[2024-01-24 11:36:20,717] [INFO] DFAST_QC pipeline started. [2024-01-24 11:36:20,718] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:36:20,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d86d867-7792-482f-bcfa-611bd73458c0/dqc_reference [2024-01-24 11:36:21,913] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:36:21,914] [INFO] Task started: Prodigal [2024-01-24 11:36:21,914] [INFO] Running command: gunzip -c /var/lib/cwl/stge83cd501-4c53-4bca-b016-a6719c2c1cd2/GCF_006385615.1_ASM638561v1_genomic.fna.gz | prodigal -d GCF_006385615.1_ASM638561v1_genomic.fna/cds.fna -a GCF_006385615.1_ASM638561v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:36:24,156] [INFO] Task succeeded: Prodigal [2024-01-24 11:36:24,156] [INFO] Task started: HMMsearch [2024-01-24 11:36:24,156] [INFO] Running command: hmmsearch --tblout GCF_006385615.1_ASM638561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d86d867-7792-482f-bcfa-611bd73458c0/dqc_reference/reference_markers.hmm GCF_006385615.1_ASM638561v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:36:24,368] [INFO] Task succeeded: HMMsearch [2024-01-24 11:36:24,370] [INFO] Found 6/6 markers. [2024-01-24 11:36:24,392] [INFO] Query marker FASTA was written to GCF_006385615.1_ASM638561v1_genomic.fna/markers.fasta [2024-01-24 11:36:24,393] [INFO] Task started: Blastn [2024-01-24 11:36:24,393] [INFO] Running command: blastn -query GCF_006385615.1_ASM638561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d86d867-7792-482f-bcfa-611bd73458c0/dqc_reference/reference_markers.fasta -out GCF_006385615.1_ASM638561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:36:27,842] [INFO] Task succeeded: Blastn [2024-01-24 11:36:27,846] [INFO] Selected 6 target genomes. [2024-01-24 11:36:27,847] [INFO] Target genome list was writen to GCF_006385615.1_ASM638561v1_genomic.fna/target_genomes.txt [2024-01-24 11:36:27,921] [INFO] Task started: fastANI [2024-01-24 11:36:27,921] [INFO] Running command: fastANI --query /var/lib/cwl/stge83cd501-4c53-4bca-b016-a6719c2c1cd2/GCF_006385615.1_ASM638561v1_genomic.fna.gz --refList GCF_006385615.1_ASM638561v1_genomic.fna/target_genomes.txt --output GCF_006385615.1_ASM638561v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:36:29,526] [INFO] Task succeeded: fastANI [2024-01-24 11:36:29,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d86d867-7792-482f-bcfa-611bd73458c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:36:29,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d86d867-7792-482f-bcfa-611bd73458c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:36:29,541] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold) [2024-01-24 11:36:29,541] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 11:36:29,541] [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 Chlamydia psittaci strain=6BC GCA_000191925.1 83554 83554 type True 98.5362 383 386 95 conclusive Chlamydia psittaci strain=6BC GCA_000204255.1 83554 83554 type True 98.5325 383 386 95 conclusive Chlamydia buteonis GCA_900634605.1 2494525 2494525 type True 93.6328 373 386 95 below_threshold Chlamydia abortus strain=GIMC 2006:CabB577 GCA_002895085.1 83555 83555 type True 93.3741 375 386 95 below_threshold Chlamydia poikilotherma strain=S15-834K GCA_900239975.1 1967783 1967783 type True 83.4147 318 386 95 below_threshold Chlamydia caviae GCA_000007605.1 83557 83557 type True 83.1536 315 386 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:36:29,544] [INFO] DFAST Taxonomy check result was written to GCF_006385615.1_ASM638561v1_genomic.fna/tc_result.tsv [2024-01-24 11:36:29,544] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:36:29,545] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:36:29,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d86d867-7792-482f-bcfa-611bd73458c0/dqc_reference/checkm_data [2024-01-24 11:36:29,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:36:29,565] [INFO] Task started: CheckM [2024-01-24 11:36:29,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385615.1_ASM638561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385615.1_ASM638561v1_genomic.fna/checkm_input GCF_006385615.1_ASM638561v1_genomic.fna/checkm_result [2024-01-24 11:36:47,890] [INFO] Task succeeded: CheckM [2024-01-24 11:36:47,891] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:36:47,909] [INFO] ===== Completeness check finished ===== [2024-01-24 11:36:47,910] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:36:47,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385615.1_ASM638561v1_genomic.fna/markers.fasta) [2024-01-24 11:36:47,911] [INFO] Task started: Blastn [2024-01-24 11:36:47,911] [INFO] Running command: blastn -query GCF_006385615.1_ASM638561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d86d867-7792-482f-bcfa-611bd73458c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385615.1_ASM638561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:36:48,641] [INFO] Task succeeded: Blastn [2024-01-24 11:36:48,645] [INFO] Selected 8 target genomes. [2024-01-24 11:36:48,645] [INFO] Target genome list was writen to GCF_006385615.1_ASM638561v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:36:48,652] [INFO] Task started: fastANI [2024-01-24 11:36:48,653] [INFO] Running command: fastANI --query /var/lib/cwl/stge83cd501-4c53-4bca-b016-a6719c2c1cd2/GCF_006385615.1_ASM638561v1_genomic.fna.gz --refList GCF_006385615.1_ASM638561v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385615.1_ASM638561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:36:50,900] [INFO] Task succeeded: fastANI [2024-01-24 11:36:50,913] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:36:50,914] [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 GCF_000204255.1 s__Chlamydophila psittaci 98.5325 383 386 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.65 97.64 1.00 0.97 66 conclusive GCF_900634605.1 s__Chlamydophila buteonis 93.6328 373 386 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.99 99.99 1.00 1.00 3 - GCF_002895085.1 s__Chlamydophila abortus 93.3754 375 386 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.82 97.53 0.99 0.97 57 - GCF_018343815.1 s__Chlamydophila sp018343815 83.4664 317 386 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_900239975.1 s__Chlamydophila sp900239975 83.3874 319 386 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_000007605.1 s__Chlamydophila caviae 83.1536 315 386 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_000009945.1 s__Chlamydophila felis 82.8421 294 386 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_000583875.1 s__Chlamydophila avium 78.3807 149 386 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.57 99.56 1.00 0.99 4 - -------------------------------------------------------------------------------- [2024-01-24 11:36:50,916] [INFO] GTDB search result was written to GCF_006385615.1_ASM638561v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:36:50,916] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:36:50,919] [INFO] DFAST_QC result json was written to GCF_006385615.1_ASM638561v1_genomic.fna/dqc_result.json [2024-01-24 11:36:50,919] [INFO] DFAST_QC completed! [2024-01-24 11:36:50,919] [INFO] Total running time: 0h0m30s