[2023-06-17 17:01:20,835] [INFO] DFAST_QC pipeline started.
[2023-06-17 17:01:20,838] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 17:01:20,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg05712ca3-7ee8-4587-b4da-d24f03a46751/dqc_reference
[2023-06-17 17:01:22,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 17:01:22,522] [INFO] Task started: Prodigal
[2023-06-17 17:01:22,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg469682ec-cda8-4097-bd75-fdab8ff299cb/GCA_009993405.1_ASM999340v1_genomic.fna.gz | prodigal -d GCA_009993405.1_ASM999340v1_genomic.fna/cds.fna -a GCA_009993405.1_ASM999340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 17:01:23,243] [INFO] Task succeeded: Prodigal
[2023-06-17 17:01:23,243] [INFO] Task started: HMMsearch
[2023-06-17 17:01:23,243] [INFO] Running command: hmmsearch --tblout GCA_009993405.1_ASM999340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05712ca3-7ee8-4587-b4da-d24f03a46751/dqc_reference/reference_markers.hmm GCA_009993405.1_ASM999340v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 17:01:23,419] [INFO] Task succeeded: HMMsearch
[2023-06-17 17:01:23,421] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg469682ec-cda8-4097-bd75-fdab8ff299cb/GCA_009993405.1_ASM999340v1_genomic.fna.gz]
[2023-06-17 17:01:23,432] [INFO] Query marker FASTA was written to GCA_009993405.1_ASM999340v1_genomic.fna/markers.fasta
[2023-06-17 17:01:23,432] [INFO] Task started: Blastn
[2023-06-17 17:01:23,432] [INFO] Running command: blastn -query GCA_009993405.1_ASM999340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05712ca3-7ee8-4587-b4da-d24f03a46751/dqc_reference/reference_markers.fasta -out GCA_009993405.1_ASM999340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 17:01:26,455] [INFO] Task succeeded: Blastn
[2023-06-17 17:01:26,459] [INFO] Selected 5 target genomes.
[2023-06-17 17:01:26,459] [INFO] Target genome list was writen to GCA_009993405.1_ASM999340v1_genomic.fna/target_genomes.txt
[2023-06-17 17:01:26,464] [INFO] Task started: fastANI
[2023-06-17 17:01:26,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg469682ec-cda8-4097-bd75-fdab8ff299cb/GCA_009993405.1_ASM999340v1_genomic.fna.gz --refList GCA_009993405.1_ASM999340v1_genomic.fna/target_genomes.txt --output GCA_009993405.1_ASM999340v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 17:01:27,882] [INFO] Task succeeded: fastANI
[2023-06-17 17:01:27,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05712ca3-7ee8-4587-b4da-d24f03a46751/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 17:01:27,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05712ca3-7ee8-4587-b4da-d24f03a46751/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 17:01:27,884] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 17:01:27,884] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 17:01:27,884] [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 17:01:27,886] [INFO] DFAST Taxonomy check result was written to GCA_009993405.1_ASM999340v1_genomic.fna/tc_result.tsv
[2023-06-17 17:01:27,887] [INFO] ===== Taxonomy check completed =====
[2023-06-17 17:01:27,887] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 17:01:27,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05712ca3-7ee8-4587-b4da-d24f03a46751/dqc_reference/checkm_data
[2023-06-17 17:01:27,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 17:01:27,897] [INFO] Task started: CheckM
[2023-06-17 17:01:27,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009993405.1_ASM999340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009993405.1_ASM999340v1_genomic.fna/checkm_input GCA_009993405.1_ASM999340v1_genomic.fna/checkm_result
[2023-06-17 17:01:40,239] [INFO] Task succeeded: CheckM
[2023-06-17 17:01:40,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 17:01:40,262] [INFO] ===== Completeness check finished =====
[2023-06-17 17:01:40,263] [INFO] ===== Start GTDB Search =====
[2023-06-17 17:01:40,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009993405.1_ASM999340v1_genomic.fna/markers.fasta)
[2023-06-17 17:01:40,263] [INFO] Task started: Blastn
[2023-06-17 17:01:40,263] [INFO] Running command: blastn -query GCA_009993405.1_ASM999340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05712ca3-7ee8-4587-b4da-d24f03a46751/dqc_reference/reference_markers_gtdb.fasta -out GCA_009993405.1_ASM999340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 17:01:40,852] [INFO] Task succeeded: Blastn
[2023-06-17 17:01:40,856] [INFO] Selected 5 target genomes.
[2023-06-17 17:01:40,856] [INFO] Target genome list was writen to GCA_009993405.1_ASM999340v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 17:01:40,859] [INFO] Task started: fastANI
[2023-06-17 17:01:40,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg469682ec-cda8-4097-bd75-fdab8ff299cb/GCA_009993405.1_ASM999340v1_genomic.fna.gz --refList GCA_009993405.1_ASM999340v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009993405.1_ASM999340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 17:01:42,102] [INFO] Task succeeded: fastANI
[2023-06-17 17:01:42,105] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 17:01:42,106] [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_002789275.1	s__Huberarchaeum crystalense	99.7869	100	122	d__Archaea;p__Huberarchaeota;c__Huberarchaeia;o__Huberarchaeales;f__Huberarchaeaceae;g__Huberarchaeum	95.0	99.74	99.48	0.86	0.82	11	conclusive
--------------------------------------------------------------------------------
[2023-06-17 17:01:42,108] [INFO] GTDB search result was written to GCA_009993405.1_ASM999340v1_genomic.fna/result_gtdb.tsv
[2023-06-17 17:01:42,109] [INFO] ===== GTDB Search completed =====
[2023-06-17 17:01:42,111] [INFO] DFAST_QC result json was written to GCA_009993405.1_ASM999340v1_genomic.fna/dqc_result.json
[2023-06-17 17:01:42,111] [INFO] DFAST_QC completed!
[2023-06-17 17:01:42,112] [INFO] Total running time: 0h0m21s