[2023-06-04 18:00:17,637] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:00:17,651] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:00:17,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dbc05a5-2073-4b9e-9c21-a52f4f7a7650/dqc_reference
[2023-06-04 18:00:18,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:00:18,892] [INFO] Task started: Prodigal
[2023-06-04 18:00:18,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg00e2188e-307a-4521-b1c4-72b1e125a3d4/GCA_010032945.1_ASM1003294v1_genomic.fna.gz | prodigal -d GCA_010032945.1_ASM1003294v1_genomic.fna/cds.fna -a GCA_010032945.1_ASM1003294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:00:20,150] [INFO] Task succeeded: Prodigal
[2023-06-04 18:00:20,151] [INFO] Task started: HMMsearch
[2023-06-04 18:00:20,151] [INFO] Running command: hmmsearch --tblout GCA_010032945.1_ASM1003294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dbc05a5-2073-4b9e-9c21-a52f4f7a7650/dqc_reference/reference_markers.hmm GCA_010032945.1_ASM1003294v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:00:20,333] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:00:20,334] [INFO] Found 6/6 markers.
[2023-06-04 18:00:20,350] [INFO] Query marker FASTA was written to GCA_010032945.1_ASM1003294v1_genomic.fna/markers.fasta
[2023-06-04 18:00:20,350] [INFO] Task started: Blastn
[2023-06-04 18:00:20,350] [INFO] Running command: blastn -query GCA_010032945.1_ASM1003294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dbc05a5-2073-4b9e-9c21-a52f4f7a7650/dqc_reference/reference_markers.fasta -out GCA_010032945.1_ASM1003294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:20,894] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:20,899] [INFO] Selected 11 target genomes.
[2023-06-04 18:00:20,900] [INFO] Target genome list was writen to GCA_010032945.1_ASM1003294v1_genomic.fna/target_genomes.txt
[2023-06-04 18:00:20,982] [INFO] Task started: fastANI
[2023-06-04 18:00:20,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e2188e-307a-4521-b1c4-72b1e125a3d4/GCA_010032945.1_ASM1003294v1_genomic.fna.gz --refList GCA_010032945.1_ASM1003294v1_genomic.fna/target_genomes.txt --output GCA_010032945.1_ASM1003294v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:00:24,699] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:24,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dbc05a5-2073-4b9e-9c21-a52f4f7a7650/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:00:24,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dbc05a5-2073-4b9e-9c21-a52f4f7a7650/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:00:24,728] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:00:24,728] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 18:00:24,728] [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
--------------------------------------------------------------------------------
[2023-06-04 18:00:24,731] [INFO] DFAST Taxonomy check result was written to GCA_010032945.1_ASM1003294v1_genomic.fna/tc_result.tsv
[2023-06-04 18:00:24,731] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:00:24,732] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:00:24,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dbc05a5-2073-4b9e-9c21-a52f4f7a7650/dqc_reference/checkm_data
[2023-06-04 18:00:24,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:00:24,748] [INFO] Task started: CheckM
[2023-06-04 18:00:24,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010032945.1_ASM1003294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010032945.1_ASM1003294v1_genomic.fna/checkm_input GCA_010032945.1_ASM1003294v1_genomic.fna/checkm_result
[2023-06-04 18:00:37,174] [INFO] Task succeeded: CheckM
[2023-06-04 18:00:37,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:00:37,195] [INFO] ===== Completeness check finished =====
[2023-06-04 18:00:37,195] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:00:37,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010032945.1_ASM1003294v1_genomic.fna/markers.fasta)
[2023-06-04 18:00:37,196] [INFO] Task started: Blastn
[2023-06-04 18:00:37,196] [INFO] Running command: blastn -query GCA_010032945.1_ASM1003294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dbc05a5-2073-4b9e-9c21-a52f4f7a7650/dqc_reference/reference_markers_gtdb.fasta -out GCA_010032945.1_ASM1003294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:37,899] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:37,904] [INFO] Selected 15 target genomes.
[2023-06-04 18:00:37,904] [INFO] Target genome list was writen to GCA_010032945.1_ASM1003294v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:00:38,114] [INFO] Task started: fastANI
[2023-06-04 18:00:38,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e2188e-307a-4521-b1c4-72b1e125a3d4/GCA_010032945.1_ASM1003294v1_genomic.fna.gz --refList GCA_010032945.1_ASM1003294v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010032945.1_ASM1003294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:00:41,314] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:41,323] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 18:00:41,323] [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_003569185.1	s__Nanopelagicus sp003569185	92.2807	62	76	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287885.2	s__Nanopelagicus limnes	89.3712	71	76	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000294575.1	s__Nanopelagicus sp000294575	81.0048	50	76	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.86	98.86	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-04 18:00:41,327] [INFO] GTDB search result was written to GCA_010032945.1_ASM1003294v1_genomic.fna/result_gtdb.tsv
[2023-06-04 18:00:41,328] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:00:41,331] [INFO] DFAST_QC result json was written to GCA_010032945.1_ASM1003294v1_genomic.fna/dqc_result.json
[2023-06-04 18:00:41,331] [INFO] DFAST_QC completed!
[2023-06-04 18:00:41,332] [INFO] Total running time: 0h0m24s