[2023-06-17 05:59:54,291] [INFO] DFAST_QC pipeline started.
[2023-06-17 05:59:54,294] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 05:59:54,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ecee3e8-f249-4a55-a65a-bbf297ef95e6/dqc_reference
[2023-06-17 05:59:55,592] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 05:59:55,593] [INFO] Task started: Prodigal
[2023-06-17 05:59:55,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b015a1b-a461-4a3d-a276-32d70ccbe207/GCA_013151495.1_ASM1315149v1_genomic.fna.gz | prodigal -d GCA_013151495.1_ASM1315149v1_genomic.fna/cds.fna -a GCA_013151495.1_ASM1315149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 05:59:58,894] [INFO] Task succeeded: Prodigal
[2023-06-17 05:59:58,894] [INFO] Task started: HMMsearch
[2023-06-17 05:59:58,894] [INFO] Running command: hmmsearch --tblout GCA_013151495.1_ASM1315149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ecee3e8-f249-4a55-a65a-bbf297ef95e6/dqc_reference/reference_markers.hmm GCA_013151495.1_ASM1315149v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 05:59:59,135] [INFO] Task succeeded: HMMsearch
[2023-06-17 05:59:59,136] [INFO] Found 6/6 markers.
[2023-06-17 05:59:59,162] [INFO] Query marker FASTA was written to GCA_013151495.1_ASM1315149v1_genomic.fna/markers.fasta
[2023-06-17 05:59:59,162] [INFO] Task started: Blastn
[2023-06-17 05:59:59,162] [INFO] Running command: blastn -query GCA_013151495.1_ASM1315149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ecee3e8-f249-4a55-a65a-bbf297ef95e6/dqc_reference/reference_markers.fasta -out GCA_013151495.1_ASM1315149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:59:59,730] [INFO] Task succeeded: Blastn
[2023-06-17 05:59:59,735] [INFO] Selected 16 target genomes.
[2023-06-17 05:59:59,736] [INFO] Target genome list was writen to GCA_013151495.1_ASM1315149v1_genomic.fna/target_genomes.txt
[2023-06-17 05:59:59,755] [INFO] Task started: fastANI
[2023-06-17 05:59:59,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b015a1b-a461-4a3d-a276-32d70ccbe207/GCA_013151495.1_ASM1315149v1_genomic.fna.gz --refList GCA_013151495.1_ASM1315149v1_genomic.fna/target_genomes.txt --output GCA_013151495.1_ASM1315149v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:00:08,033] [INFO] Task succeeded: fastANI
[2023-06-17 06:00:08,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ecee3e8-f249-4a55-a65a-bbf297ef95e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:00:08,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ecee3e8-f249-4a55-a65a-bbf297ef95e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:00:08,037] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:00:08,037] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 06:00:08,037] [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
--------------------------------------------------------------------------------
[2023-06-17 06:00:08,039] [INFO] DFAST Taxonomy check result was written to GCA_013151495.1_ASM1315149v1_genomic.fna/tc_result.tsv
[2023-06-17 06:00:08,040] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:00:08,041] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:00:08,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ecee3e8-f249-4a55-a65a-bbf297ef95e6/dqc_reference/checkm_data
[2023-06-17 06:00:08,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:00:08,070] [INFO] Task started: CheckM
[2023-06-17 06:00:08,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013151495.1_ASM1315149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013151495.1_ASM1315149v1_genomic.fna/checkm_input GCA_013151495.1_ASM1315149v1_genomic.fna/checkm_result
[2023-06-17 06:00:25,914] [INFO] Task succeeded: CheckM
[2023-06-17 06:00:25,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:00:25,939] [INFO] ===== Completeness check finished =====
[2023-06-17 06:00:25,940] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:00:25,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013151495.1_ASM1315149v1_genomic.fna/markers.fasta)
[2023-06-17 06:00:25,940] [INFO] Task started: Blastn
[2023-06-17 06:00:25,940] [INFO] Running command: blastn -query GCA_013151495.1_ASM1315149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ecee3e8-f249-4a55-a65a-bbf297ef95e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_013151495.1_ASM1315149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:00:26,765] [INFO] Task succeeded: Blastn
[2023-06-17 06:00:26,769] [INFO] Selected 20 target genomes.
[2023-06-17 06:00:26,769] [INFO] Target genome list was writen to GCA_013151495.1_ASM1315149v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:00:26,786] [INFO] Task started: fastANI
[2023-06-17 06:00:26,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b015a1b-a461-4a3d-a276-32d70ccbe207/GCA_013151495.1_ASM1315149v1_genomic.fna.gz --refList GCA_013151495.1_ASM1315149v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013151495.1_ASM1315149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:00:34,447] [INFO] Task succeeded: fastANI
[2023-06-17 06:00:34,453] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 06:00:34,454] [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_013151495.1	s__JAADIE01 sp013151495	100.0	516	520	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__JdFR-85;g__JAADIE01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015484595.1	s__JAADIE01 sp015484595	77.7985	167	520	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__JdFR-85;g__JAADIE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 06:00:34,456] [INFO] GTDB search result was written to GCA_013151495.1_ASM1315149v1_genomic.fna/result_gtdb.tsv
[2023-06-17 06:00:34,458] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:00:34,460] [INFO] DFAST_QC result json was written to GCA_013151495.1_ASM1315149v1_genomic.fna/dqc_result.json
[2023-06-17 06:00:34,460] [INFO] DFAST_QC completed!
[2023-06-17 06:00:34,460] [INFO] Total running time: 0h0m40s