[2024-01-24 14:23:05,156] [INFO] DFAST_QC pipeline started. [2024-01-24 14:23:05,158] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:23:05,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg044da524-bd83-408f-b391-34f3117a08ae/dqc_reference [2024-01-24 14:23:06,562] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:23:06,563] [INFO] Task started: Prodigal [2024-01-24 14:23:06,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg8441300e-360e-4e49-9622-e3153a704c9b/GCF_000255705.1_ASM25570v1_genomic.fna.gz | prodigal -d GCF_000255705.1_ASM25570v1_genomic.fna/cds.fna -a GCF_000255705.1_ASM25570v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:23:44,450] [INFO] Task succeeded: Prodigal [2024-01-24 14:23:44,451] [INFO] Task started: HMMsearch [2024-01-24 14:23:44,451] [INFO] Running command: hmmsearch --tblout GCF_000255705.1_ASM25570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg044da524-bd83-408f-b391-34f3117a08ae/dqc_reference/reference_markers.hmm GCF_000255705.1_ASM25570v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:23:44,878] [INFO] Task succeeded: HMMsearch [2024-01-24 14:23:44,880] [INFO] Found 6/6 markers. [2024-01-24 14:23:44,968] [INFO] Query marker FASTA was written to GCF_000255705.1_ASM25570v1_genomic.fna/markers.fasta [2024-01-24 14:23:44,968] [INFO] Task started: Blastn [2024-01-24 14:23:44,968] [INFO] Running command: blastn -query GCF_000255705.1_ASM25570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg044da524-bd83-408f-b391-34f3117a08ae/dqc_reference/reference_markers.fasta -out GCF_000255705.1_ASM25570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:23:45,611] [INFO] Task succeeded: Blastn [2024-01-24 14:23:45,623] [INFO] Selected 18 target genomes. [2024-01-24 14:23:45,624] [INFO] Target genome list was writen to GCF_000255705.1_ASM25570v1_genomic.fna/target_genomes.txt [2024-01-24 14:23:45,631] [INFO] Task started: fastANI [2024-01-24 14:23:45,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg8441300e-360e-4e49-9622-e3153a704c9b/GCF_000255705.1_ASM25570v1_genomic.fna.gz --refList GCF_000255705.1_ASM25570v1_genomic.fna/target_genomes.txt --output GCF_000255705.1_ASM25570v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:24:06,719] [INFO] Task succeeded: fastANI [2024-01-24 14:24:06,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg044da524-bd83-408f-b391-34f3117a08ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:24:06,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg044da524-bd83-408f-b391-34f3117a08ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:24:06,738] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold) [2024-01-24 14:24:06,738] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 14:24:06,738] [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 Zavarzinella formosa strain=DSM 19928 GCA_000255705.1 360055 360055 type True 99.9836 3278 3320 95 conclusive Limnoglobus roseus strain=PX52 GCA_008254045.1 2598579 2598579 type True 76.1926 320 3320 95 below_threshold Gemmata obscuriglobus strain=UQM 2246 GCA_000171775.1 114 114 type True 75.831 235 3320 95 below_threshold Gemmata obscuriglobus strain=DSM 5831 GCA_008065095.1 114 114 type True 75.7893 249 3320 95 below_threshold Gemmata obscuriglobus GCA_901538385.1 114 114 type True 75.7759 249 3320 95 below_threshold Gemmata obscuriglobus strain=DSM 5831 GCA_003149495.1 114 114 type True 75.7545 248 3320 95 below_threshold Tuwongella immobilis GCA_901538355.1 692036 692036 type True 75.5628 122 3320 95 below_threshold Botrimarina colliarenosi strain=Pla108 GCA_007859955.1 2528001 2528001 type True 75.5509 74 3320 95 below_threshold Lacipirellula limnantheis strain=I41 GCA_007746075.1 2528024 2528024 type True 75.2272 93 3320 95 below_threshold Botrimarina mediterranea strain=Spa11 GCA_007753265.1 2528022 2528022 type True 75.1525 76 3320 95 below_threshold Lacipirellula parvula strain=PX69 GCA_009177095.1 2650471 2650471 type True 75.069 103 3320 95 below_threshold Paracoccus sphaerophysae strain=HAMBI 3106 GCA_000763805.1 690417 690417 type True 74.9613 56 3320 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:24:06,740] [INFO] DFAST Taxonomy check result was written to GCF_000255705.1_ASM25570v1_genomic.fna/tc_result.tsv [2024-01-24 14:24:06,741] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:24:06,742] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:24:06,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg044da524-bd83-408f-b391-34f3117a08ae/dqc_reference/checkm_data [2024-01-24 14:24:06,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:24:06,842] [INFO] Task started: CheckM [2024-01-24 14:24:06,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000255705.1_ASM25570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000255705.1_ASM25570v1_genomic.fna/checkm_input GCF_000255705.1_ASM25570v1_genomic.fna/checkm_result [2024-01-24 14:25:52,146] [INFO] Task succeeded: CheckM [2024-01-24 14:25:52,147] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:25:52,177] [INFO] ===== Completeness check finished ===== [2024-01-24 14:25:52,177] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:25:52,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000255705.1_ASM25570v1_genomic.fna/markers.fasta) [2024-01-24 14:25:52,178] [INFO] Task started: Blastn [2024-01-24 14:25:52,178] [INFO] Running command: blastn -query GCF_000255705.1_ASM25570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg044da524-bd83-408f-b391-34f3117a08ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_000255705.1_ASM25570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:25:52,932] [INFO] Task succeeded: Blastn [2024-01-24 14:25:52,935] [INFO] Selected 22 target genomes. [2024-01-24 14:25:52,935] [INFO] Target genome list was writen to GCF_000255705.1_ASM25570v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:25:53,051] [INFO] Task started: fastANI [2024-01-24 14:25:53,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg8441300e-360e-4e49-9622-e3153a704c9b/GCF_000255705.1_ASM25570v1_genomic.fna.gz --refList GCF_000255705.1_ASM25570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000255705.1_ASM25570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:26:21,456] [INFO] Task succeeded: fastANI [2024-01-24 14:26:21,476] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:26:21,477] [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_000255705.1 s__Zavarzinella formosa 99.9836 3278 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Zavarzinella 95.0 N/A N/A N/A N/A 1 conclusive GCF_008254045.1 s__Limnoglobus roseus 76.2569 314 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Limnoglobus 95.0 N/A N/A N/A N/A 1 - GCA_009691845.1 s__SIAJ01 sp009691845 76.0161 218 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAJ01 95.0 99.37 99.37 0.91 0.91 2 - GCA_901538445.1 s__Gemmata sp901538445 75.8262 249 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata 95.0 N/A N/A N/A N/A 1 - GCA_000531095.1 s__Gemmata massiliana 75.7892 226 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata 95.0 97.81 97.81 0.89 0.89 2 - GCF_008065095.1 s__Gemmata obscuriglobus 75.7861 239 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata 95.0 99.98 99.95 1.00 1.00 4 - GCF_013128195.2 s__Gemmata tundricola 75.7447 284 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata 95.0 N/A N/A N/A N/A 1 - GCA_017306025.1 s__Gemmata sp017306025 75.7444 200 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata 95.0 N/A N/A N/A N/A 1 - GCA_016872595.1 s__Gemmata sp016872595 75.7216 232 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata 95.0 N/A N/A N/A N/A 1 - GCA_017308215.1 s__Urbifossiella sp017308215 75.6875 283 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella 95.0 N/A N/A N/A N/A 1 - GCF_901538355.1 s__Tuwongella immobilis 75.5873 122 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Tuwongella 95.0 N/A N/A N/A N/A 1 - GCA_013822345.1 s__Gemmata sp013822345 75.5127 240 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata 95.0 N/A N/A N/A N/A 1 - GCA_009692065.1 s__SIAQ01 sp009692065 75.3889 123 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01 95.0 N/A N/A N/A N/A 1 - GCA_011331615.1 s__DSRJ01 sp011331615 75.3315 100 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__DSRJ01 95.0 N/A N/A N/A N/A 1 - GCA_016872605.1 s__SIAQ01 sp016872605 75.2151 109 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01 95.0 N/A N/A N/A N/A 1 - GCA_017853285.1 s__UBA6894 sp017853285 75.1806 72 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA6894 95.0 N/A N/A N/A N/A 1 - GCA_016200155.1 s__SIAQ01 sp016200155 75.1606 92 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01 95.0 N/A N/A N/A N/A 1 - GCA_005773755.1 s__Gemmata sp005773755 75.1478 139 3320 d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata 95.0 N/A N/A N/A N/A 1 - GCA_903857665.1 s__CAIZWN01 sp903857665 74.9261 64 3320 d__Bacteria;p__Myxococcota;c__UBA9042;o__DTJE01;f__DTJE01;g__CAIZWN01 95.0 99.68 99.68 0.89 0.89 2 - -------------------------------------------------------------------------------- [2024-01-24 14:26:21,478] [INFO] GTDB search result was written to GCF_000255705.1_ASM25570v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:26:21,479] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:26:21,482] [INFO] DFAST_QC result json was written to GCF_000255705.1_ASM25570v1_genomic.fna/dqc_result.json [2024-01-24 14:26:21,483] [INFO] DFAST_QC completed! [2024-01-24 14:26:21,483] [INFO] Total running time: 0h3m16s