[2023-06-29 02:27:46,213] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:27:46,216] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:27:46,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg355c97d9-be53-4241-bdf9-a084ffc70bb5/dqc_reference
[2023-06-29 02:27:47,425] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:27:47,426] [INFO] Task started: Prodigal
[2023-06-29 02:27:47,426] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1cbe102-f2d3-4e4b-85ee-f309630dd612/GCA_027318005.1_ASM2731800v1_genomic.fna.gz | prodigal -d GCA_027318005.1_ASM2731800v1_genomic.fna/cds.fna -a GCA_027318005.1_ASM2731800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:27:57,679] [INFO] Task succeeded: Prodigal
[2023-06-29 02:27:57,679] [INFO] Task started: HMMsearch
[2023-06-29 02:27:57,680] [INFO] Running command: hmmsearch --tblout GCA_027318005.1_ASM2731800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg355c97d9-be53-4241-bdf9-a084ffc70bb5/dqc_reference/reference_markers.hmm GCA_027318005.1_ASM2731800v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:27:57,930] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:27:57,932] [INFO] Found 6/6 markers.
[2023-06-29 02:27:57,964] [INFO] Query marker FASTA was written to GCA_027318005.1_ASM2731800v1_genomic.fna/markers.fasta
[2023-06-29 02:27:57,964] [INFO] Task started: Blastn
[2023-06-29 02:27:57,965] [INFO] Running command: blastn -query GCA_027318005.1_ASM2731800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg355c97d9-be53-4241-bdf9-a084ffc70bb5/dqc_reference/reference_markers.fasta -out GCA_027318005.1_ASM2731800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:27:58,569] [INFO] Task succeeded: Blastn
[2023-06-29 02:27:58,574] [INFO] Selected 25 target genomes.
[2023-06-29 02:27:58,575] [INFO] Target genome list was writen to GCA_027318005.1_ASM2731800v1_genomic.fna/target_genomes.txt
[2023-06-29 02:27:58,581] [INFO] Task started: fastANI
[2023-06-29 02:27:58,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1cbe102-f2d3-4e4b-85ee-f309630dd612/GCA_027318005.1_ASM2731800v1_genomic.fna.gz --refList GCA_027318005.1_ASM2731800v1_genomic.fna/target_genomes.txt --output GCA_027318005.1_ASM2731800v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:28:18,180] [INFO] Task succeeded: fastANI
[2023-06-29 02:28:18,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg355c97d9-be53-4241-bdf9-a084ffc70bb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:28:18,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg355c97d9-be53-4241-bdf9-a084ffc70bb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:28:18,183] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:28:18,183] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 02:28:18,183] [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
--------------------------------------------------------------------------------
[2023-06-29 02:28:18,186] [INFO] DFAST Taxonomy check result was written to GCA_027318005.1_ASM2731800v1_genomic.fna/tc_result.tsv
[2023-06-29 02:28:18,187] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:28:18,187] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:28:18,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg355c97d9-be53-4241-bdf9-a084ffc70bb5/dqc_reference/checkm_data
[2023-06-29 02:28:18,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:28:18,252] [INFO] Task started: CheckM
[2023-06-29 02:28:18,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027318005.1_ASM2731800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027318005.1_ASM2731800v1_genomic.fna/checkm_input GCA_027318005.1_ASM2731800v1_genomic.fna/checkm_result
[2023-06-29 02:28:51,618] [INFO] Task succeeded: CheckM
[2023-06-29 02:28:51,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 02:28:51,644] [INFO] ===== Completeness check finished =====
[2023-06-29 02:28:51,644] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:28:51,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027318005.1_ASM2731800v1_genomic.fna/markers.fasta)
[2023-06-29 02:28:51,645] [INFO] Task started: Blastn
[2023-06-29 02:28:51,645] [INFO] Running command: blastn -query GCA_027318005.1_ASM2731800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg355c97d9-be53-4241-bdf9-a084ffc70bb5/dqc_reference/reference_markers_gtdb.fasta -out GCA_027318005.1_ASM2731800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:28:52,501] [INFO] Task succeeded: Blastn
[2023-06-29 02:28:52,506] [INFO] Selected 25 target genomes.
[2023-06-29 02:28:52,506] [INFO] Target genome list was writen to GCA_027318005.1_ASM2731800v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:28:52,547] [INFO] Task started: fastANI
[2023-06-29 02:28:52,548] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1cbe102-f2d3-4e4b-85ee-f309630dd612/GCA_027318005.1_ASM2731800v1_genomic.fna.gz --refList GCA_027318005.1_ASM2731800v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027318005.1_ASM2731800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:29:08,846] [INFO] Task succeeded: fastANI
[2023-06-29 02:29:08,857] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 02:29:08,857] [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_011388475.1	s__SCRD01 sp011388475	77.548	66	1103	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__SCRD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298155.1	s__SCRD01 sp004298155	76.519	77	1103	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__SCRD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003225365.1	s__Gp13-AA74 sp003225365	76.1256	81	1103	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__Gp13-AA74	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478145.1	s__UBA7540 sp002478145	76.0057	72	1103	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__UBA7540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003224695.1	s__Gp13-AA74 sp003224695	75.9129	74	1103	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__Gp13-AA74	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 02:29:08,860] [INFO] GTDB search result was written to GCA_027318005.1_ASM2731800v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:29:08,860] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:29:08,864] [INFO] DFAST_QC result json was written to GCA_027318005.1_ASM2731800v1_genomic.fna/dqc_result.json
[2023-06-29 02:29:08,864] [INFO] DFAST_QC completed!
[2023-06-29 02:29:08,864] [INFO] Total running time: 0h1m23s