[2023-06-28 18:26:52,917] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:26:52,919] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:26:52,919] [INFO] DQC Reference Directory: /var/lib/cwl/stg47363b4b-6df3-4ef8-825b-893563391548/dqc_reference
[2023-06-28 18:26:54,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:26:54,245] [INFO] Task started: Prodigal
[2023-06-28 18:26:54,245] [INFO] Running command: gunzip -c /var/lib/cwl/stg3dcba4fa-ec14-465d-8e74-1b74d84f3714/GCA_020721655.1_ASM2072165v1_genomic.fna.gz | prodigal -d GCA_020721655.1_ASM2072165v1_genomic.fna/cds.fna -a GCA_020721655.1_ASM2072165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:27:01,484] [INFO] Task succeeded: Prodigal
[2023-06-28 18:27:01,484] [INFO] Task started: HMMsearch
[2023-06-28 18:27:01,484] [INFO] Running command: hmmsearch --tblout GCA_020721655.1_ASM2072165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47363b4b-6df3-4ef8-825b-893563391548/dqc_reference/reference_markers.hmm GCA_020721655.1_ASM2072165v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:27:01,756] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:27:01,758] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3dcba4fa-ec14-465d-8e74-1b74d84f3714/GCA_020721655.1_ASM2072165v1_genomic.fna.gz]
[2023-06-28 18:27:01,787] [INFO] Query marker FASTA was written to GCA_020721655.1_ASM2072165v1_genomic.fna/markers.fasta
[2023-06-28 18:27:01,788] [INFO] Task started: Blastn
[2023-06-28 18:27:01,788] [INFO] Running command: blastn -query GCA_020721655.1_ASM2072165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47363b4b-6df3-4ef8-825b-893563391548/dqc_reference/reference_markers.fasta -out GCA_020721655.1_ASM2072165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:02,397] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:02,404] [INFO] Selected 24 target genomes.
[2023-06-28 18:27:02,405] [INFO] Target genome list was writen to GCA_020721655.1_ASM2072165v1_genomic.fna/target_genomes.txt
[2023-06-28 18:27:02,410] [INFO] Task started: fastANI
[2023-06-28 18:27:02,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dcba4fa-ec14-465d-8e74-1b74d84f3714/GCA_020721655.1_ASM2072165v1_genomic.fna.gz --refList GCA_020721655.1_ASM2072165v1_genomic.fna/target_genomes.txt --output GCA_020721655.1_ASM2072165v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:27:19,960] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:19,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47363b4b-6df3-4ef8-825b-893563391548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:27:19,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47363b4b-6df3-4ef8-825b-893563391548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:27:19,962] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:27:19,963] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:27:19,963] [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
--------------------------------------------------------------------------------
[2023-06-28 18:27:19,965] [INFO] DFAST Taxonomy check result was written to GCA_020721655.1_ASM2072165v1_genomic.fna/tc_result.tsv
[2023-06-28 18:27:19,965] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:27:19,966] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:27:19,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47363b4b-6df3-4ef8-825b-893563391548/dqc_reference/checkm_data
[2023-06-28 18:27:19,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:27:20,006] [INFO] Task started: CheckM
[2023-06-28 18:27:20,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020721655.1_ASM2072165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020721655.1_ASM2072165v1_genomic.fna/checkm_input GCA_020721655.1_ASM2072165v1_genomic.fna/checkm_result
[2023-06-28 18:27:47,662] [INFO] Task succeeded: CheckM
[2023-06-28 18:27:47,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:27:47,690] [INFO] ===== Completeness check finished =====
[2023-06-28 18:27:47,691] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:27:47,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020721655.1_ASM2072165v1_genomic.fna/markers.fasta)
[2023-06-28 18:27:47,692] [INFO] Task started: Blastn
[2023-06-28 18:27:47,692] [INFO] Running command: blastn -query GCA_020721655.1_ASM2072165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47363b4b-6df3-4ef8-825b-893563391548/dqc_reference/reference_markers_gtdb.fasta -out GCA_020721655.1_ASM2072165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:48,485] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:48,489] [INFO] Selected 24 target genomes.
[2023-06-28 18:27:48,490] [INFO] Target genome list was writen to GCA_020721655.1_ASM2072165v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:27:48,500] [INFO] Task started: fastANI
[2023-06-28 18:27:48,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dcba4fa-ec14-465d-8e74-1b74d84f3714/GCA_020721655.1_ASM2072165v1_genomic.fna.gz --refList GCA_020721655.1_ASM2072165v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020721655.1_ASM2072165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:28:04,460] [INFO] Task succeeded: fastANI
[2023-06-28 18:28:04,464] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:28:04,464] [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_001769505.1	s__GWF2-33-38 sp001769505	75.2339	65	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWF2-33-38;g__GWF2-33-38	95.0	99.92	99.84	0.98	0.98	4	-
GCA_003648455.1	s__B39-G9 sp003648455	74.9226	59	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__B39-G9;g__B39-G9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:28:04,467] [INFO] GTDB search result was written to GCA_020721655.1_ASM2072165v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:28:04,467] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:28:04,470] [INFO] DFAST_QC result json was written to GCA_020721655.1_ASM2072165v1_genomic.fna/dqc_result.json
[2023-06-28 18:28:04,471] [INFO] DFAST_QC completed!
[2023-06-28 18:28:04,471] [INFO] Total running time: 0h1m12s