[2023-06-13 22:21:47,662] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:21:47,664] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:21:47,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg51909e8b-de3b-4488-ac75-44f082c273d6/dqc_reference
[2023-06-13 22:21:48,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:21:48,863] [INFO] Task started: Prodigal
[2023-06-13 22:21:48,863] [INFO] Running command: gunzip -c /var/lib/cwl/stgab014988-f5ca-4c54-913a-e4d199250ab0/GCA_022708685.1_ASM2270868v1_genomic.fna.gz | prodigal -d GCA_022708685.1_ASM2270868v1_genomic.fna/cds.fna -a GCA_022708685.1_ASM2270868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:22:02,332] [INFO] Task succeeded: Prodigal
[2023-06-13 22:22:02,332] [INFO] Task started: HMMsearch
[2023-06-13 22:22:02,333] [INFO] Running command: hmmsearch --tblout GCA_022708685.1_ASM2270868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51909e8b-de3b-4488-ac75-44f082c273d6/dqc_reference/reference_markers.hmm GCA_022708685.1_ASM2270868v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:22:02,568] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:22:02,569] [INFO] Found 6/6 markers.
[2023-06-13 22:22:02,598] [INFO] Query marker FASTA was written to GCA_022708685.1_ASM2270868v1_genomic.fna/markers.fasta
[2023-06-13 22:22:02,599] [INFO] Task started: Blastn
[2023-06-13 22:22:02,599] [INFO] Running command: blastn -query GCA_022708685.1_ASM2270868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51909e8b-de3b-4488-ac75-44f082c273d6/dqc_reference/reference_markers.fasta -out GCA_022708685.1_ASM2270868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:22:03,231] [INFO] Task succeeded: Blastn
[2023-06-13 22:22:03,237] [INFO] Selected 34 target genomes.
[2023-06-13 22:22:03,238] [INFO] Target genome list was writen to GCA_022708685.1_ASM2270868v1_genomic.fna/target_genomes.txt
[2023-06-13 22:22:03,241] [INFO] Task started: fastANI
[2023-06-13 22:22:03,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgab014988-f5ca-4c54-913a-e4d199250ab0/GCA_022708685.1_ASM2270868v1_genomic.fna.gz --refList GCA_022708685.1_ASM2270868v1_genomic.fna/target_genomes.txt --output GCA_022708685.1_ASM2270868v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:22:24,728] [INFO] Task succeeded: fastANI
[2023-06-13 22:22:24,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51909e8b-de3b-4488-ac75-44f082c273d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:22:24,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51909e8b-de3b-4488-ac75-44f082c273d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:22:24,730] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:22:24,730] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 22:22:24,731] [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
--------------------------------------------------------------------------------
[2023-06-13 22:22:24,733] [INFO] DFAST Taxonomy check result was written to GCA_022708685.1_ASM2270868v1_genomic.fna/tc_result.tsv
[2023-06-13 22:22:24,733] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:22:24,733] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:22:24,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51909e8b-de3b-4488-ac75-44f082c273d6/dqc_reference/checkm_data
[2023-06-13 22:22:24,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:22:24,767] [INFO] Task started: CheckM
[2023-06-13 22:22:24,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708685.1_ASM2270868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708685.1_ASM2270868v1_genomic.fna/checkm_input GCA_022708685.1_ASM2270868v1_genomic.fna/checkm_result
[2023-06-13 22:23:08,194] [INFO] Task succeeded: CheckM
[2023-06-13 22:23:08,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 22:23:08,223] [INFO] ===== Completeness check finished =====
[2023-06-13 22:23:08,223] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:23:08,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708685.1_ASM2270868v1_genomic.fna/markers.fasta)
[2023-06-13 22:23:08,224] [INFO] Task started: Blastn
[2023-06-13 22:23:08,224] [INFO] Running command: blastn -query GCA_022708685.1_ASM2270868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51909e8b-de3b-4488-ac75-44f082c273d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708685.1_ASM2270868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:23:09,213] [INFO] Task succeeded: Blastn
[2023-06-13 22:23:09,218] [INFO] Selected 13 target genomes.
[2023-06-13 22:23:09,218] [INFO] Target genome list was writen to GCA_022708685.1_ASM2270868v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:23:09,221] [INFO] Task started: fastANI
[2023-06-13 22:23:09,221] [INFO] Running command: fastANI --query /var/lib/cwl/stgab014988-f5ca-4c54-913a-e4d199250ab0/GCA_022708685.1_ASM2270868v1_genomic.fna.gz --refList GCA_022708685.1_ASM2270868v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708685.1_ASM2270868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:23:17,150] [INFO] Task succeeded: fastANI
[2023-06-13 22:23:17,156] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 22:23:17,157] [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_001567275.1	s__OLB10 sp001567275	98.6237	896	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	98.86	98.55	0.94	0.93	4	conclusive
GCA_019136655.1	s__OLB10 sp019136655	91.1562	870	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268195.1	s__OLB10 sp018268195	80.2512	608	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699635.1	s__OLB10 sp016699635	77.2122	250	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	99.73	99.71	0.98	0.98	4	-
GCA_002455375.1	s__OLB10 sp002455375	76.7954	238	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__OLB10	95.0	99.14	99.00	0.89	0.83	5	-
GCA_016714005.1	s__JADJOA01 sp016714005	76.2528	73	985	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__JADJOA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 22:23:17,160] [INFO] GTDB search result was written to GCA_022708685.1_ASM2270868v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:23:17,161] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:23:17,163] [INFO] DFAST_QC result json was written to GCA_022708685.1_ASM2270868v1_genomic.fna/dqc_result.json
[2023-06-13 22:23:17,163] [INFO] DFAST_QC completed!
[2023-06-13 22:23:17,163] [INFO] Total running time: 0h1m30s