[2023-06-29 18:14:15,125] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:14:15,127] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:14:15,127] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf5a3d60-ea15-44dd-91a5-389f3902e88a/dqc_reference
[2023-06-29 18:14:16,290] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:14:16,291] [INFO] Task started: Prodigal
[2023-06-29 18:14:16,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg91b2a79e-878b-4d03-93a2-e4b8ea0d7dc7/GCA_021779515.1_ASM2177951v1_genomic.fna.gz | prodigal -d GCA_021779515.1_ASM2177951v1_genomic.fna/cds.fna -a GCA_021779515.1_ASM2177951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:14:25,443] [INFO] Task succeeded: Prodigal
[2023-06-29 18:14:25,443] [INFO] Task started: HMMsearch
[2023-06-29 18:14:25,444] [INFO] Running command: hmmsearch --tblout GCA_021779515.1_ASM2177951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf5a3d60-ea15-44dd-91a5-389f3902e88a/dqc_reference/reference_markers.hmm GCA_021779515.1_ASM2177951v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:14:25,671] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:14:25,673] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg91b2a79e-878b-4d03-93a2-e4b8ea0d7dc7/GCA_021779515.1_ASM2177951v1_genomic.fna.gz]
[2023-06-29 18:14:25,696] [INFO] Query marker FASTA was written to GCA_021779515.1_ASM2177951v1_genomic.fna/markers.fasta
[2023-06-29 18:14:25,696] [INFO] Task started: Blastn
[2023-06-29 18:14:25,697] [INFO] Running command: blastn -query GCA_021779515.1_ASM2177951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf5a3d60-ea15-44dd-91a5-389f3902e88a/dqc_reference/reference_markers.fasta -out GCA_021779515.1_ASM2177951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:14:26,285] [INFO] Task succeeded: Blastn
[2023-06-29 18:14:26,291] [INFO] Selected 15 target genomes.
[2023-06-29 18:14:26,292] [INFO] Target genome list was writen to GCA_021779515.1_ASM2177951v1_genomic.fna/target_genomes.txt
[2023-06-29 18:14:26,296] [INFO] Task started: fastANI
[2023-06-29 18:14:26,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b2a79e-878b-4d03-93a2-e4b8ea0d7dc7/GCA_021779515.1_ASM2177951v1_genomic.fna.gz --refList GCA_021779515.1_ASM2177951v1_genomic.fna/target_genomes.txt --output GCA_021779515.1_ASM2177951v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:14:37,209] [INFO] Task succeeded: fastANI
[2023-06-29 18:14:37,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf5a3d60-ea15-44dd-91a5-389f3902e88a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:14:37,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf5a3d60-ea15-44dd-91a5-389f3902e88a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:14:37,215] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 18:14:37,215] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 18:14:37,215] [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
Paludibacter propionicigenes	strain=WB4	GCA_000183135.1	185300	185300	type	True	80.0733	131	434	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 18:14:37,217] [INFO] DFAST Taxonomy check result was written to GCA_021779515.1_ASM2177951v1_genomic.fna/tc_result.tsv
[2023-06-29 18:14:37,218] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:14:37,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:14:37,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf5a3d60-ea15-44dd-91a5-389f3902e88a/dqc_reference/checkm_data
[2023-06-29 18:14:37,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:14:37,248] [INFO] Task started: CheckM
[2023-06-29 18:14:37,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021779515.1_ASM2177951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021779515.1_ASM2177951v1_genomic.fna/checkm_input GCA_021779515.1_ASM2177951v1_genomic.fna/checkm_result
[2023-06-29 18:15:09,718] [INFO] Task succeeded: CheckM
[2023-06-29 18:15:09,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.51%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 18:15:09,745] [INFO] ===== Completeness check finished =====
[2023-06-29 18:15:09,745] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:15:09,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021779515.1_ASM2177951v1_genomic.fna/markers.fasta)
[2023-06-29 18:15:09,746] [INFO] Task started: Blastn
[2023-06-29 18:15:09,746] [INFO] Running command: blastn -query GCA_021779515.1_ASM2177951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf5a3d60-ea15-44dd-91a5-389f3902e88a/dqc_reference/reference_markers_gtdb.fasta -out GCA_021779515.1_ASM2177951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:15:10,634] [INFO] Task succeeded: Blastn
[2023-06-29 18:15:10,640] [INFO] Selected 14 target genomes.
[2023-06-29 18:15:10,640] [INFO] Target genome list was writen to GCA_021779515.1_ASM2177951v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:15:10,646] [INFO] Task started: fastANI
[2023-06-29 18:15:10,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b2a79e-878b-4d03-93a2-e4b8ea0d7dc7/GCA_021779515.1_ASM2177951v1_genomic.fna.gz --refList GCA_021779515.1_ASM2177951v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021779515.1_ASM2177951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:15:18,763] [INFO] Task succeeded: fastANI
[2023-06-29 18:15:18,776] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 18:15:18,777] [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
GCF_000183135.1	s__Paludibacter propionicigenes	80.0733	131	434	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163375.1	s__Paludibacter sp019163375	79.8783	115	434	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882285.1	s__Paludibacter sp017882285	79.488	88	434	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654525.1	s__Paludibacter sp015654525	78.8954	122	434	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365115.1	s__Paludibacter sp010365115	77.9663	58	434	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929065.1	s__Paludibacter sp903929065	77.7043	70	434	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901975.1	s__Paludibacter sp903901975	77.6887	72	434	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.91	99.88	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2023-06-29 18:15:18,779] [INFO] GTDB search result was written to GCA_021779515.1_ASM2177951v1_genomic.fna/result_gtdb.tsv
[2023-06-29 18:15:18,780] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:15:18,782] [INFO] DFAST_QC result json was written to GCA_021779515.1_ASM2177951v1_genomic.fna/dqc_result.json
[2023-06-29 18:15:18,783] [INFO] DFAST_QC completed!
[2023-06-29 18:15:18,783] [INFO] Total running time: 0h1m4s