[2024-01-24 13:58:10,221] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,222] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg47d6e222-0f9a-4ac6-9ebe-c1b5481bfb8a/dqc_reference
[2024-01-24 13:58:11,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,346] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,346] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cfde37e-c70b-4f7b-b134-175d16ce6aad/GCF_016863335.1_ASM1686333v1_genomic.fna.gz | prodigal -d GCF_016863335.1_ASM1686333v1_genomic.fna/cds.fna -a GCF_016863335.1_ASM1686333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:33,443] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:33,443] [INFO] Task started: HMMsearch
[2024-01-24 13:58:33,443] [INFO] Running command: hmmsearch --tblout GCF_016863335.1_ASM1686333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47d6e222-0f9a-4ac6-9ebe-c1b5481bfb8a/dqc_reference/reference_markers.hmm GCF_016863335.1_ASM1686333v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:33,754] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:33,755] [INFO] Found 6/6 markers.
[2024-01-24 13:58:33,817] [INFO] Query marker FASTA was written to GCF_016863335.1_ASM1686333v1_genomic.fna/markers.fasta
[2024-01-24 13:58:33,817] [INFO] Task started: Blastn
[2024-01-24 13:58:33,817] [INFO] Running command: blastn -query GCF_016863335.1_ASM1686333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d6e222-0f9a-4ac6-9ebe-c1b5481bfb8a/dqc_reference/reference_markers.fasta -out GCF_016863335.1_ASM1686333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:34,975] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:34,978] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:34,978] [INFO] Target genome list was writen to GCF_016863335.1_ASM1686333v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:34,986] [INFO] Task started: fastANI
[2024-01-24 13:58:34,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cfde37e-c70b-4f7b-b134-175d16ce6aad/GCF_016863335.1_ASM1686333v1_genomic.fna.gz --refList GCF_016863335.1_ASM1686333v1_genomic.fna/target_genomes.txt --output GCF_016863335.1_ASM1686333v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:57,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:57,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47d6e222-0f9a-4ac6-9ebe-c1b5481bfb8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:57,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47d6e222-0f9a-4ac6-9ebe-c1b5481bfb8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:57,018] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:57,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:57,018] [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
Planotetraspora thailandica	strain=NBRC 104271	GCA_016863335.1	487172	487172	type	True	100.0	2919	2926	95	conclusive
Planotetraspora phitsanulokensis	strain=NBRC 104273	GCA_016863295.1	575192	575192	type	True	85.9298	2073	2926	95	below_threshold
Planotetraspora silvatica	strain=NBRC 100141	GCA_016863315.1	234614	234614	type	True	85.5678	1990	2926	95	below_threshold
Planotetraspora mira	strain=NBRC 15435	GCA_016863275.1	58121	58121	type	True	85.553	2009	2926	95	below_threshold
Planotetraspora kaengkrachanensis	strain=NBRC 104272	GCA_016862895.1	575193	575193	type	True	85.471	2028	2926	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	81.4961	1236	2926	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	81.41	1004	2926	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	79.8461	1242	2926	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.1521	1156	2926	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	78.9886	1184	2926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:57,019] [INFO] DFAST Taxonomy check result was written to GCF_016863335.1_ASM1686333v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:57,020] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:57,020] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:57,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47d6e222-0f9a-4ac6-9ebe-c1b5481bfb8a/dqc_reference/checkm_data
[2024-01-24 13:58:57,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:57,101] [INFO] Task started: CheckM
[2024-01-24 13:58:57,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863335.1_ASM1686333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863335.1_ASM1686333v1_genomic.fna/checkm_input GCF_016863335.1_ASM1686333v1_genomic.fna/checkm_result
[2024-01-24 14:00:13,937] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:13,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:00:13,959] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:13,959] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:13,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863335.1_ASM1686333v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:13,960] [INFO] Task started: Blastn
[2024-01-24 14:00:13,960] [INFO] Running command: blastn -query GCF_016863335.1_ASM1686333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d6e222-0f9a-4ac6-9ebe-c1b5481bfb8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863335.1_ASM1686333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:15,799] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:15,801] [INFO] Selected 5 target genomes.
[2024-01-24 14:00:15,801] [INFO] Target genome list was writen to GCF_016863335.1_ASM1686333v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:15,804] [INFO] Task started: fastANI
[2024-01-24 14:00:15,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cfde37e-c70b-4f7b-b134-175d16ce6aad/GCF_016863335.1_ASM1686333v1_genomic.fna.gz --refList GCF_016863335.1_ASM1686333v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863335.1_ASM1686333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:27,669] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:27,673] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:27,673] [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
GCF_016863335.1	s__Planotetraspora thailandica	100.0	2919	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016863295.1	s__Planotetraspora phitsanulokensis	85.9305	2072	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863315.1	s__Planotetraspora silvatica	85.5876	1985	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.2969	N/A	N/A	N/A	N/A	1	-
GCF_016863275.1	s__Planotetraspora mira	85.5331	2013	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.2969	N/A	N/A	N/A	N/A	1	-
GCF_016862895.1	s__Planotetraspora kaengkrachanensis	85.4706	2028	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:27,675] [INFO] GTDB search result was written to GCF_016863335.1_ASM1686333v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:27,675] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:27,677] [INFO] DFAST_QC result json was written to GCF_016863335.1_ASM1686333v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:27,677] [INFO] DFAST_QC completed!
[2024-01-24 14:00:27,678] [INFO] Total running time: 0h2m17s