[2023-06-19 10:56:31,324] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:56:31,329] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:56:31,329] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f08c484-b248-402c-80f5-c7ad6606c832/dqc_reference
[2023-06-19 10:56:33,391] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:56:33,392] [INFO] Task started: Prodigal
[2023-06-19 10:56:33,393] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3380167-eb67-4a89-9404-5d1746685f4f/GCA_018238545.1_ASM1823854v1_genomic.fna.gz | prodigal -d GCA_018238545.1_ASM1823854v1_genomic.fna/cds.fna -a GCA_018238545.1_ASM1823854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:56:39,817] [INFO] Task succeeded: Prodigal
[2023-06-19 10:56:39,818] [INFO] Task started: HMMsearch
[2023-06-19 10:56:39,818] [INFO] Running command: hmmsearch --tblout GCA_018238545.1_ASM1823854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f08c484-b248-402c-80f5-c7ad6606c832/dqc_reference/reference_markers.hmm GCA_018238545.1_ASM1823854v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:56:40,082] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:56:40,084] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf3380167-eb67-4a89-9404-5d1746685f4f/GCA_018238545.1_ASM1823854v1_genomic.fna.gz]
[2023-06-19 10:56:40,116] [INFO] Query marker FASTA was written to GCA_018238545.1_ASM1823854v1_genomic.fna/markers.fasta
[2023-06-19 10:56:40,117] [INFO] Task started: Blastn
[2023-06-19 10:56:40,117] [INFO] Running command: blastn -query GCA_018238545.1_ASM1823854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f08c484-b248-402c-80f5-c7ad6606c832/dqc_reference/reference_markers.fasta -out GCA_018238545.1_ASM1823854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:40,660] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:40,664] [INFO] Selected 5 target genomes.
[2023-06-19 10:56:40,665] [INFO] Target genome list was writen to GCA_018238545.1_ASM1823854v1_genomic.fna/target_genomes.txt
[2023-06-19 10:56:40,668] [INFO] Task started: fastANI
[2023-06-19 10:56:40,668] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3380167-eb67-4a89-9404-5d1746685f4f/GCA_018238545.1_ASM1823854v1_genomic.fna.gz --refList GCA_018238545.1_ASM1823854v1_genomic.fna/target_genomes.txt --output GCA_018238545.1_ASM1823854v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:56:42,536] [INFO] Task succeeded: fastANI
[2023-06-19 10:56:42,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f08c484-b248-402c-80f5-c7ad6606c832/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:56:42,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f08c484-b248-402c-80f5-c7ad6606c832/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:56:42,539] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:56:42,539] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 10:56:42,540] [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
--------------------------------------------------------------------------------
[2023-06-19 10:56:42,542] [INFO] DFAST Taxonomy check result was written to GCA_018238545.1_ASM1823854v1_genomic.fna/tc_result.tsv
[2023-06-19 10:56:42,543] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:56:42,543] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:56:42,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f08c484-b248-402c-80f5-c7ad6606c832/dqc_reference/checkm_data
[2023-06-19 10:56:42,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:56:42,583] [INFO] Task started: CheckM
[2023-06-19 10:56:42,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018238545.1_ASM1823854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018238545.1_ASM1823854v1_genomic.fna/checkm_input GCA_018238545.1_ASM1823854v1_genomic.fna/checkm_result
[2023-06-19 10:57:08,408] [INFO] Task succeeded: CheckM
[2023-06-19 10:57:08,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:57:08,433] [INFO] ===== Completeness check finished =====
[2023-06-19 10:57:08,433] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:57:08,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018238545.1_ASM1823854v1_genomic.fna/markers.fasta)
[2023-06-19 10:57:08,434] [INFO] Task started: Blastn
[2023-06-19 10:57:08,434] [INFO] Running command: blastn -query GCA_018238545.1_ASM1823854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f08c484-b248-402c-80f5-c7ad6606c832/dqc_reference/reference_markers_gtdb.fasta -out GCA_018238545.1_ASM1823854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:57:09,138] [INFO] Task succeeded: Blastn
[2023-06-19 10:57:09,144] [INFO] Selected 6 target genomes.
[2023-06-19 10:57:09,144] [INFO] Target genome list was writen to GCA_018238545.1_ASM1823854v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:57:09,148] [INFO] Task started: fastANI
[2023-06-19 10:57:09,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3380167-eb67-4a89-9404-5d1746685f4f/GCA_018238545.1_ASM1823854v1_genomic.fna.gz --refList GCA_018238545.1_ASM1823854v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018238545.1_ASM1823854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:57:12,217] [INFO] Task succeeded: fastANI
[2023-06-19 10:57:12,221] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:57:12,222] [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_018238545.1	s__UBA460 sp018238545	100.0	1137	1143	d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__UBA460;g__UBA460	95.0	98.49	96.64	0.93	0.84	6	conclusive
GCA_019057375.1	s__UBA460 sp002505645	77.6919	133	1143	d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__UBA460;g__UBA460	95.0	99.91	99.89	0.94	0.94	3	-
GCA_001940755.1	s__UBA460 sp001940755	76.5525	67	1143	d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__UBA460;g__UBA460	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:57:12,223] [INFO] GTDB search result was written to GCA_018238545.1_ASM1823854v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:57:12,224] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:57:12,226] [INFO] DFAST_QC result json was written to GCA_018238545.1_ASM1823854v1_genomic.fna/dqc_result.json
[2023-06-19 10:57:12,226] [INFO] DFAST_QC completed!
[2023-06-19 10:57:12,226] [INFO] Total running time: 0h0m41s