[2023-06-17 13:13:35,946] [INFO] DFAST_QC pipeline started.
[2023-06-17 13:13:35,949] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 13:13:35,949] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0812cfe-ea87-410d-b8e1-b116f0697f79/dqc_reference
[2023-06-17 13:13:37,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 13:13:37,129] [INFO] Task started: Prodigal
[2023-06-17 13:13:37,129] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a381b55-17c2-4ef0-8960-453e1349860b/GCA_028708945.1_ASM2870894v1_genomic.fna.gz | prodigal -d GCA_028708945.1_ASM2870894v1_genomic.fna/cds.fna -a GCA_028708945.1_ASM2870894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 13:13:38,814] [INFO] Task succeeded: Prodigal
[2023-06-17 13:13:38,814] [INFO] Task started: HMMsearch
[2023-06-17 13:13:38,814] [INFO] Running command: hmmsearch --tblout GCA_028708945.1_ASM2870894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0812cfe-ea87-410d-b8e1-b116f0697f79/dqc_reference/reference_markers.hmm GCA_028708945.1_ASM2870894v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 13:13:38,963] [INFO] Task succeeded: HMMsearch
[2023-06-17 13:13:38,965] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4a381b55-17c2-4ef0-8960-453e1349860b/GCA_028708945.1_ASM2870894v1_genomic.fna.gz]
[2023-06-17 13:13:38,983] [INFO] Query marker FASTA was written to GCA_028708945.1_ASM2870894v1_genomic.fna/markers.fasta
[2023-06-17 13:13:38,983] [INFO] Task started: Blastn
[2023-06-17 13:13:38,983] [INFO] Running command: blastn -query GCA_028708945.1_ASM2870894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0812cfe-ea87-410d-b8e1-b116f0697f79/dqc_reference/reference_markers.fasta -out GCA_028708945.1_ASM2870894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:13:39,581] [INFO] Task succeeded: Blastn
[2023-06-17 13:13:39,586] [INFO] Selected 27 target genomes.
[2023-06-17 13:13:39,587] [INFO] Target genome list was writen to GCA_028708945.1_ASM2870894v1_genomic.fna/target_genomes.txt
[2023-06-17 13:13:39,590] [INFO] Task started: fastANI
[2023-06-17 13:13:39,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a381b55-17c2-4ef0-8960-453e1349860b/GCA_028708945.1_ASM2870894v1_genomic.fna.gz --refList GCA_028708945.1_ASM2870894v1_genomic.fna/target_genomes.txt --output GCA_028708945.1_ASM2870894v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 13:13:50,531] [INFO] Task succeeded: fastANI
[2023-06-17 13:13:50,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0812cfe-ea87-410d-b8e1-b116f0697f79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 13:13:50,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0812cfe-ea87-410d-b8e1-b116f0697f79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 13:13:50,533] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 13:13:50,533] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 13:13:50,534] [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 13:13:50,535] [INFO] DFAST Taxonomy check result was written to GCA_028708945.1_ASM2870894v1_genomic.fna/tc_result.tsv
[2023-06-17 13:13:50,536] [INFO] ===== Taxonomy check completed =====
[2023-06-17 13:13:50,536] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 13:13:50,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0812cfe-ea87-410d-b8e1-b116f0697f79/dqc_reference/checkm_data
[2023-06-17 13:13:50,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 13:13:50,553] [INFO] Task started: CheckM
[2023-06-17 13:13:50,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708945.1_ASM2870894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708945.1_ASM2870894v1_genomic.fna/checkm_input GCA_028708945.1_ASM2870894v1_genomic.fna/checkm_result
[2023-06-17 13:14:03,374] [INFO] Task succeeded: CheckM
[2023-06-17 13:14:03,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 13:14:03,394] [INFO] ===== Completeness check finished =====
[2023-06-17 13:14:03,395] [INFO] ===== Start GTDB Search =====
[2023-06-17 13:14:03,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708945.1_ASM2870894v1_genomic.fna/markers.fasta)
[2023-06-17 13:14:03,395] [INFO] Task started: Blastn
[2023-06-17 13:14:03,395] [INFO] Running command: blastn -query GCA_028708945.1_ASM2870894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0812cfe-ea87-410d-b8e1-b116f0697f79/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708945.1_ASM2870894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:14:04,334] [INFO] Task succeeded: Blastn
[2023-06-17 13:14:04,339] [INFO] Selected 28 target genomes.
[2023-06-17 13:14:04,339] [INFO] Target genome list was writen to GCA_028708945.1_ASM2870894v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 13:14:04,349] [INFO] Task started: fastANI
[2023-06-17 13:14:04,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a381b55-17c2-4ef0-8960-453e1349860b/GCA_028708945.1_ASM2870894v1_genomic.fna.gz --refList GCA_028708945.1_ASM2870894v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708945.1_ASM2870894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 13:14:10,406] [INFO] Task succeeded: fastANI
[2023-06-17 13:14:10,413] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 13:14:10,413] [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_000432255.1	s__Faecisoma sp000432255	76.9326	52	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	99.02	98.86	0.88	0.87	4	-
GCA_900550255.1	s__UBA5026 sp900550255	76.9294	52	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.55	98.27	0.87	0.84	3	-
GCA_012520435.1	s__JAAYOI01 sp012520435	76.4997	57	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__JAAYOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716405.1	s__Faecisoma merdavium	76.4992	62	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	97.86	97.86	0.74	0.74	2	-
GCA_017936845.1	s__UBA5026 sp017936845	76.3596	72	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773675.1	s__RUG11890 sp902773675	75.9039	52	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11890	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 13:14:10,415] [INFO] GTDB search result was written to GCA_028708945.1_ASM2870894v1_genomic.fna/result_gtdb.tsv
[2023-06-17 13:14:10,416] [INFO] ===== GTDB Search completed =====
[2023-06-17 13:14:10,418] [INFO] DFAST_QC result json was written to GCA_028708945.1_ASM2870894v1_genomic.fna/dqc_result.json
[2023-06-17 13:14:10,419] [INFO] DFAST_QC completed!
[2023-06-17 13:14:10,419] [INFO] Total running time: 0h0m34s