[2023-06-08 09:31:55,299] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:31:55,302] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:31:55,302] [INFO] DQC Reference Directory: /var/lib/cwl/stgb69ce0e6-83f7-4a3d-8267-0d3aae821631/dqc_reference
[2023-06-08 09:31:57,260] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:31:57,261] [INFO] Task started: Prodigal
[2023-06-08 09:31:57,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg84b88972-5616-437d-a807-266f30bb68a3/GCA_902623725.1_AG-893-O11_genomic.fna.gz | prodigal -d GCA_902623725.1_AG-893-O11_genomic.fna/cds.fna -a GCA_902623725.1_AG-893-O11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:32:00,552] [INFO] Task succeeded: Prodigal
[2023-06-08 09:32:00,552] [INFO] Task started: HMMsearch
[2023-06-08 09:32:00,552] [INFO] Running command: hmmsearch --tblout GCA_902623725.1_AG-893-O11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb69ce0e6-83f7-4a3d-8267-0d3aae821631/dqc_reference/reference_markers.hmm GCA_902623725.1_AG-893-O11_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:32:00,768] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:32:00,770] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg84b88972-5616-437d-a807-266f30bb68a3/GCA_902623725.1_AG-893-O11_genomic.fna.gz]
[2023-06-08 09:32:00,794] [INFO] Query marker FASTA was written to GCA_902623725.1_AG-893-O11_genomic.fna/markers.fasta
[2023-06-08 09:32:00,795] [INFO] Task started: Blastn
[2023-06-08 09:32:00,795] [INFO] Running command: blastn -query GCA_902623725.1_AG-893-O11_genomic.fna/markers.fasta -db /var/lib/cwl/stgb69ce0e6-83f7-4a3d-8267-0d3aae821631/dqc_reference/reference_markers.fasta -out GCA_902623725.1_AG-893-O11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:01,751] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:01,755] [INFO] Selected 10 target genomes.
[2023-06-08 09:32:01,756] [INFO] Target genome list was writen to GCA_902623725.1_AG-893-O11_genomic.fna/target_genomes.txt
[2023-06-08 09:32:01,761] [INFO] Task started: fastANI
[2023-06-08 09:32:01,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg84b88972-5616-437d-a807-266f30bb68a3/GCA_902623725.1_AG-893-O11_genomic.fna.gz --refList GCA_902623725.1_AG-893-O11_genomic.fna/target_genomes.txt --output GCA_902623725.1_AG-893-O11_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:32:08,779] [INFO] Task succeeded: fastANI
[2023-06-08 09:32:08,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb69ce0e6-83f7-4a3d-8267-0d3aae821631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:32:08,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb69ce0e6-83f7-4a3d-8267-0d3aae821631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:32:08,782] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:32:08,782] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:32:08,782] [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
--------------------------------------------------------------------------------
[2023-06-08 09:32:08,785] [INFO] DFAST Taxonomy check result was written to GCA_902623725.1_AG-893-O11_genomic.fna/tc_result.tsv
[2023-06-08 09:32:08,786] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:32:08,786] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:32:08,787] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb69ce0e6-83f7-4a3d-8267-0d3aae821631/dqc_reference/checkm_data
[2023-06-08 09:32:08,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:32:08,812] [INFO] Task started: CheckM
[2023-06-08 09:32:08,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902623725.1_AG-893-O11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902623725.1_AG-893-O11_genomic.fna/checkm_input GCA_902623725.1_AG-893-O11_genomic.fna/checkm_result
[2023-06-08 09:32:26,810] [INFO] Task succeeded: CheckM
[2023-06-08 09:32:26,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:32:26,830] [INFO] ===== Completeness check finished =====
[2023-06-08 09:32:26,830] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:32:26,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902623725.1_AG-893-O11_genomic.fna/markers.fasta)
[2023-06-08 09:32:26,831] [INFO] Task started: Blastn
[2023-06-08 09:32:26,831] [INFO] Running command: blastn -query GCA_902623725.1_AG-893-O11_genomic.fna/markers.fasta -db /var/lib/cwl/stgb69ce0e6-83f7-4a3d-8267-0d3aae821631/dqc_reference/reference_markers_gtdb.fasta -out GCA_902623725.1_AG-893-O11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:27,462] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:27,465] [INFO] Selected 13 target genomes.
[2023-06-08 09:32:27,465] [INFO] Target genome list was writen to GCA_902623725.1_AG-893-O11_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:32:27,471] [INFO] Task started: fastANI
[2023-06-08 09:32:27,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg84b88972-5616-437d-a807-266f30bb68a3/GCA_902623725.1_AG-893-O11_genomic.fna.gz --refList GCA_902623725.1_AG-893-O11_genomic.fna/target_genomes_gtdb.txt --output GCA_902623725.1_AG-893-O11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:32:31,187] [INFO] Task succeeded: fastANI
[2023-06-08 09:32:31,205] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:32:31,205] [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_902621305.1	s__AG-337-I02 sp902621305	96.0686	303	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	96.07	96.07	0.82	0.82	2	conclusive
GCA_902590695.1	s__AG-337-I02 sp902590695	93.1454	272	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588745.1	s__AG-337-I02 sp902588745	92.9642	291	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902584805.1	s__AG-337-I02 sp902584805	92.9634	274	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	95.88	95.85	0.75	0.74	3	-
GCA_902612825.1	s__AG-337-I02 sp902612825	92.9247	262	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614085.1	s__AG-337-I02 sp902614085	92.6185	325	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902582755.1	s__AG-337-I02 sp902582755	92.61	288	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.81	99.81	0.85	0.85	2	-
GCA_902541435.1	s__AG-337-I02 sp902541435	92.5332	219	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902575815.1	s__AG-337-I02 sp902575815	92.0221	192	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902585605.1	s__AG-337-I02 sp902585605	91.3831	268	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902525035.1	s__AG-337-I02 sp902525035	89.9812	262	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602695.1	s__AG-337-I02 sp902602695	89.375	252	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628835.1	s__AG-337-I02 sp902628835	89.0833	277	371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:32:31,207] [INFO] GTDB search result was written to GCA_902623725.1_AG-893-O11_genomic.fna/result_gtdb.tsv
[2023-06-08 09:32:31,208] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:32:31,220] [INFO] DFAST_QC result json was written to GCA_902623725.1_AG-893-O11_genomic.fna/dqc_result.json
[2023-06-08 09:32:31,220] [INFO] DFAST_QC completed!
[2023-06-08 09:32:31,220] [INFO] Total running time: 0h0m36s