[2023-06-28 08:55:24,649] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:55:24,652] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:55:24,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg17cfde59-61ff-4b69-8853-c704ac02166d/dqc_reference
[2023-06-28 08:55:25,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:55:25,889] [INFO] Task started: Prodigal
[2023-06-28 08:55:25,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgec8fc32f-57ab-4b9f-8f90-5bf69e4c30d5/GCA_017621175.1_ASM1762117v1_genomic.fna.gz | prodigal -d GCA_017621175.1_ASM1762117v1_genomic.fna/cds.fna -a GCA_017621175.1_ASM1762117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:55:32,381] [INFO] Task succeeded: Prodigal
[2023-06-28 08:55:32,381] [INFO] Task started: HMMsearch
[2023-06-28 08:55:32,382] [INFO] Running command: hmmsearch --tblout GCA_017621175.1_ASM1762117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17cfde59-61ff-4b69-8853-c704ac02166d/dqc_reference/reference_markers.hmm GCA_017621175.1_ASM1762117v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:55:32,651] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:55:32,652] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgec8fc32f-57ab-4b9f-8f90-5bf69e4c30d5/GCA_017621175.1_ASM1762117v1_genomic.fna.gz]
[2023-06-28 08:55:32,672] [INFO] Query marker FASTA was written to GCA_017621175.1_ASM1762117v1_genomic.fna/markers.fasta
[2023-06-28 08:55:32,673] [INFO] Task started: Blastn
[2023-06-28 08:55:32,673] [INFO] Running command: blastn -query GCA_017621175.1_ASM1762117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17cfde59-61ff-4b69-8853-c704ac02166d/dqc_reference/reference_markers.fasta -out GCA_017621175.1_ASM1762117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:55:33,243] [INFO] Task succeeded: Blastn
[2023-06-28 08:55:33,247] [INFO] Selected 26 target genomes.
[2023-06-28 08:55:33,247] [INFO] Target genome list was writen to GCA_017621175.1_ASM1762117v1_genomic.fna/target_genomes.txt
[2023-06-28 08:55:33,250] [INFO] Task started: fastANI
[2023-06-28 08:55:33,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgec8fc32f-57ab-4b9f-8f90-5bf69e4c30d5/GCA_017621175.1_ASM1762117v1_genomic.fna.gz --refList GCA_017621175.1_ASM1762117v1_genomic.fna/target_genomes.txt --output GCA_017621175.1_ASM1762117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:55:50,148] [INFO] Task succeeded: fastANI
[2023-06-28 08:55:50,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17cfde59-61ff-4b69-8853-c704ac02166d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:55:50,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17cfde59-61ff-4b69-8853-c704ac02166d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:55:50,151] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:55:50,151] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:55:50,151] [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
--------------------------------------------------------------------------------
[2023-06-28 08:55:50,153] [INFO] DFAST Taxonomy check result was written to GCA_017621175.1_ASM1762117v1_genomic.fna/tc_result.tsv
[2023-06-28 08:55:50,154] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:55:50,154] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:55:50,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17cfde59-61ff-4b69-8853-c704ac02166d/dqc_reference/checkm_data
[2023-06-28 08:55:50,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:55:50,179] [INFO] Task started: CheckM
[2023-06-28 08:55:50,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017621175.1_ASM1762117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017621175.1_ASM1762117v1_genomic.fna/checkm_input GCA_017621175.1_ASM1762117v1_genomic.fna/checkm_result
[2023-06-28 08:56:15,030] [INFO] Task succeeded: CheckM
[2023-06-28 08:56:15,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:56:15,053] [INFO] ===== Completeness check finished =====
[2023-06-28 08:56:15,053] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:56:15,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017621175.1_ASM1762117v1_genomic.fna/markers.fasta)
[2023-06-28 08:56:15,054] [INFO] Task started: Blastn
[2023-06-28 08:56:15,054] [INFO] Running command: blastn -query GCA_017621175.1_ASM1762117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17cfde59-61ff-4b69-8853-c704ac02166d/dqc_reference/reference_markers_gtdb.fasta -out GCA_017621175.1_ASM1762117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:56:15,811] [INFO] Task succeeded: Blastn
[2023-06-28 08:56:15,816] [INFO] Selected 10 target genomes.
[2023-06-28 08:56:15,816] [INFO] Target genome list was writen to GCA_017621175.1_ASM1762117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:56:15,822] [INFO] Task started: fastANI
[2023-06-28 08:56:15,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgec8fc32f-57ab-4b9f-8f90-5bf69e4c30d5/GCA_017621175.1_ASM1762117v1_genomic.fna.gz --refList GCA_017621175.1_ASM1762117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017621175.1_ASM1762117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:56:19,377] [INFO] Task succeeded: fastANI
[2023-06-28 08:56:19,397] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:56:19,397] [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_015061165.1	s__RF16 sp015061165	96.5337	219	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	95.95	95.95	0.91	0.91	2	conclusive
GCA_017457295.1	s__RF16 sp017457295	82.1828	122	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.17	96.16	0.79	0.77	3	-
GCA_017625155.1	s__RF16 sp017625155	81.8701	92	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017451525.1	s__RF16 sp017451525	81.7813	115	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017558065.1	s__RF16 sp017558065	81.2774	156	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017556705.1	s__RF16 sp017556705	80.708	114	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017628395.1	s__RF16 sp017628395	80.0426	137	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017546705.1	s__RF16 sp017546705	80.0291	121	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017384225.1	s__RF16 sp017384225	79.8738	124	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555595.1	s__RF16 sp017555595	79.5127	131	243	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:56:19,400] [INFO] GTDB search result was written to GCA_017621175.1_ASM1762117v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:56:19,401] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:56:19,404] [INFO] DFAST_QC result json was written to GCA_017621175.1_ASM1762117v1_genomic.fna/dqc_result.json
[2023-06-28 08:56:19,404] [INFO] DFAST_QC completed!
[2023-06-28 08:56:19,404] [INFO] Total running time: 0h0m55s