[2023-06-07 22:21:35,530] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:21:35,533] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:21:35,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg644ce3cb-24a7-4cd0-a2c2-0805b665d402/dqc_reference
[2023-06-07 22:21:38,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:21:38,569] [INFO] Task started: Prodigal
[2023-06-07 22:21:38,569] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d022e7f-8640-404d-9de7-89d0d9099794/GCA_947504665.1_ZH-3nov15-59_genomic.fna.gz | prodigal -d GCA_947504665.1_ZH-3nov15-59_genomic.fna/cds.fna -a GCA_947504665.1_ZH-3nov15-59_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:21:49,858] [INFO] Task succeeded: Prodigal
[2023-06-07 22:21:49,858] [INFO] Task started: HMMsearch
[2023-06-07 22:21:49,858] [INFO] Running command: hmmsearch --tblout GCA_947504665.1_ZH-3nov15-59_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg644ce3cb-24a7-4cd0-a2c2-0805b665d402/dqc_reference/reference_markers.hmm GCA_947504665.1_ZH-3nov15-59_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:21:50,176] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:21:50,177] [INFO] Found 6/6 markers.
[2023-06-07 22:21:50,200] [INFO] Query marker FASTA was written to GCA_947504665.1_ZH-3nov15-59_genomic.fna/markers.fasta
[2023-06-07 22:21:50,200] [INFO] Task started: Blastn
[2023-06-07 22:21:50,200] [INFO] Running command: blastn -query GCA_947504665.1_ZH-3nov15-59_genomic.fna/markers.fasta -db /var/lib/cwl/stg644ce3cb-24a7-4cd0-a2c2-0805b665d402/dqc_reference/reference_markers.fasta -out GCA_947504665.1_ZH-3nov15-59_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:21:50,861] [INFO] Task succeeded: Blastn
[2023-06-07 22:21:50,866] [INFO] Selected 25 target genomes.
[2023-06-07 22:21:50,866] [INFO] Target genome list was writen to GCA_947504665.1_ZH-3nov15-59_genomic.fna/target_genomes.txt
[2023-06-07 22:21:50,875] [INFO] Task started: fastANI
[2023-06-07 22:21:50,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d022e7f-8640-404d-9de7-89d0d9099794/GCA_947504665.1_ZH-3nov15-59_genomic.fna.gz --refList GCA_947504665.1_ZH-3nov15-59_genomic.fna/target_genomes.txt --output GCA_947504665.1_ZH-3nov15-59_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:22:06,816] [INFO] Task succeeded: fastANI
[2023-06-07 22:22:06,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg644ce3cb-24a7-4cd0-a2c2-0805b665d402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:22:06,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg644ce3cb-24a7-4cd0-a2c2-0805b665d402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:22:06,819] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:22:06,820] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 22:22:06,820] [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
--------------------------------------------------------------------------------
[2023-06-07 22:22:06,822] [INFO] DFAST Taxonomy check result was written to GCA_947504665.1_ZH-3nov15-59_genomic.fna/tc_result.tsv
[2023-06-07 22:22:06,823] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:22:06,824] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:22:06,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg644ce3cb-24a7-4cd0-a2c2-0805b665d402/dqc_reference/checkm_data
[2023-06-07 22:22:06,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:22:06,863] [INFO] Task started: CheckM
[2023-06-07 22:22:06,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947504665.1_ZH-3nov15-59_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947504665.1_ZH-3nov15-59_genomic.fna/checkm_input GCA_947504665.1_ZH-3nov15-59_genomic.fna/checkm_result
[2023-06-07 22:22:43,205] [INFO] Task succeeded: CheckM
[2023-06-07 22:22:43,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:22:43,228] [INFO] ===== Completeness check finished =====
[2023-06-07 22:22:43,228] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:22:43,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947504665.1_ZH-3nov15-59_genomic.fna/markers.fasta)
[2023-06-07 22:22:43,229] [INFO] Task started: Blastn
[2023-06-07 22:22:43,229] [INFO] Running command: blastn -query GCA_947504665.1_ZH-3nov15-59_genomic.fna/markers.fasta -db /var/lib/cwl/stg644ce3cb-24a7-4cd0-a2c2-0805b665d402/dqc_reference/reference_markers_gtdb.fasta -out GCA_947504665.1_ZH-3nov15-59_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:22:43,989] [INFO] Task succeeded: Blastn
[2023-06-07 22:22:43,994] [INFO] Selected 16 target genomes.
[2023-06-07 22:22:43,994] [INFO] Target genome list was writen to GCA_947504665.1_ZH-3nov15-59_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:22:44,005] [INFO] Task started: fastANI
[2023-06-07 22:22:44,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d022e7f-8640-404d-9de7-89d0d9099794/GCA_947504665.1_ZH-3nov15-59_genomic.fna.gz --refList GCA_947504665.1_ZH-3nov15-59_genomic.fna/target_genomes_gtdb.txt --output GCA_947504665.1_ZH-3nov15-59_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:22:50,419] [INFO] Task succeeded: fastANI
[2023-06-07 22:22:50,427] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:22:50,427] [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_002737625.1	s__UBA955 sp002737625	97.9969	383	618	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	97.97	95.99	0.82	0.69	3	conclusive
GCA_903959115.1	s__UBA955 sp903959115	87.0297	407	618	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	98.58	98.30	0.81	0.78	5	-
GCA_002347985.1	s__UBA955 sp002347985	82.7889	425	618	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	99.54	99.54	0.88	0.88	2	-
GCA_002737705.1	s__UBA955 sp002737705	79.4064	96	618	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	99.19	99.19	0.94	0.94	2	-
GCA_002293105.1	s__UBA955 sp002293105	78.8071	194	618	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	98.32	98.13	0.83	0.80	10	-
GCA_016868785.1	s__UBA955 sp016868785	78.3316	213	618	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788145.1	s__UBA955 sp005788145	78.2572	189	618	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA955;g__UBA955	95.0	96.27	95.94	0.80	0.76	5	-
--------------------------------------------------------------------------------
[2023-06-07 22:22:50,429] [INFO] GTDB search result was written to GCA_947504665.1_ZH-3nov15-59_genomic.fna/result_gtdb.tsv
[2023-06-07 22:22:50,430] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:22:50,433] [INFO] DFAST_QC result json was written to GCA_947504665.1_ZH-3nov15-59_genomic.fna/dqc_result.json
[2023-06-07 22:22:50,433] [INFO] DFAST_QC completed!
[2023-06-07 22:22:50,434] [INFO] Total running time: 0h1m15s