[2023-06-28 02:32:13,117] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:32:13,121] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:32:13,121] [INFO] DQC Reference Directory: /var/lib/cwl/stged99a7e4-2022-4b32-8eff-fc01d4fd615b/dqc_reference
[2023-06-28 02:32:15,212] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:32:15,212] [INFO] Task started: Prodigal
[2023-06-28 02:32:15,213] [INFO] Running command: gunzip -c /var/lib/cwl/stg53292c55-ead3-4232-ad08-848c778dcbda/GCA_019894835.1_ASM1989483v1_genomic.fna.gz | prodigal -d GCA_019894835.1_ASM1989483v1_genomic.fna/cds.fna -a GCA_019894835.1_ASM1989483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:32:17,815] [INFO] Task succeeded: Prodigal
[2023-06-28 02:32:17,815] [INFO] Task started: HMMsearch
[2023-06-28 02:32:17,815] [INFO] Running command: hmmsearch --tblout GCA_019894835.1_ASM1989483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged99a7e4-2022-4b32-8eff-fc01d4fd615b/dqc_reference/reference_markers.hmm GCA_019894835.1_ASM1989483v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:32:18,015] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:32:18,017] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg53292c55-ead3-4232-ad08-848c778dcbda/GCA_019894835.1_ASM1989483v1_genomic.fna.gz]
[2023-06-28 02:32:18,038] [INFO] Query marker FASTA was written to GCA_019894835.1_ASM1989483v1_genomic.fna/markers.fasta
[2023-06-28 02:32:18,038] [INFO] Task started: Blastn
[2023-06-28 02:32:18,038] [INFO] Running command: blastn -query GCA_019894835.1_ASM1989483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged99a7e4-2022-4b32-8eff-fc01d4fd615b/dqc_reference/reference_markers.fasta -out GCA_019894835.1_ASM1989483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:32:20,136] [INFO] Task succeeded: Blastn
[2023-06-28 02:32:20,141] [INFO] Selected 5 target genomes.
[2023-06-28 02:32:20,141] [INFO] Target genome list was writen to GCA_019894835.1_ASM1989483v1_genomic.fna/target_genomes.txt
[2023-06-28 02:32:20,168] [INFO] Task started: fastANI
[2023-06-28 02:32:20,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg53292c55-ead3-4232-ad08-848c778dcbda/GCA_019894835.1_ASM1989483v1_genomic.fna.gz --refList GCA_019894835.1_ASM1989483v1_genomic.fna/target_genomes.txt --output GCA_019894835.1_ASM1989483v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:32:22,643] [INFO] Task succeeded: fastANI
[2023-06-28 02:32:22,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged99a7e4-2022-4b32-8eff-fc01d4fd615b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:32:22,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged99a7e4-2022-4b32-8eff-fc01d4fd615b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:32:22,646] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:32:22,647] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 02:32:22,647] [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 02:32:22,659] [INFO] DFAST Taxonomy check result was written to GCA_019894835.1_ASM1989483v1_genomic.fna/tc_result.tsv
[2023-06-28 02:32:22,659] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:32:22,659] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:32:22,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged99a7e4-2022-4b32-8eff-fc01d4fd615b/dqc_reference/checkm_data
[2023-06-28 02:32:22,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:32:22,689] [INFO] Task started: CheckM
[2023-06-28 02:32:22,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019894835.1_ASM1989483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019894835.1_ASM1989483v1_genomic.fna/checkm_input GCA_019894835.1_ASM1989483v1_genomic.fna/checkm_result
[2023-06-28 02:32:41,449] [INFO] Task succeeded: CheckM
[2023-06-28 02:32:41,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.22%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:32:41,473] [INFO] ===== Completeness check finished =====
[2023-06-28 02:32:41,473] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:32:41,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019894835.1_ASM1989483v1_genomic.fna/markers.fasta)
[2023-06-28 02:32:41,474] [INFO] Task started: Blastn
[2023-06-28 02:32:41,474] [INFO] Running command: blastn -query GCA_019894835.1_ASM1989483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged99a7e4-2022-4b32-8eff-fc01d4fd615b/dqc_reference/reference_markers_gtdb.fasta -out GCA_019894835.1_ASM1989483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:32:41,973] [INFO] Task succeeded: Blastn
[2023-06-28 02:32:41,978] [INFO] Selected 5 target genomes.
[2023-06-28 02:32:41,978] [INFO] Target genome list was writen to GCA_019894835.1_ASM1989483v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:32:42,014] [INFO] Task started: fastANI
[2023-06-28 02:32:42,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg53292c55-ead3-4232-ad08-848c778dcbda/GCA_019894835.1_ASM1989483v1_genomic.fna.gz --refList GCA_019894835.1_ASM1989483v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019894835.1_ASM1989483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:32:44,994] [INFO] Task succeeded: fastANI
[2023-06-28 02:32:44,998] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:32:44,998] [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_016926735.1	s__JAFGOA01 sp016926735	77.6327	164	327	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__JAFGOA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 02:32:45,000] [INFO] GTDB search result was written to GCA_019894835.1_ASM1989483v1_genomic.fna/result_gtdb.tsv
[2023-06-28 02:32:45,000] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:32:45,003] [INFO] DFAST_QC result json was written to GCA_019894835.1_ASM1989483v1_genomic.fna/dqc_result.json
[2023-06-28 02:32:45,003] [INFO] DFAST_QC completed!
[2023-06-28 02:32:45,004] [INFO] Total running time: 0h0m32s