[2023-06-18 13:27:36,384] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:27:36,388] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:27:36,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg373a2050-4b38-4feb-ac59-31d87c911f60/dqc_reference
[2023-06-18 13:27:37,590] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:27:37,591] [INFO] Task started: Prodigal
[2023-06-18 13:27:37,591] [INFO] Running command: gunzip -c /var/lib/cwl/stg240736e7-6a83-45b4-b120-f8a389112fc4/GCA_018897535.1_ASM1889753v1_genomic.fna.gz | prodigal -d GCA_018897535.1_ASM1889753v1_genomic.fna/cds.fna -a GCA_018897535.1_ASM1889753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:27:39,254] [INFO] Task succeeded: Prodigal
[2023-06-18 13:27:39,254] [INFO] Task started: HMMsearch
[2023-06-18 13:27:39,254] [INFO] Running command: hmmsearch --tblout GCA_018897535.1_ASM1889753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg373a2050-4b38-4feb-ac59-31d87c911f60/dqc_reference/reference_markers.hmm GCA_018897535.1_ASM1889753v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:27:39,493] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:27:39,495] [INFO] Found 6/6 markers.
[2023-06-18 13:27:39,514] [INFO] Query marker FASTA was written to GCA_018897535.1_ASM1889753v1_genomic.fna/markers.fasta
[2023-06-18 13:27:39,514] [INFO] Task started: Blastn
[2023-06-18 13:27:39,515] [INFO] Running command: blastn -query GCA_018897535.1_ASM1889753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg373a2050-4b38-4feb-ac59-31d87c911f60/dqc_reference/reference_markers.fasta -out GCA_018897535.1_ASM1889753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:27:40,125] [INFO] Task succeeded: Blastn
[2023-06-18 13:27:40,130] [INFO] Selected 10 target genomes.
[2023-06-18 13:27:40,130] [INFO] Target genome list was writen to GCA_018897535.1_ASM1889753v1_genomic.fna/target_genomes.txt
[2023-06-18 13:27:40,136] [INFO] Task started: fastANI
[2023-06-18 13:27:40,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg240736e7-6a83-45b4-b120-f8a389112fc4/GCA_018897535.1_ASM1889753v1_genomic.fna.gz --refList GCA_018897535.1_ASM1889753v1_genomic.fna/target_genomes.txt --output GCA_018897535.1_ASM1889753v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:27:44,922] [INFO] Task succeeded: fastANI
[2023-06-18 13:27:44,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg373a2050-4b38-4feb-ac59-31d87c911f60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:27:44,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg373a2050-4b38-4feb-ac59-31d87c911f60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:27:44,926] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:27:44,926] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 13:27:44,926] [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
--------------------------------------------------------------------------------
[2023-06-18 13:27:44,929] [INFO] DFAST Taxonomy check result was written to GCA_018897535.1_ASM1889753v1_genomic.fna/tc_result.tsv
[2023-06-18 13:27:44,932] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:27:44,932] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:27:44,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg373a2050-4b38-4feb-ac59-31d87c911f60/dqc_reference/checkm_data
[2023-06-18 13:27:44,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:27:44,956] [INFO] Task started: CheckM
[2023-06-18 13:27:44,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018897535.1_ASM1889753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018897535.1_ASM1889753v1_genomic.fna/checkm_input GCA_018897535.1_ASM1889753v1_genomic.fna/checkm_result
[2023-06-18 13:27:58,548] [INFO] Task succeeded: CheckM
[2023-06-18 13:27:58,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:27:58,580] [INFO] ===== Completeness check finished =====
[2023-06-18 13:27:58,580] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:27:58,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018897535.1_ASM1889753v1_genomic.fna/markers.fasta)
[2023-06-18 13:27:58,581] [INFO] Task started: Blastn
[2023-06-18 13:27:58,581] [INFO] Running command: blastn -query GCA_018897535.1_ASM1889753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg373a2050-4b38-4feb-ac59-31d87c911f60/dqc_reference/reference_markers_gtdb.fasta -out GCA_018897535.1_ASM1889753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:27:59,373] [INFO] Task succeeded: Blastn
[2023-06-18 13:27:59,377] [INFO] Selected 14 target genomes.
[2023-06-18 13:27:59,378] [INFO] Target genome list was writen to GCA_018897535.1_ASM1889753v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:27:59,389] [INFO] Task started: fastANI
[2023-06-18 13:27:59,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg240736e7-6a83-45b4-b120-f8a389112fc4/GCA_018897535.1_ASM1889753v1_genomic.fna.gz --refList GCA_018897535.1_ASM1889753v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018897535.1_ASM1889753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:28:04,414] [INFO] Task succeeded: fastANI
[2023-06-18 13:28:04,422] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:28:04,423] [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_018897535.1	s__UASB340 sp018897535	100.0	304	307	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UASB340;g__UASB340	95.0	99.90	99.90	0.96	0.96	2	conclusive
GCA_001468925.1	s__UASB340 sp001468925	94.7355	254	307	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UASB340;g__UASB340	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000989185.1	s__UASB340 sp000989185	77.45	134	307	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UASB340;g__UASB340	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014728525.1	s__WJLJ01 sp014728525	76.8431	73	307	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UASB340;g__WJLJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 13:28:04,426] [INFO] GTDB search result was written to GCA_018897535.1_ASM1889753v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:28:04,426] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:28:04,429] [INFO] DFAST_QC result json was written to GCA_018897535.1_ASM1889753v1_genomic.fna/dqc_result.json
[2023-06-18 13:28:04,429] [INFO] DFAST_QC completed!
[2023-06-18 13:28:04,429] [INFO] Total running time: 0h0m28s