[2023-06-08 11:46:54,626] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:46:54,629] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:46:54,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ec4c1ae-742c-420a-a6b9-3636f956c62a/dqc_reference
[2023-06-08 11:46:55,994] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:46:55,995] [INFO] Task started: Prodigal
[2023-06-08 11:46:55,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg56be6c51-8903-42f8-9e6d-2708963b5dd4/GCA_000997385.1_ASM99738v1_genomic.fna.gz | prodigal -d GCA_000997385.1_ASM99738v1_genomic.fna/cds.fna -a GCA_000997385.1_ASM99738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:46:59,726] [INFO] Task succeeded: Prodigal
[2023-06-08 11:46:59,726] [INFO] Task started: HMMsearch
[2023-06-08 11:46:59,726] [INFO] Running command: hmmsearch --tblout GCA_000997385.1_ASM99738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ec4c1ae-742c-420a-a6b9-3636f956c62a/dqc_reference/reference_markers.hmm GCA_000997385.1_ASM99738v1_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:46:59,948] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:46:59,949] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg56be6c51-8903-42f8-9e6d-2708963b5dd4/GCA_000997385.1_ASM99738v1_genomic.fna.gz]
[2023-06-08 11:46:59,970] [INFO] Query marker FASTA was written to GCA_000997385.1_ASM99738v1_genomic.fna/markers.fasta
[2023-06-08 11:46:59,970] [INFO] Task started: Blastn
[2023-06-08 11:46:59,971] [INFO] Running command: blastn -query GCA_000997385.1_ASM99738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ec4c1ae-742c-420a-a6b9-3636f956c62a/dqc_reference/reference_markers.fasta -out GCA_000997385.1_ASM99738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:47:00,527] [INFO] Task succeeded: Blastn
[2023-06-08 11:47:00,537] [INFO] Selected 13 target genomes.
[2023-06-08 11:47:00,537] [INFO] Target genome list was writen to GCA_000997385.1_ASM99738v1_genomic.fna/target_genomes.txt
[2023-06-08 11:47:00,542] [INFO] Task started: fastANI
[2023-06-08 11:47:00,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg56be6c51-8903-42f8-9e6d-2708963b5dd4/GCA_000997385.1_ASM99738v1_genomic.fna.gz --refList GCA_000997385.1_ASM99738v1_genomic.fna/target_genomes.txt --output GCA_000997385.1_ASM99738v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:47:08,305] [INFO] Task succeeded: fastANI
[2023-06-08 11:47:08,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ec4c1ae-742c-420a-a6b9-3636f956c62a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:47:08,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ec4c1ae-742c-420a-a6b9-3636f956c62a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:47:08,308] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:47:08,308] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:47:08,308] [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
--------------------------------------------------------------------------------
[2023-06-08 11:47:08,311] [INFO] DFAST Taxonomy check result was written to GCA_000997385.1_ASM99738v1_genomic.fna/tc_result.tsv
[2023-06-08 11:47:08,311] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:47:08,312] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:47:08,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ec4c1ae-742c-420a-a6b9-3636f956c62a/dqc_reference/checkm_data
[2023-06-08 11:47:08,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:47:08,334] [INFO] Task started: CheckM
[2023-06-08 11:47:08,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_000997385.1_ASM99738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_000997385.1_ASM99738v1_genomic.fna/checkm_input GCA_000997385.1_ASM99738v1_genomic.fna/checkm_result
[2023-06-08 11:47:26,680] [INFO] Task succeeded: CheckM
[2023-06-08 11:47:26,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:47:26,708] [INFO] ===== Completeness check finished =====
[2023-06-08 11:47:26,708] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:47:26,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_000997385.1_ASM99738v1_genomic.fna/markers.fasta)
[2023-06-08 11:47:26,709] [INFO] Task started: Blastn
[2023-06-08 11:47:26,709] [INFO] Running command: blastn -query GCA_000997385.1_ASM99738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ec4c1ae-742c-420a-a6b9-3636f956c62a/dqc_reference/reference_markers_gtdb.fasta -out GCA_000997385.1_ASM99738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:47:27,416] [INFO] Task succeeded: Blastn
[2023-06-08 11:47:27,421] [INFO] Selected 11 target genomes.
[2023-06-08 11:47:27,421] [INFO] Target genome list was writen to GCA_000997385.1_ASM99738v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:47:27,448] [INFO] Task started: fastANI
[2023-06-08 11:47:27,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg56be6c51-8903-42f8-9e6d-2708963b5dd4/GCA_000997385.1_ASM99738v1_genomic.fna.gz --refList GCA_000997385.1_ASM99738v1_genomic.fna/target_genomes_gtdb.txt --output GCA_000997385.1_ASM99738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:47:30,124] [INFO] Task succeeded: fastANI
[2023-06-08 11:47:30,128] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:47:30,129] [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_000997385.1	s__GWC1-40-9 sp000997385	100.0	347	348	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__Daviesbacterales;f__UBA10151;g__GWC1-40-9	95.0	99.97	99.94	0.99	0.99	3	conclusive
--------------------------------------------------------------------------------
[2023-06-08 11:47:30,131] [INFO] GTDB search result was written to GCA_000997385.1_ASM99738v1_genomic.fna/result_gtdb.tsv
[2023-06-08 11:47:30,131] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:47:30,134] [INFO] DFAST_QC result json was written to GCA_000997385.1_ASM99738v1_genomic.fna/dqc_result.json
[2023-06-08 11:47:30,134] [INFO] DFAST_QC completed!
[2023-06-08 11:47:30,134] [INFO] Total running time: 0h0m36s