[2023-06-28 13:05:36,366] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:05:36,368] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:05:36,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg9be98018-e87c-49ed-8fd7-175bad807499/dqc_reference
[2023-06-28 13:05:37,686] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:05:37,687] [INFO] Task started: Prodigal
[2023-06-28 13:05:37,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg15cbd305-c04a-4a80-876b-ab9a81237c6f/GCA_005777985.1_ASM577798v1_genomic.fna.gz | prodigal -d GCA_005777985.1_ASM577798v1_genomic.fna/cds.fna -a GCA_005777985.1_ASM577798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:05:48,377] [INFO] Task succeeded: Prodigal
[2023-06-28 13:05:48,378] [INFO] Task started: HMMsearch
[2023-06-28 13:05:48,378] [INFO] Running command: hmmsearch --tblout GCA_005777985.1_ASM577798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9be98018-e87c-49ed-8fd7-175bad807499/dqc_reference/reference_markers.hmm GCA_005777985.1_ASM577798v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:05:48,659] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:05:48,660] [INFO] Found 6/6 markers.
[2023-06-28 13:05:48,691] [INFO] Query marker FASTA was written to GCA_005777985.1_ASM577798v1_genomic.fna/markers.fasta
[2023-06-28 13:05:48,692] [INFO] Task started: Blastn
[2023-06-28 13:05:48,692] [INFO] Running command: blastn -query GCA_005777985.1_ASM577798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9be98018-e87c-49ed-8fd7-175bad807499/dqc_reference/reference_markers.fasta -out GCA_005777985.1_ASM577798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:05:49,333] [INFO] Task succeeded: Blastn
[2023-06-28 13:05:49,338] [INFO] Selected 20 target genomes.
[2023-06-28 13:05:49,338] [INFO] Target genome list was writen to GCA_005777985.1_ASM577798v1_genomic.fna/target_genomes.txt
[2023-06-28 13:05:49,344] [INFO] Task started: fastANI
[2023-06-28 13:05:49,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg15cbd305-c04a-4a80-876b-ab9a81237c6f/GCA_005777985.1_ASM577798v1_genomic.fna.gz --refList GCA_005777985.1_ASM577798v1_genomic.fna/target_genomes.txt --output GCA_005777985.1_ASM577798v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:06:04,524] [INFO] Task succeeded: fastANI
[2023-06-28 13:06:04,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9be98018-e87c-49ed-8fd7-175bad807499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:06:04,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9be98018-e87c-49ed-8fd7-175bad807499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:06:04,526] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:06:04,526] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 13:06:04,527] [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 13:06:04,532] [INFO] DFAST Taxonomy check result was written to GCA_005777985.1_ASM577798v1_genomic.fna/tc_result.tsv
[2023-06-28 13:06:04,533] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:06:04,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:06:04,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9be98018-e87c-49ed-8fd7-175bad807499/dqc_reference/checkm_data
[2023-06-28 13:06:04,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:06:04,571] [INFO] Task started: CheckM
[2023-06-28 13:06:04,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005777985.1_ASM577798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005777985.1_ASM577798v1_genomic.fna/checkm_input GCA_005777985.1_ASM577798v1_genomic.fna/checkm_result
[2023-06-28 13:06:39,587] [INFO] Task succeeded: CheckM
[2023-06-28 13:06:39,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:06:39,610] [INFO] ===== Completeness check finished =====
[2023-06-28 13:06:39,610] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:06:39,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005777985.1_ASM577798v1_genomic.fna/markers.fasta)
[2023-06-28 13:06:39,611] [INFO] Task started: Blastn
[2023-06-28 13:06:39,611] [INFO] Running command: blastn -query GCA_005777985.1_ASM577798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9be98018-e87c-49ed-8fd7-175bad807499/dqc_reference/reference_markers_gtdb.fasta -out GCA_005777985.1_ASM577798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:06:40,380] [INFO] Task succeeded: Blastn
[2023-06-28 13:06:40,385] [INFO] Selected 13 target genomes.
[2023-06-28 13:06:40,386] [INFO] Target genome list was writen to GCA_005777985.1_ASM577798v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:06:40,398] [INFO] Task started: fastANI
[2023-06-28 13:06:40,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg15cbd305-c04a-4a80-876b-ab9a81237c6f/GCA_005777985.1_ASM577798v1_genomic.fna.gz --refList GCA_005777985.1_ASM577798v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005777985.1_ASM577798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:06:46,949] [INFO] Task succeeded: fastANI
[2023-06-28 13:06:46,954] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:06:46,954] [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_005799065.1	s__F1-60-MAGs140 sp005799065	99.6854	451	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__F1-60-MAGs140	95.0	97.89	96.09	0.81	0.78	3	conclusive
GCA_016868485.1	s__F1-60-MAGs140 sp016868485	93.2762	359	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__F1-60-MAGs140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908015.1	s__F1-60-MAGs140 sp903908015	80.4863	303	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__F1-60-MAGs140	95.0	98.75	98.75	0.77	0.77	2	-
GCA_016872215.1	s__F1-60-MAGs140 sp016872215	79.2154	274	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__UBA7662;f__UBA7662;g__F1-60-MAGs140	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:06:46,956] [INFO] GTDB search result was written to GCA_005777985.1_ASM577798v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:06:46,957] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:06:46,959] [INFO] DFAST_QC result json was written to GCA_005777985.1_ASM577798v1_genomic.fna/dqc_result.json
[2023-06-28 13:06:46,959] [INFO] DFAST_QC completed!
[2023-06-28 13:06:46,959] [INFO] Total running time: 0h1m11s