna -a GCA_945903285.1_TrH-03may19-99_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:07:51,525] [INFO] Task succeeded: Prodigal
[2023-06-07 20:07:51,525] [INFO] Task started: HMMsearch
[2023-06-07 20:07:51,525] [INFO] Running command: hmmsearch --tblout GCA_945903285.1_TrH-03may19-99_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb24205b8-5da7-4cec-ac17-e45b0f63beea/dqc_reference/reference_markers.hmm GCA_945903285.1_TrH-03may19-99_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:07:51,718] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:07:51,721] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg038f5287-a386-47af-8cea-e047bc5fc515/GCA_945903285.1_TrH-03may19-99_genomic.fna.gz]
[2023-06-07 20:07:51,743] [INFO] Query marker FASTA was written to GCA_945903285.1_TrH-03may19-99_genomic.fna/markers.fasta
[2023-06-07 20:07:51,743] [INFO] Task started: Blastn
[2023-06-07 20:07:51,743] [INFO] Running command: blastn -query GCA_945903285.1_TrH-03may19-99_genomic.fna/markers.fasta -db /var/lib/cwl/stgb24205b8-5da7-4cec-ac17-e45b0f63beea/dqc_reference/reference_markers.fasta -out GCA_945903285.1_TrH-03may19-99_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:07:52,378] [INFO] Task succeeded: Blastn
[2023-06-07 20:07:52,385] [INFO] Selected 16 target genomes.
[2023-06-07 20:07:52,386] [INFO] Target genome list was writen to GCA_945903285.1_TrH-03may19-99_genomic.fna/target_genomes.txt
[2023-06-07 20:07:52,389] [INFO] Task started: fastANI
[2023-06-07 20:07:52,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg038f5287-a386-47af-8cea-e047bc5fc515/GCA_945903285.1_TrH-03may19-99_genomic.fna.gz --refList GCA_945903285.1_TrH-03may19-99_genomic.fna/target_genomes.txt --output GCA_945903285.1_TrH-03may19-99_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:08:02,413] [INFO] Task succeeded: fastANI
[2023-06-07 20:08:02,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb24205b8-5da7-4cec-ac17-e45b0f63beea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:08:02,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb24205b8-5da7-4cec-ac17-e45b0f63beea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:08:02,416] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:08:02,416] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 20:08:02,416] [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
--------------------------------------------------------------------------------
[2023-06-07 20:08:02,418] [INFO] DFAST Taxonomy check result was written to GCA_945903285.1_TrH-03may19-99_genomic.fna/tc_result.tsv
[2023-06-07 20:08:02,418] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:08:02,419] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:08:02,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb24205b8-5da7-4cec-ac17-e45b0f63beea/dqc_reference/checkm_data
[2023-06-07 20:08:02,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:08:02,437] [INFO] Task started: CheckM
[2023-06-07 20:08:02,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945903285.1_TrH-03may19-99_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945903285.1_TrH-03may19-99_genomic.fna/checkm_input GCA_945903285.1_TrH-03may19-99_genomic.fna/checkm_result
[2023-06-07 20:08:22,637] [INFO] Task succeeded: CheckM
[2023-06-07 20:08:22,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 5.73%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-07 20:08:22,661] [INFO] ===== Completeness check finished =====
[2023-06-07 20:08:22,661] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:08:22,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945903285.1_TrH-03may19-99_genomic.fna/markers.fasta)
[2023-06-07 20:08:22,662] [INFO] Task started: Blastn
[2023-06-07 20:08:22,662] [INFO] Running command: blastn -query GCA_945903285.1_TrH-03may19-99_genomic.fna/markers.fasta -db /var/lib/cwl/stgb24205b8-5da7-4cec-ac17-e45b0f63beea/dqc_reference/reference_markers_gtdb.fasta -out GCA_945903285.1_TrH-03may19-99_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:08:23,437] [INFO] Task succeeded: Blastn
[2023-06-07 20:08:23,442] [INFO] Selected 15 target genomes.
[2023-06-07 20:08:23,442] [INFO] Target genome list was writen to GCA_945903285.1_TrH-03may19-99_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:08:23,454] [INFO] Task started: fastANI
[2023-06-07 20:08:23,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg038f5287-a386-47af-8cea-e047bc5fc515/GCA_945903285.1_TrH-03may19-99_genomic.fna.gz --refList GCA_945903285.1_TrH-03may19-99_genomic.fna/target_genomes_gtdb.txt --output GCA_945903285.1_TrH-03may19-99_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:08:29,793] [INFO] Task succeeded: fastANI
[2023-06-07 20:08:29,802] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 20:08:29,802] [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_016463775.1	s__F1-60-MAGs027 sp016463775	93.9114	312	343	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005800965.1	s__F1-60-MAGs027 sp005800965	80.559	207	343	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926705.1	s__F1-60-MAGs027 sp009926705	78.3929	75	343	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870295.1	s__F1-60-MAGs027 sp016870295	78.0991	110	343	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005793785.1	s__F1-60-MAGs027 sp005793785	77.7514	118	343	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	98.94	98.60	0.81	0.74	4	-
GCA_010025655.1	s__F1-60-MAGs027 sp010025655	77.6394	91	343	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-60-MAGs027	95.0	98.35	98.13	0.74	0.70	11	-
--------------------------------------------------------------------------------
[2023-06-07 20:08:29,804] [INFO] GTDB search result was written to GCA_945903285.1_TrH-03may19-99_genomic.fna/result_gtdb.tsv
[2023-06-07 20:08:29,804] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:08:29,806] [INFO] DFAST_QC result json was written to GCA_945903285.1_TrH-03may19-99_genomic.fna/dqc_result.json
[2023-06-07 20:08:29,807] [INFO] DFAST_QC completed!
[2023-06-07 20:08:29,807] [INFO] Total running time: 0h0m44s