[2023-06-17 02:01:31,724] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:01:31,725] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:01:31,726] [INFO] DQC Reference Directory: /var/lib/cwl/stg78a65540-fd94-4c5c-9181-7b3d68706b1d/dqc_reference
[2023-06-17 02:01:33,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:01:33,337] [INFO] Task started: Prodigal
[2023-06-17 02:01:33,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg1245ee9f-ffa7-47c7-9fc8-20fc20c6e6da/GCA_028708335.1_ASM2870833v1_genomic.fna.gz | prodigal -d GCA_028708335.1_ASM2870833v1_genomic.fna/cds.fna -a GCA_028708335.1_ASM2870833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:01:39,861] [INFO] Task succeeded: Prodigal
[2023-06-17 02:01:39,861] [INFO] Task started: HMMsearch
[2023-06-17 02:01:39,861] [INFO] Running command: hmmsearch --tblout GCA_028708335.1_ASM2870833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78a65540-fd94-4c5c-9181-7b3d68706b1d/dqc_reference/reference_markers.hmm GCA_028708335.1_ASM2870833v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:01:40,045] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:01:40,046] [INFO] Found 6/6 markers.
[2023-06-17 02:01:40,066] [INFO] Query marker FASTA was written to GCA_028708335.1_ASM2870833v1_genomic.fna/markers.fasta
[2023-06-17 02:01:40,066] [INFO] Task started: Blastn
[2023-06-17 02:01:40,066] [INFO] Running command: blastn -query GCA_028708335.1_ASM2870833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78a65540-fd94-4c5c-9181-7b3d68706b1d/dqc_reference/reference_markers.fasta -out GCA_028708335.1_ASM2870833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:01:40,615] [INFO] Task succeeded: Blastn
[2023-06-17 02:01:40,620] [INFO] Selected 20 target genomes.
[2023-06-17 02:01:40,620] [INFO] Target genome list was writen to GCA_028708335.1_ASM2870833v1_genomic.fna/target_genomes.txt
[2023-06-17 02:01:40,625] [INFO] Task started: fastANI
[2023-06-17 02:01:40,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg1245ee9f-ffa7-47c7-9fc8-20fc20c6e6da/GCA_028708335.1_ASM2870833v1_genomic.fna.gz --refList GCA_028708335.1_ASM2870833v1_genomic.fna/target_genomes.txt --output GCA_028708335.1_ASM2870833v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:01:52,978] [INFO] Task succeeded: fastANI
[2023-06-17 02:01:52,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78a65540-fd94-4c5c-9181-7b3d68706b1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:01:52,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78a65540-fd94-4c5c-9181-7b3d68706b1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:01:52,980] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:01:52,980] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 02:01:52,980] [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 02:01:52,982] [INFO] DFAST Taxonomy check result was written to GCA_028708335.1_ASM2870833v1_genomic.fna/tc_result.tsv
[2023-06-17 02:01:52,983] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:01:52,983] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:01:52,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78a65540-fd94-4c5c-9181-7b3d68706b1d/dqc_reference/checkm_data
[2023-06-17 02:01:52,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:01:53,009] [INFO] Task started: CheckM
[2023-06-17 02:01:53,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708335.1_ASM2870833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708335.1_ASM2870833v1_genomic.fna/checkm_input GCA_028708335.1_ASM2870833v1_genomic.fna/checkm_result
[2023-06-17 02:02:17,080] [INFO] Task succeeded: CheckM
[2023-06-17 02:02:17,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:02:17,097] [INFO] ===== Completeness check finished =====
[2023-06-17 02:02:17,097] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:02:17,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708335.1_ASM2870833v1_genomic.fna/markers.fasta)
[2023-06-17 02:02:17,098] [INFO] Task started: Blastn
[2023-06-17 02:02:17,098] [INFO] Running command: blastn -query GCA_028708335.1_ASM2870833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78a65540-fd94-4c5c-9181-7b3d68706b1d/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708335.1_ASM2870833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:02:17,825] [INFO] Task succeeded: Blastn
[2023-06-17 02:02:17,828] [INFO] Selected 21 target genomes.
[2023-06-17 02:02:17,829] [INFO] Target genome list was writen to GCA_028708335.1_ASM2870833v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:02:17,837] [INFO] Task started: fastANI
[2023-06-17 02:02:17,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg1245ee9f-ffa7-47c7-9fc8-20fc20c6e6da/GCA_028708335.1_ASM2870833v1_genomic.fna.gz --refList GCA_028708335.1_ASM2870833v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708335.1_ASM2870833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:02:26,099] [INFO] Task succeeded: fastANI
[2023-06-17 02:02:26,105] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:02:26,105] [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_001513425.1	s__DTU024 sp001513425	99.6539	595	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__DTU024	95.0	99.75	99.75	0.92	0.92	2	conclusive
GCA_012728815.1	s__DTU024 sp012728815	76.2119	50	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__DTU024	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305755.1	s__UBA1038 sp002305755	75.909	59	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA1038	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521895.1	s__DTU024 sp012521895	75.8814	59	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__DTU024	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513645.1	s__UBA1038 sp012513645	75.7164	57	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA1038	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 02:02:26,107] [INFO] GTDB search result was written to GCA_028708335.1_ASM2870833v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:02:26,107] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:02:26,110] [INFO] DFAST_QC result json was written to GCA_028708335.1_ASM2870833v1_genomic.fna/dqc_result.json
[2023-06-17 02:02:26,110] [INFO] DFAST_QC completed!
[2023-06-17 02:02:26,110] [INFO] Total running time: 0h0m54s