[2023-06-29 04:57:23,174] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:57:23,177] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:57:23,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg09b3755b-3777-4539-aeec-104dd892c7e6/dqc_reference
[2023-06-29 04:57:24,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:57:24,729] [INFO] Task started: Prodigal
[2023-06-29 04:57:24,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fd1da00-c354-4b9a-8821-45f58ca7ad96/GCA_027045295.1_ASM2704529v1_genomic.fna.gz | prodigal -d GCA_027045295.1_ASM2704529v1_genomic.fna/cds.fna -a GCA_027045295.1_ASM2704529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:57:28,440] [INFO] Task succeeded: Prodigal
[2023-06-29 04:57:28,440] [INFO] Task started: HMMsearch
[2023-06-29 04:57:28,440] [INFO] Running command: hmmsearch --tblout GCA_027045295.1_ASM2704529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09b3755b-3777-4539-aeec-104dd892c7e6/dqc_reference/reference_markers.hmm GCA_027045295.1_ASM2704529v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:57:28,685] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:57:28,686] [INFO] Found 6/6 markers.
[2023-06-29 04:57:28,708] [INFO] Query marker FASTA was written to GCA_027045295.1_ASM2704529v1_genomic.fna/markers.fasta
[2023-06-29 04:57:28,708] [INFO] Task started: Blastn
[2023-06-29 04:57:28,708] [INFO] Running command: blastn -query GCA_027045295.1_ASM2704529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09b3755b-3777-4539-aeec-104dd892c7e6/dqc_reference/reference_markers.fasta -out GCA_027045295.1_ASM2704529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:57:29,307] [INFO] Task succeeded: Blastn
[2023-06-29 04:57:29,311] [INFO] Selected 16 target genomes.
[2023-06-29 04:57:29,311] [INFO] Target genome list was writen to GCA_027045295.1_ASM2704529v1_genomic.fna/target_genomes.txt
[2023-06-29 04:57:29,351] [INFO] Task started: fastANI
[2023-06-29 04:57:29,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fd1da00-c354-4b9a-8821-45f58ca7ad96/GCA_027045295.1_ASM2704529v1_genomic.fna.gz --refList GCA_027045295.1_ASM2704529v1_genomic.fna/target_genomes.txt --output GCA_027045295.1_ASM2704529v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:57:35,899] [INFO] Task succeeded: fastANI
[2023-06-29 04:57:35,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09b3755b-3777-4539-aeec-104dd892c7e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:57:35,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09b3755b-3777-4539-aeec-104dd892c7e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:57:35,903] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:57:35,903] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:57:35,903] [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
Hippea maritima	strain=DSM 10411	GCA_000194135.1	84405	84405	type	True	77.0892	56	445	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:57:35,905] [INFO] DFAST Taxonomy check result was written to GCA_027045295.1_ASM2704529v1_genomic.fna/tc_result.tsv
[2023-06-29 04:57:35,906] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:57:35,906] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:57:35,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09b3755b-3777-4539-aeec-104dd892c7e6/dqc_reference/checkm_data
[2023-06-29 04:57:35,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:57:35,935] [INFO] Task started: CheckM
[2023-06-29 04:57:35,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027045295.1_ASM2704529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027045295.1_ASM2704529v1_genomic.fna/checkm_input GCA_027045295.1_ASM2704529v1_genomic.fna/checkm_result
[2023-06-29 04:57:55,362] [INFO] Task succeeded: CheckM
[2023-06-29 04:57:55,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.32%
Contamintation: 4.86%
Strain heterogeneity: 15.38%
--------------------------------------------------------------------------------
[2023-06-29 04:57:55,386] [INFO] ===== Completeness check finished =====
[2023-06-29 04:57:55,386] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:57:55,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027045295.1_ASM2704529v1_genomic.fna/markers.fasta)
[2023-06-29 04:57:55,387] [INFO] Task started: Blastn
[2023-06-29 04:57:55,387] [INFO] Running command: blastn -query GCA_027045295.1_ASM2704529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09b3755b-3777-4539-aeec-104dd892c7e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_027045295.1_ASM2704529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:57:56,258] [INFO] Task succeeded: Blastn
[2023-06-29 04:57:56,262] [INFO] Selected 16 target genomes.
[2023-06-29 04:57:56,262] [INFO] Target genome list was writen to GCA_027045295.1_ASM2704529v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:57:56,275] [INFO] Task started: fastANI
[2023-06-29 04:57:56,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fd1da00-c354-4b9a-8821-45f58ca7ad96/GCA_027045295.1_ASM2704529v1_genomic.fna.gz --refList GCA_027045295.1_ASM2704529v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027045295.1_ASM2704529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:58:00,829] [INFO] Task succeeded: fastANI
[2023-06-29 04:58:00,980] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 04:58:00,980] [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_015490005.1	s__Hippea sp015490005	99.5953	319	445	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015486705.1	s__Hippea sp015486705	84.698	162	445	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015486955.1	s__Hippea sp015486955	80.7723	172	445	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015486965.1	s__Hippea sp015486965	77.7414	64	445	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea	95.0	98.25	97.79	0.84	0.82	3	-
GCF_000526195.1	s__Hippea sp000526195	77.6354	57	445	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194135.1	s__Hippea maritima	77.0892	56	445	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:58:00,983] [INFO] GTDB search result was written to GCA_027045295.1_ASM2704529v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:58:00,983] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:58:00,986] [INFO] DFAST_QC result json was written to GCA_027045295.1_ASM2704529v1_genomic.fna/dqc_result.json
[2023-06-29 04:58:00,986] [INFO] DFAST_QC completed!
[2023-06-29 04:58:00,986] [INFO] Total running time: 0h0m38s