[2023-06-08 12:26:52,519] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:26:52,525] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:26:52,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgcabfb13b-6a66-41e7-bf48-509ca4f5739e/dqc_reference
[2023-06-08 12:26:53,888] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:26:53,889] [INFO] Task started: Prodigal
[2023-06-08 12:26:53,889] [INFO] Running command: gunzip -c /var/lib/cwl/stga3113b6f-0982-446e-a24e-4268e52df507/GCA_902526545.1_AG-896-B20_genomic.fna.gz | prodigal -d GCA_902526545.1_AG-896-B20_genomic.fna/cds.fna -a GCA_902526545.1_AG-896-B20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:26:55,669] [INFO] Task succeeded: Prodigal
[2023-06-08 12:26:55,670] [INFO] Task started: HMMsearch
[2023-06-08 12:26:55,670] [INFO] Running command: hmmsearch --tblout GCA_902526545.1_AG-896-B20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcabfb13b-6a66-41e7-bf48-509ca4f5739e/dqc_reference/reference_markers.hmm GCA_902526545.1_AG-896-B20_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:26:55,878] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:26:55,879] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga3113b6f-0982-446e-a24e-4268e52df507/GCA_902526545.1_AG-896-B20_genomic.fna.gz]
[2023-06-08 12:26:55,896] [INFO] Query marker FASTA was written to GCA_902526545.1_AG-896-B20_genomic.fna/markers.fasta
[2023-06-08 12:26:55,896] [INFO] Task started: Blastn
[2023-06-08 12:26:55,897] [INFO] Running command: blastn -query GCA_902526545.1_AG-896-B20_genomic.fna/markers.fasta -db /var/lib/cwl/stgcabfb13b-6a66-41e7-bf48-509ca4f5739e/dqc_reference/reference_markers.fasta -out GCA_902526545.1_AG-896-B20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:26:56,477] [INFO] Task succeeded: Blastn
[2023-06-08 12:26:56,482] [INFO] Selected 11 target genomes.
[2023-06-08 12:26:56,482] [INFO] Target genome list was writen to GCA_902526545.1_AG-896-B20_genomic.fna/target_genomes.txt
[2023-06-08 12:26:56,484] [INFO] Task started: fastANI
[2023-06-08 12:26:56,484] [INFO] Running command: fastANI --query /var/lib/cwl/stga3113b6f-0982-446e-a24e-4268e52df507/GCA_902526545.1_AG-896-B20_genomic.fna.gz --refList GCA_902526545.1_AG-896-B20_genomic.fna/target_genomes.txt --output GCA_902526545.1_AG-896-B20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:27:00,386] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:00,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcabfb13b-6a66-41e7-bf48-509ca4f5739e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:27:00,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcabfb13b-6a66-41e7-bf48-509ca4f5739e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:27:00,389] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:27:00,389] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:27:00,390] [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 12:27:00,392] [INFO] DFAST Taxonomy check result was written to GCA_902526545.1_AG-896-B20_genomic.fna/tc_result.tsv
[2023-06-08 12:27:00,392] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:27:00,393] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:27:00,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcabfb13b-6a66-41e7-bf48-509ca4f5739e/dqc_reference/checkm_data
[2023-06-08 12:27:00,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:27:00,411] [INFO] Task started: CheckM
[2023-06-08 12:27:00,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902526545.1_AG-896-B20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902526545.1_AG-896-B20_genomic.fna/checkm_input GCA_902526545.1_AG-896-B20_genomic.fna/checkm_result
[2023-06-08 12:27:14,784] [INFO] Task succeeded: CheckM
[2023-06-08 12:27:14,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:27:14,804] [INFO] ===== Completeness check finished =====
[2023-06-08 12:27:14,805] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:27:14,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902526545.1_AG-896-B20_genomic.fna/markers.fasta)
[2023-06-08 12:27:14,806] [INFO] Task started: Blastn
[2023-06-08 12:27:14,806] [INFO] Running command: blastn -query GCA_902526545.1_AG-896-B20_genomic.fna/markers.fasta -db /var/lib/cwl/stgcabfb13b-6a66-41e7-bf48-509ca4f5739e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902526545.1_AG-896-B20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:15,757] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:15,761] [INFO] Selected 15 target genomes.
[2023-06-08 12:27:15,761] [INFO] Target genome list was writen to GCA_902526545.1_AG-896-B20_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:27:15,763] [INFO] Task started: fastANI
[2023-06-08 12:27:15,763] [INFO] Running command: fastANI --query /var/lib/cwl/stga3113b6f-0982-446e-a24e-4268e52df507/GCA_902526545.1_AG-896-B20_genomic.fna.gz --refList GCA_902526545.1_AG-896-B20_genomic.fna/target_genomes_gtdb.txt --output GCA_902526545.1_AG-896-B20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:27:20,492] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:20,512] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:27:20,512] [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_902560505.1	s__CACIJG01 sp902560505	92.7212	137	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576905.1	s__CACIJG01 sp902576905	92.6501	208	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902540655.1	s__CACIJG01 sp902540655	92.6362	171	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596605.1	s__CACIJG01 sp902596605	92.3739	215	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902530595.1	s__CACIJG01 sp902530595	92.3489	134	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619165.1	s__CACIJG01 sp902619165	92.1069	241	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537415.1	s__CACIJG01 sp902537415	92.0107	170	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537215.1	s__CACIJG01 sp902537215	92.0043	211	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611475.1	s__CACIJG01 sp902611475	91.7327	159	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596985.1	s__CACIJG01 sp902596985	91.7215	195	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574225.1	s__CACIJG01 sp902574225	91.6976	215	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902581005.1	s__CACIJG01 sp902581005	91.4044	159	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524655.1	s__CACIJG01 sp902524655	88.8592	166	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556405.1	s__CACIJG01 sp902556405	87.8903	208	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537235.1	s__CACIJG01 sp902537235	87.5608	184	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:27:20,522] [INFO] GTDB search result was written to GCA_902526545.1_AG-896-B20_genomic.fna/result_gtdb.tsv
[2023-06-08 12:27:20,523] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:27:20,529] [INFO] DFAST_QC result json was written to GCA_902526545.1_AG-896-B20_genomic.fna/dqc_result.json
[2023-06-08 12:27:20,529] [INFO] DFAST_QC completed!
[2023-06-08 12:27:20,530] [INFO] Total running time: 0h0m28s