[2023-06-28 23:44:53,622] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:44:53,625] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:44:53,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg63736ccb-7f83-4268-a67c-254fa78144ef/dqc_reference
[2023-06-28 23:44:55,005] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:44:55,006] [INFO] Task started: Prodigal
[2023-06-28 23:44:55,006] [INFO] Running command: gunzip -c /var/lib/cwl/stg6888e077-4083-4cf0-bffd-15a62410e920/GCA_015656475.1_ASM1565647v1_genomic.fna.gz | prodigal -d GCA_015656475.1_ASM1565647v1_genomic.fna/cds.fna -a GCA_015656475.1_ASM1565647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:45:07,092] [INFO] Task succeeded: Prodigal
[2023-06-28 23:45:07,093] [INFO] Task started: HMMsearch
[2023-06-28 23:45:07,093] [INFO] Running command: hmmsearch --tblout GCA_015656475.1_ASM1565647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63736ccb-7f83-4268-a67c-254fa78144ef/dqc_reference/reference_markers.hmm GCA_015656475.1_ASM1565647v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:45:07,325] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:45:07,326] [INFO] Found 6/6 markers.
[2023-06-28 23:45:07,348] [INFO] Query marker FASTA was written to GCA_015656475.1_ASM1565647v1_genomic.fna/markers.fasta
[2023-06-28 23:45:07,348] [INFO] Task started: Blastn
[2023-06-28 23:45:07,348] [INFO] Running command: blastn -query GCA_015656475.1_ASM1565647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63736ccb-7f83-4268-a67c-254fa78144ef/dqc_reference/reference_markers.fasta -out GCA_015656475.1_ASM1565647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:45:07,984] [INFO] Task succeeded: Blastn
[2023-06-28 23:45:07,988] [INFO] Selected 29 target genomes.
[2023-06-28 23:45:07,988] [INFO] Target genome list was writen to GCA_015656475.1_ASM1565647v1_genomic.fna/target_genomes.txt
[2023-06-28 23:45:07,991] [INFO] Task started: fastANI
[2023-06-28 23:45:07,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg6888e077-4083-4cf0-bffd-15a62410e920/GCA_015656475.1_ASM1565647v1_genomic.fna.gz --refList GCA_015656475.1_ASM1565647v1_genomic.fna/target_genomes.txt --output GCA_015656475.1_ASM1565647v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:45:27,099] [INFO] Task succeeded: fastANI
[2023-06-28 23:45:27,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63736ccb-7f83-4268-a67c-254fa78144ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:45:27,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63736ccb-7f83-4268-a67c-254fa78144ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:45:27,101] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:45:27,101] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:45:27,101] [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 23:45:27,103] [INFO] DFAST Taxonomy check result was written to GCA_015656475.1_ASM1565647v1_genomic.fna/tc_result.tsv
[2023-06-28 23:45:27,104] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:45:27,104] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:45:27,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63736ccb-7f83-4268-a67c-254fa78144ef/dqc_reference/checkm_data
[2023-06-28 23:45:27,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:45:27,134] [INFO] Task started: CheckM
[2023-06-28 23:45:27,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015656475.1_ASM1565647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015656475.1_ASM1565647v1_genomic.fna/checkm_input GCA_015656475.1_ASM1565647v1_genomic.fna/checkm_result
[2023-06-28 23:46:04,707] [INFO] Task succeeded: CheckM
[2023-06-28 23:46:04,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 23:46:04,734] [INFO] ===== Completeness check finished =====
[2023-06-28 23:46:04,734] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:46:04,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015656475.1_ASM1565647v1_genomic.fna/markers.fasta)
[2023-06-28 23:46:04,735] [INFO] Task started: Blastn
[2023-06-28 23:46:04,735] [INFO] Running command: blastn -query GCA_015656475.1_ASM1565647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63736ccb-7f83-4268-a67c-254fa78144ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_015656475.1_ASM1565647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:46:05,558] [INFO] Task succeeded: Blastn
[2023-06-28 23:46:05,563] [INFO] Selected 12 target genomes.
[2023-06-28 23:46:05,563] [INFO] Target genome list was writen to GCA_015656475.1_ASM1565647v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:46:05,569] [INFO] Task started: fastANI
[2023-06-28 23:46:05,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg6888e077-4083-4cf0-bffd-15a62410e920/GCA_015656475.1_ASM1565647v1_genomic.fna.gz --refList GCA_015656475.1_ASM1565647v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015656475.1_ASM1565647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:46:11,164] [INFO] Task succeeded: fastANI
[2023-06-28 23:46:11,181] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:46:11,181] [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_904502185.1	s__HGM04593 sp904502185	100.0	631	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCA_017547585.1	s__HGM04593 sp017547585	79.9241	318	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	97.67	97.67	0.92	0.92	2	-
GCA_017560125.1	s__HGM04593 sp017560125	79.8165	316	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060835.1	s__HGM04593 sp015060835	79.5499	305	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	95.63	95.32	0.85	0.84	3	-
GCA_017557045.1	s__HGM04593 sp017557045	79.382	278	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060905.1	s__HGM04593 sp015060905	79.0775	287	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	98.28	98.28	0.94	0.94	2	-
GCA_017467015.1	s__HGM04593 sp017467015	78.9564	255	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	98.48	98.48	0.91	0.91	2	-
GCA_017554605.1	s__HGM04593 sp017554605	77.5379	131	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060885.1	s__HGM04593 sp015060885	77.2148	124	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	97.79	97.34	0.92	0.91	3	-
GCA_900769465.1	s__HGM04593 sp900769465	76.8183	98	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770665.1	s__HGM04593 sp900770665	76.7221	111	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017407905.1	s__HGM04593 sp017407905	76.4201	119	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__HGM04593	95.0	97.99	97.99	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-28 23:46:11,183] [INFO] GTDB search result was written to GCA_015656475.1_ASM1565647v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:46:11,184] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:46:11,187] [INFO] DFAST_QC result json was written to GCA_015656475.1_ASM1565647v1_genomic.fna/dqc_result.json
[2023-06-28 23:46:11,187] [INFO] DFAST_QC completed!
[2023-06-28 23:46:11,187] [INFO] Total running time: 0h1m18s