[2023-06-28 01:42:58,229] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:42:58,250] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:42:58,251] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb24d0e6-8033-40bf-8b8c-1c1e97a1f45a/dqc_reference
[2023-06-28 01:42:59,696] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:42:59,697] [INFO] Task started: Prodigal
[2023-06-28 01:42:59,697] [INFO] Running command: gunzip -c /var/lib/cwl/stg90105d9d-3422-448f-92e2-c99694f75095/GCA_026461675.1_ASM2646167v1_genomic.fna.gz | prodigal -d GCA_026461675.1_ASM2646167v1_genomic.fna/cds.fna -a GCA_026461675.1_ASM2646167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:43:03,924] [INFO] Task succeeded: Prodigal
[2023-06-28 01:43:03,924] [INFO] Task started: HMMsearch
[2023-06-28 01:43:03,924] [INFO] Running command: hmmsearch --tblout GCA_026461675.1_ASM2646167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb24d0e6-8033-40bf-8b8c-1c1e97a1f45a/dqc_reference/reference_markers.hmm GCA_026461675.1_ASM2646167v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:43:04,129] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:43:04,133] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg90105d9d-3422-448f-92e2-c99694f75095/GCA_026461675.1_ASM2646167v1_genomic.fna.gz]
[2023-06-28 01:43:04,162] [INFO] Query marker FASTA was written to GCA_026461675.1_ASM2646167v1_genomic.fna/markers.fasta
[2023-06-28 01:43:04,163] [INFO] Task started: Blastn
[2023-06-28 01:43:04,163] [INFO] Running command: blastn -query GCA_026461675.1_ASM2646167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb24d0e6-8033-40bf-8b8c-1c1e97a1f45a/dqc_reference/reference_markers.fasta -out GCA_026461675.1_ASM2646167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:43:04,905] [INFO] Task succeeded: Blastn
[2023-06-28 01:43:04,910] [INFO] Selected 35 target genomes.
[2023-06-28 01:43:04,910] [INFO] Target genome list was writen to GCA_026461675.1_ASM2646167v1_genomic.fna/target_genomes.txt
[2023-06-28 01:43:04,931] [INFO] Task started: fastANI
[2023-06-28 01:43:04,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg90105d9d-3422-448f-92e2-c99694f75095/GCA_026461675.1_ASM2646167v1_genomic.fna.gz --refList GCA_026461675.1_ASM2646167v1_genomic.fna/target_genomes.txt --output GCA_026461675.1_ASM2646167v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:43:39,390] [INFO] Task succeeded: fastANI
[2023-06-28 01:43:39,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb24d0e6-8033-40bf-8b8c-1c1e97a1f45a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:43:39,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb24d0e6-8033-40bf-8b8c-1c1e97a1f45a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:43:39,393] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:43:39,393] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 01:43:39,394] [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 01:43:39,396] [INFO] DFAST Taxonomy check result was written to GCA_026461675.1_ASM2646167v1_genomic.fna/tc_result.tsv
[2023-06-28 01:43:39,407] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:43:39,407] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:43:39,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb24d0e6-8033-40bf-8b8c-1c1e97a1f45a/dqc_reference/checkm_data
[2023-06-28 01:43:39,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:43:39,436] [INFO] Task started: CheckM
[2023-06-28 01:43:39,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026461675.1_ASM2646167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026461675.1_ASM2646167v1_genomic.fna/checkm_input GCA_026461675.1_ASM2646167v1_genomic.fna/checkm_result
[2023-06-28 01:43:58,938] [INFO] Task succeeded: CheckM
[2023-06-28 01:43:58,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.19%
Contamintation: 9.56%
Strain heterogeneity: 10.00%
--------------------------------------------------------------------------------
[2023-06-28 01:43:58,964] [INFO] ===== Completeness check finished =====
[2023-06-28 01:43:58,964] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:43:58,964] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026461675.1_ASM2646167v1_genomic.fna/markers.fasta)
[2023-06-28 01:43:58,965] [INFO] Task started: Blastn
[2023-06-28 01:43:58,965] [INFO] Running command: blastn -query GCA_026461675.1_ASM2646167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb24d0e6-8033-40bf-8b8c-1c1e97a1f45a/dqc_reference/reference_markers_gtdb.fasta -out GCA_026461675.1_ASM2646167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:43:59,992] [INFO] Task succeeded: Blastn
[2023-06-28 01:43:59,997] [INFO] Selected 28 target genomes.
[2023-06-28 01:43:59,998] [INFO] Target genome list was writen to GCA_026461675.1_ASM2646167v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:44:00,076] [INFO] Task started: fastANI
[2023-06-28 01:44:00,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg90105d9d-3422-448f-92e2-c99694f75095/GCA_026461675.1_ASM2646167v1_genomic.fna.gz --refList GCA_026461675.1_ASM2646167v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026461675.1_ASM2646167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:44:19,143] [INFO] Task succeeded: fastANI
[2023-06-28 01:44:19,151] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 01:44:19,151] [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_016717115.1	s__UBA10649 sp016717115	77.9932	57	188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856385.1	s__UBA10649 sp017856385	77.7243	60	188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125355.1	s__UBA10649 sp016125355	77.1246	56	188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:44:19,154] [INFO] GTDB search result was written to GCA_026461675.1_ASM2646167v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:44:19,154] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:44:19,157] [INFO] DFAST_QC result json was written to GCA_026461675.1_ASM2646167v1_genomic.fna/dqc_result.json
[2023-06-28 01:44:19,157] [INFO] DFAST_QC completed!
[2023-06-28 01:44:19,157] [INFO] Total running time: 0h1m21s