[2023-06-29 20:02:10,049] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:02:10,051] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:02:10,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b91a406-8443-4ca1-82a3-35e3f24919a8/dqc_reference
[2023-06-29 20:02:11,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:02:11,802] [INFO] Task started: Prodigal
[2023-06-29 20:02:11,803] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9a9c650-6e51-46f3-afee-e3707ae7700e/GCA_021604105.1_ASM2160410v1_genomic.fna.gz | prodigal -d GCA_021604105.1_ASM2160410v1_genomic.fna/cds.fna -a GCA_021604105.1_ASM2160410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:02:25,004] [INFO] Task succeeded: Prodigal
[2023-06-29 20:02:25,005] [INFO] Task started: HMMsearch
[2023-06-29 20:02:25,005] [INFO] Running command: hmmsearch --tblout GCA_021604105.1_ASM2160410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b91a406-8443-4ca1-82a3-35e3f24919a8/dqc_reference/reference_markers.hmm GCA_021604105.1_ASM2160410v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:02:25,315] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:02:25,317] [INFO] Found 6/6 markers.
[2023-06-29 20:02:25,363] [INFO] Query marker FASTA was written to GCA_021604105.1_ASM2160410v1_genomic.fna/markers.fasta
[2023-06-29 20:02:25,363] [INFO] Task started: Blastn
[2023-06-29 20:02:25,363] [INFO] Running command: blastn -query GCA_021604105.1_ASM2160410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b91a406-8443-4ca1-82a3-35e3f24919a8/dqc_reference/reference_markers.fasta -out GCA_021604105.1_ASM2160410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:02:27,703] [INFO] Task succeeded: Blastn
[2023-06-29 20:02:27,708] [INFO] Selected 25 target genomes.
[2023-06-29 20:02:27,709] [INFO] Target genome list was writen to GCA_021604105.1_ASM2160410v1_genomic.fna/target_genomes.txt
[2023-06-29 20:02:27,717] [INFO] Task started: fastANI
[2023-06-29 20:02:27,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9a9c650-6e51-46f3-afee-e3707ae7700e/GCA_021604105.1_ASM2160410v1_genomic.fna.gz --refList GCA_021604105.1_ASM2160410v1_genomic.fna/target_genomes.txt --output GCA_021604105.1_ASM2160410v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:02:44,556] [INFO] Task succeeded: fastANI
[2023-06-29 20:02:44,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b91a406-8443-4ca1-82a3-35e3f24919a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:02:44,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b91a406-8443-4ca1-82a3-35e3f24919a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:02:44,560] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:02:44,560] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:02:44,560] [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
--------------------------------------------------------------------------------
[2023-06-29 20:02:44,563] [INFO] DFAST Taxonomy check result was written to GCA_021604105.1_ASM2160410v1_genomic.fna/tc_result.tsv
[2023-06-29 20:02:44,563] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:02:44,564] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:02:44,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b91a406-8443-4ca1-82a3-35e3f24919a8/dqc_reference/checkm_data
[2023-06-29 20:02:44,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:02:44,616] [INFO] Task started: CheckM
[2023-06-29 20:02:44,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021604105.1_ASM2160410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021604105.1_ASM2160410v1_genomic.fna/checkm_input GCA_021604105.1_ASM2160410v1_genomic.fna/checkm_result
[2023-06-29 20:03:28,349] [INFO] Task succeeded: CheckM
[2023-06-29 20:03:28,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:03:28,376] [INFO] ===== Completeness check finished =====
[2023-06-29 20:03:28,376] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:03:28,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021604105.1_ASM2160410v1_genomic.fna/markers.fasta)
[2023-06-29 20:03:28,377] [INFO] Task started: Blastn
[2023-06-29 20:03:28,377] [INFO] Running command: blastn -query GCA_021604105.1_ASM2160410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b91a406-8443-4ca1-82a3-35e3f24919a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_021604105.1_ASM2160410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:03:29,199] [INFO] Task succeeded: Blastn
[2023-06-29 20:03:29,203] [INFO] Selected 14 target genomes.
[2023-06-29 20:03:29,203] [INFO] Target genome list was writen to GCA_021604105.1_ASM2160410v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:03:29,233] [INFO] Task started: fastANI
[2023-06-29 20:03:29,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9a9c650-6e51-46f3-afee-e3707ae7700e/GCA_021604105.1_ASM2160410v1_genomic.fna.gz --refList GCA_021604105.1_ASM2160410v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021604105.1_ASM2160410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:03:38,896] [INFO] Task succeeded: fastANI
[2023-06-29 20:03:38,909] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:03:38,910] [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_902500695.1	s__UBA8639 sp902500695	85.238	1015	1528	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817135.1	s__UBA8639 sp013817135	85.1481	579	1528	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523945.1	s__UBA8639 sp003523945	83.0144	784	1528	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377845.1	s__UBA8639 sp009377845	79.8313	564	1528	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003235785.1	s__UBA8639 sp003235785	77.2926	128	1528	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228495.1	s__UBA8639 sp003228495	76.6166	106	1528	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003233615.1	s__UBA8639 sp003233615	76.3026	87	1528	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:03:38,912] [INFO] GTDB search result was written to GCA_021604105.1_ASM2160410v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:03:38,912] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:03:38,915] [INFO] DFAST_QC result json was written to GCA_021604105.1_ASM2160410v1_genomic.fna/dqc_result.json
[2023-06-29 20:03:38,915] [INFO] DFAST_QC completed!
[2023-06-29 20:03:38,915] [INFO] Total running time: 0h1m29s