[2023-06-13 10:10:41,055] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:10:41,058] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:10:41,058] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb4ccc98-b536-4744-9766-ed77e4868cfe/dqc_reference
[2023-06-13 10:10:45,135] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:10:45,136] [INFO] Task started: Prodigal
[2023-06-13 10:10:45,137] [INFO] Running command: gunzip -c /var/lib/cwl/stg823342c7-1dd1-42e0-adba-74a96202455d/GCA_022784645.1_ASM2278464v1_genomic.fna.gz | prodigal -d GCA_022784645.1_ASM2278464v1_genomic.fna/cds.fna -a GCA_022784645.1_ASM2278464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:10:57,808] [INFO] Task succeeded: Prodigal
[2023-06-13 10:10:57,809] [INFO] Task started: HMMsearch
[2023-06-13 10:10:57,809] [INFO] Running command: hmmsearch --tblout GCA_022784645.1_ASM2278464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb4ccc98-b536-4744-9766-ed77e4868cfe/dqc_reference/reference_markers.hmm GCA_022784645.1_ASM2278464v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:10:58,048] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:10:58,049] [INFO] Found 6/6 markers.
[2023-06-13 10:10:58,075] [INFO] Query marker FASTA was written to GCA_022784645.1_ASM2278464v1_genomic.fna/markers.fasta
[2023-06-13 10:10:58,075] [INFO] Task started: Blastn
[2023-06-13 10:10:58,075] [INFO] Running command: blastn -query GCA_022784645.1_ASM2278464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb4ccc98-b536-4744-9766-ed77e4868cfe/dqc_reference/reference_markers.fasta -out GCA_022784645.1_ASM2278464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:10:58,655] [INFO] Task succeeded: Blastn
[2023-06-13 10:10:58,659] [INFO] Selected 33 target genomes.
[2023-06-13 10:10:58,660] [INFO] Target genome list was writen to GCA_022784645.1_ASM2278464v1_genomic.fna/target_genomes.txt
[2023-06-13 10:10:58,667] [INFO] Task started: fastANI
[2023-06-13 10:10:58,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg823342c7-1dd1-42e0-adba-74a96202455d/GCA_022784645.1_ASM2278464v1_genomic.fna.gz --refList GCA_022784645.1_ASM2278464v1_genomic.fna/target_genomes.txt --output GCA_022784645.1_ASM2278464v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:16,024] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:16,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb4ccc98-b536-4744-9766-ed77e4868cfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:16,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb4ccc98-b536-4744-9766-ed77e4868cfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:16,027] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:11:16,028] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:11:16,028] [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 10:11:16,030] [INFO] DFAST Taxonomy check result was written to GCA_022784645.1_ASM2278464v1_genomic.fna/tc_result.tsv
[2023-06-13 10:11:16,031] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:16,031] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:16,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb4ccc98-b536-4744-9766-ed77e4868cfe/dqc_reference/checkm_data
[2023-06-13 10:11:16,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:16,062] [INFO] Task started: CheckM
[2023-06-13 10:11:16,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022784645.1_ASM2278464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022784645.1_ASM2278464v1_genomic.fna/checkm_input GCA_022784645.1_ASM2278464v1_genomic.fna/checkm_result
[2023-06-13 10:11:55,525] [INFO] Task succeeded: CheckM
[2023-06-13 10:11:55,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:11:55,567] [INFO] ===== Completeness check finished =====
[2023-06-13 10:11:55,568] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:11:55,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022784645.1_ASM2278464v1_genomic.fna/markers.fasta)
[2023-06-13 10:11:55,569] [INFO] Task started: Blastn
[2023-06-13 10:11:55,569] [INFO] Running command: blastn -query GCA_022784645.1_ASM2278464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb4ccc98-b536-4744-9766-ed77e4868cfe/dqc_reference/reference_markers_gtdb.fasta -out GCA_022784645.1_ASM2278464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:56,415] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:56,420] [INFO] Selected 34 target genomes.
[2023-06-13 10:11:56,420] [INFO] Target genome list was writen to GCA_022784645.1_ASM2278464v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:11:56,482] [INFO] Task started: fastANI
[2023-06-13 10:11:56,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg823342c7-1dd1-42e0-adba-74a96202455d/GCA_022784645.1_ASM2278464v1_genomic.fna.gz --refList GCA_022784645.1_ASM2278464v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022784645.1_ASM2278464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:12:10,226] [INFO] Task succeeded: fastANI
[2023-06-13 10:12:10,233] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 10:12:10,234] [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_018064985.1	s__RF16 sp018064985	78.8046	153	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321775.1	s__RF16 sp900321775	77.1781	65	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.90	95.79	0.79	0.59	13	-
GCA_002373505.1	s__RF16 sp002373505	76.5008	52	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.32	96.25	0.84	0.83	3	-
GCA_900766775.1	s__RF16 sp900766775	76.4256	52	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233255.1	s__RF16 sp905233255	76.3195	61	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551025.1	s__RF16 sp017551025	76.2278	54	715	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:12:10,236] [INFO] GTDB search result was written to GCA_022784645.1_ASM2278464v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:12:10,236] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:12:10,239] [INFO] DFAST_QC result json was written to GCA_022784645.1_ASM2278464v1_genomic.fna/dqc_result.json
[2023-06-13 10:12:10,239] [INFO] DFAST_QC completed!
[2023-06-13 10:12:10,239] [INFO] Total running time: 0h1m29s