[2023-06-27 05:58:18,492] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:58:18,494] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:58:18,494] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4f29b01-f8d3-4c13-90d5-882b62e163e6/dqc_reference
[2023-06-27 05:58:19,739] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:58:19,739] [INFO] Task started: Prodigal
[2023-06-27 05:58:19,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg81bba3ac-997f-4392-abff-fd8757d98e5d/GCA_002434045.1_ASM243404v1_genomic.fna.gz | prodigal -d GCA_002434045.1_ASM243404v1_genomic.fna/cds.fna -a GCA_002434045.1_ASM243404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:58:22,532] [INFO] Task succeeded: Prodigal
[2023-06-27 05:58:22,532] [INFO] Task started: HMMsearch
[2023-06-27 05:58:22,533] [INFO] Running command: hmmsearch --tblout GCA_002434045.1_ASM243404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4f29b01-f8d3-4c13-90d5-882b62e163e6/dqc_reference/reference_markers.hmm GCA_002434045.1_ASM243404v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:58:22,730] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:58:22,731] [INFO] Found 6/6 markers.
[2023-06-27 05:58:22,767] [INFO] Query marker FASTA was written to GCA_002434045.1_ASM243404v1_genomic.fna/markers.fasta
[2023-06-27 05:58:22,767] [INFO] Task started: Blastn
[2023-06-27 05:58:22,767] [INFO] Running command: blastn -query GCA_002434045.1_ASM243404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4f29b01-f8d3-4c13-90d5-882b62e163e6/dqc_reference/reference_markers.fasta -out GCA_002434045.1_ASM243404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:58:23,338] [INFO] Task succeeded: Blastn
[2023-06-27 05:58:23,345] [INFO] Selected 10 target genomes.
[2023-06-27 05:58:23,345] [INFO] Target genome list was writen to GCA_002434045.1_ASM243404v1_genomic.fna/target_genomes.txt
[2023-06-27 05:58:23,351] [INFO] Task started: fastANI
[2023-06-27 05:58:23,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg81bba3ac-997f-4392-abff-fd8757d98e5d/GCA_002434045.1_ASM243404v1_genomic.fna.gz --refList GCA_002434045.1_ASM243404v1_genomic.fna/target_genomes.txt --output GCA_002434045.1_ASM243404v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:58:29,713] [INFO] Task succeeded: fastANI
[2023-06-27 05:58:29,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4f29b01-f8d3-4c13-90d5-882b62e163e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:58:29,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4f29b01-f8d3-4c13-90d5-882b62e163e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:58:29,717] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:58:29,717] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 05:58:29,717] [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
--------------------------------------------------------------------------------
[2023-06-27 05:58:29,720] [INFO] DFAST Taxonomy check result was written to GCA_002434045.1_ASM243404v1_genomic.fna/tc_result.tsv
[2023-06-27 05:58:29,720] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:58:29,721] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:58:29,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4f29b01-f8d3-4c13-90d5-882b62e163e6/dqc_reference/checkm_data
[2023-06-27 05:58:29,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:58:29,739] [INFO] Task started: CheckM
[2023-06-27 05:58:29,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002434045.1_ASM243404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002434045.1_ASM243404v1_genomic.fna/checkm_input GCA_002434045.1_ASM243404v1_genomic.fna/checkm_result
[2023-06-27 05:58:45,330] [INFO] Task succeeded: CheckM
[2023-06-27 05:58:45,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:58:45,348] [INFO] ===== Completeness check finished =====
[2023-06-27 05:58:45,349] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:58:45,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002434045.1_ASM243404v1_genomic.fna/markers.fasta)
[2023-06-27 05:58:45,349] [INFO] Task started: Blastn
[2023-06-27 05:58:45,349] [INFO] Running command: blastn -query GCA_002434045.1_ASM243404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4f29b01-f8d3-4c13-90d5-882b62e163e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_002434045.1_ASM243404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:58:46,144] [INFO] Task succeeded: Blastn
[2023-06-27 05:58:46,148] [INFO] Selected 19 target genomes.
[2023-06-27 05:58:46,149] [INFO] Target genome list was writen to GCA_002434045.1_ASM243404v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:58:46,158] [INFO] Task started: fastANI
[2023-06-27 05:58:46,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg81bba3ac-997f-4392-abff-fd8757d98e5d/GCA_002434045.1_ASM243404v1_genomic.fna.gz --refList GCA_002434045.1_ASM243404v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002434045.1_ASM243404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:58:49,989] [INFO] Task succeeded: fastANI
[2023-06-27 05:58:49,994] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:58:49,994] [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_002434045.1	s__UBA5946 sp002434045	100.0	298	298	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA5946;g__UBA5946	95.0	96.84	96.78	0.92	0.89	5	conclusive
--------------------------------------------------------------------------------
[2023-06-27 05:58:49,996] [INFO] GTDB search result was written to GCA_002434045.1_ASM243404v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:58:49,997] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:58:50,013] [INFO] DFAST_QC result json was written to GCA_002434045.1_ASM243404v1_genomic.fna/dqc_result.json
[2023-06-27 05:58:50,014] [INFO] DFAST_QC completed!
[2023-06-27 05:58:50,014] [INFO] Total running time: 0h0m32s