[2023-06-17 11:26:14,467] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:26:14,493] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:26:14,493] [INFO] DQC Reference Directory: /var/lib/cwl/stg39d04dff-6a8c-441c-b547-d817a233d80a/dqc_reference
[2023-06-17 11:26:17,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:26:17,190] [INFO] Task started: Prodigal
[2023-06-17 11:26:17,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg55fe6b8c-1188-4aa1-8a93-12fc3a29e578/GCA_028697815.1_ASM2869781v1_genomic.fna.gz | prodigal -d GCA_028697815.1_ASM2869781v1_genomic.fna/cds.fna -a GCA_028697815.1_ASM2869781v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:26:22,812] [INFO] Task succeeded: Prodigal
[2023-06-17 11:26:22,812] [INFO] Task started: HMMsearch
[2023-06-17 11:26:22,812] [INFO] Running command: hmmsearch --tblout GCA_028697815.1_ASM2869781v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39d04dff-6a8c-441c-b547-d817a233d80a/dqc_reference/reference_markers.hmm GCA_028697815.1_ASM2869781v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:26:23,049] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:26:23,050] [INFO] Found 6/6 markers.
[2023-06-17 11:26:23,071] [INFO] Query marker FASTA was written to GCA_028697815.1_ASM2869781v1_genomic.fna/markers.fasta
[2023-06-17 11:26:23,072] [INFO] Task started: Blastn
[2023-06-17 11:26:23,072] [INFO] Running command: blastn -query GCA_028697815.1_ASM2869781v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39d04dff-6a8c-441c-b547-d817a233d80a/dqc_reference/reference_markers.fasta -out GCA_028697815.1_ASM2869781v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:26:23,709] [INFO] Task succeeded: Blastn
[2023-06-17 11:26:23,714] [INFO] Selected 21 target genomes.
[2023-06-17 11:26:23,714] [INFO] Target genome list was writen to GCA_028697815.1_ASM2869781v1_genomic.fna/target_genomes.txt
[2023-06-17 11:26:23,727] [INFO] Task started: fastANI
[2023-06-17 11:26:23,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg55fe6b8c-1188-4aa1-8a93-12fc3a29e578/GCA_028697815.1_ASM2869781v1_genomic.fna.gz --refList GCA_028697815.1_ASM2869781v1_genomic.fna/target_genomes.txt --output GCA_028697815.1_ASM2869781v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:26:34,738] [INFO] Task succeeded: fastANI
[2023-06-17 11:26:34,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39d04dff-6a8c-441c-b547-d817a233d80a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:26:34,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39d04dff-6a8c-441c-b547-d817a233d80a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:26:34,741] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:26:34,741] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 11:26:34,741] [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 11:26:34,743] [INFO] DFAST Taxonomy check result was written to GCA_028697815.1_ASM2869781v1_genomic.fna/tc_result.tsv
[2023-06-17 11:26:34,744] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:26:34,744] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:26:34,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39d04dff-6a8c-441c-b547-d817a233d80a/dqc_reference/checkm_data
[2023-06-17 11:26:34,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:26:34,774] [INFO] Task started: CheckM
[2023-06-17 11:26:34,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028697815.1_ASM2869781v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028697815.1_ASM2869781v1_genomic.fna/checkm_input GCA_028697815.1_ASM2869781v1_genomic.fna/checkm_result
[2023-06-17 11:26:57,761] [INFO] Task succeeded: CheckM
[2023-06-17 11:26:57,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:26:57,782] [INFO] ===== Completeness check finished =====
[2023-06-17 11:26:57,783] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:26:57,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028697815.1_ASM2869781v1_genomic.fna/markers.fasta)
[2023-06-17 11:26:57,783] [INFO] Task started: Blastn
[2023-06-17 11:26:57,783] [INFO] Running command: blastn -query GCA_028697815.1_ASM2869781v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39d04dff-6a8c-441c-b547-d817a233d80a/dqc_reference/reference_markers_gtdb.fasta -out GCA_028697815.1_ASM2869781v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:26:58,768] [INFO] Task succeeded: Blastn
[2023-06-17 11:26:58,772] [INFO] Selected 17 target genomes.
[2023-06-17 11:26:58,772] [INFO] Target genome list was writen to GCA_028697815.1_ASM2869781v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:26:58,782] [INFO] Task started: fastANI
[2023-06-17 11:26:58,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg55fe6b8c-1188-4aa1-8a93-12fc3a29e578/GCA_028697815.1_ASM2869781v1_genomic.fna.gz --refList GCA_028697815.1_ASM2869781v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028697815.1_ASM2869781v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:27:06,118] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:06,127] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:27:06,127] [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_001512885.1	s__DTU049 sp001512885	99.7358	539	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__DTU049;g__DTU049	95.0	99.85	99.76	0.91	0.87	5	conclusive
GCA_018056215.1	s__DTU049 sp018056215	78.9211	205	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__DTU049;g__DTU049	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432645.1	s__DTU049 sp018432645	78.4502	252	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__DTU049;g__DTU049	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001513285.1	s__DTU049 sp001513285	78.3336	218	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__DTU049;g__DTU049	95.0	99.83	99.83	0.87	0.87	2	-
GCA_001603615.1	s__DTU049 sp001603615	78.0358	171	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__DTU049;g__DTU049	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:27:06,129] [INFO] GTDB search result was written to GCA_028697815.1_ASM2869781v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:27:06,130] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:27:06,133] [INFO] DFAST_QC result json was written to GCA_028697815.1_ASM2869781v1_genomic.fna/dqc_result.json
[2023-06-17 11:27:06,133] [INFO] DFAST_QC completed!
[2023-06-17 11:27:06,133] [INFO] Total running time: 0h0m52s