[2023-06-17 13:43:51,575] [INFO] DFAST_QC pipeline started.
[2023-06-17 13:43:51,585] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 13:43:51,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dd96248-d692-4a10-b824-ceff9101da06/dqc_reference
[2023-06-17 13:43:52,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 13:43:52,820] [INFO] Task started: Prodigal
[2023-06-17 13:43:52,821] [INFO] Running command: gunzip -c /var/lib/cwl/stgd71d8319-3c0a-4c24-938a-f1d6e2a7bdbb/GCA_028874585.1_ASM2887458v1_genomic.fna.gz | prodigal -d GCA_028874585.1_ASM2887458v1_genomic.fna/cds.fna -a GCA_028874585.1_ASM2887458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 13:44:01,715] [INFO] Task succeeded: Prodigal
[2023-06-17 13:44:01,716] [INFO] Task started: HMMsearch
[2023-06-17 13:44:01,716] [INFO] Running command: hmmsearch --tblout GCA_028874585.1_ASM2887458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dd96248-d692-4a10-b824-ceff9101da06/dqc_reference/reference_markers.hmm GCA_028874585.1_ASM2887458v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 13:44:01,969] [INFO] Task succeeded: HMMsearch
[2023-06-17 13:44:01,970] [INFO] Found 6/6 markers.
[2023-06-17 13:44:02,007] [INFO] Query marker FASTA was written to GCA_028874585.1_ASM2887458v1_genomic.fna/markers.fasta
[2023-06-17 13:44:02,007] [INFO] Task started: Blastn
[2023-06-17 13:44:02,007] [INFO] Running command: blastn -query GCA_028874585.1_ASM2887458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dd96248-d692-4a10-b824-ceff9101da06/dqc_reference/reference_markers.fasta -out GCA_028874585.1_ASM2887458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:44:02,636] [INFO] Task succeeded: Blastn
[2023-06-17 13:44:02,641] [INFO] Selected 20 target genomes.
[2023-06-17 13:44:02,641] [INFO] Target genome list was writen to GCA_028874585.1_ASM2887458v1_genomic.fna/target_genomes.txt
[2023-06-17 13:44:02,645] [INFO] Task started: fastANI
[2023-06-17 13:44:02,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgd71d8319-3c0a-4c24-938a-f1d6e2a7bdbb/GCA_028874585.1_ASM2887458v1_genomic.fna.gz --refList GCA_028874585.1_ASM2887458v1_genomic.fna/target_genomes.txt --output GCA_028874585.1_ASM2887458v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 13:44:18,521] [INFO] Task succeeded: fastANI
[2023-06-17 13:44:18,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dd96248-d692-4a10-b824-ceff9101da06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 13:44:18,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dd96248-d692-4a10-b824-ceff9101da06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 13:44:18,532] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 13:44:18,532] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 13:44:18,532] [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
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	74.8089	50	1012	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	74.7703	55	1012	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	74.6546	58	1012	95	below_threshold
Trebonia kvetii	strain=15TR583	GCA_007827045.1	2480626	2480626	type	True	74.5761	61	1012	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 13:44:18,534] [INFO] DFAST Taxonomy check result was written to GCA_028874585.1_ASM2887458v1_genomic.fna/tc_result.tsv
[2023-06-17 13:44:18,535] [INFO] ===== Taxonomy check completed =====
[2023-06-17 13:44:18,535] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 13:44:18,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dd96248-d692-4a10-b824-ceff9101da06/dqc_reference/checkm_data
[2023-06-17 13:44:18,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 13:44:18,574] [INFO] Task started: CheckM
[2023-06-17 13:44:18,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028874585.1_ASM2887458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028874585.1_ASM2887458v1_genomic.fna/checkm_input GCA_028874585.1_ASM2887458v1_genomic.fna/checkm_result
[2023-06-17 13:44:48,720] [INFO] Task succeeded: CheckM
[2023-06-17 13:44:48,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 13:44:48,745] [INFO] ===== Completeness check finished =====
[2023-06-17 13:44:48,746] [INFO] ===== Start GTDB Search =====
[2023-06-17 13:44:48,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028874585.1_ASM2887458v1_genomic.fna/markers.fasta)
[2023-06-17 13:44:48,747] [INFO] Task started: Blastn
[2023-06-17 13:44:48,747] [INFO] Running command: blastn -query GCA_028874585.1_ASM2887458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dd96248-d692-4a10-b824-ceff9101da06/dqc_reference/reference_markers_gtdb.fasta -out GCA_028874585.1_ASM2887458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:44:49,636] [INFO] Task succeeded: Blastn
[2023-06-17 13:44:49,640] [INFO] Selected 17 target genomes.
[2023-06-17 13:44:49,640] [INFO] Target genome list was writen to GCA_028874585.1_ASM2887458v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 13:44:49,644] [INFO] Task started: fastANI
[2023-06-17 13:44:49,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgd71d8319-3c0a-4c24-938a-f1d6e2a7bdbb/GCA_028874585.1_ASM2887458v1_genomic.fna.gz --refList GCA_028874585.1_ASM2887458v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028874585.1_ASM2887458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 13:44:58,993] [INFO] Task succeeded: fastANI
[2023-06-17 13:44:58,999] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 13:44:59,000] [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_009839425.1	s__UBA11872 sp009839425	90.5293	699	1012	d__Bacteria;p__Chloroflexota;c__UBA11872;o__UBA11872;f__UBA11872;g__UBA11872	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523785.1	s__UBA11872 sp011523785	87.763	772	1012	d__Bacteria;p__Chloroflexota;c__UBA11872;o__UBA11872;f__UBA11872;g__UBA11872	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 13:44:59,002] [INFO] GTDB search result was written to GCA_028874585.1_ASM2887458v1_genomic.fna/result_gtdb.tsv
[2023-06-17 13:44:59,003] [INFO] ===== GTDB Search completed =====
[2023-06-17 13:44:59,005] [INFO] DFAST_QC result json was written to GCA_028874585.1_ASM2887458v1_genomic.fna/dqc_result.json
[2023-06-17 13:44:59,006] [INFO] DFAST_QC completed!
[2023-06-17 13:44:59,006] [INFO] Total running time: 0h1m7s