[2023-06-19 15:01:20,307] [INFO] DFAST_QC pipeline started.
[2023-06-19 15:01:20,309] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 15:01:20,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f4849b0-d2bd-4dde-b9ae-dcaadb3e0f57/dqc_reference
[2023-06-19 15:01:21,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 15:01:21,548] [INFO] Task started: Prodigal
[2023-06-19 15:01:21,548] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ad7e7bb-2280-4931-a631-d6b53ed128d8/GCA_018822775.1_ASM1882277v1_genomic.fna.gz | prodigal -d GCA_018822775.1_ASM1882277v1_genomic.fna/cds.fna -a GCA_018822775.1_ASM1882277v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 15:01:32,107] [INFO] Task succeeded: Prodigal
[2023-06-19 15:01:32,108] [INFO] Task started: HMMsearch
[2023-06-19 15:01:32,108] [INFO] Running command: hmmsearch --tblout GCA_018822775.1_ASM1882277v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f4849b0-d2bd-4dde-b9ae-dcaadb3e0f57/dqc_reference/reference_markers.hmm GCA_018822775.1_ASM1882277v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 15:01:32,362] [INFO] Task succeeded: HMMsearch
[2023-06-19 15:01:32,364] [INFO] Found 6/6 markers.
[2023-06-19 15:01:32,410] [INFO] Query marker FASTA was written to GCA_018822775.1_ASM1882277v1_genomic.fna/markers.fasta
[2023-06-19 15:01:32,411] [INFO] Task started: Blastn
[2023-06-19 15:01:32,411] [INFO] Running command: blastn -query GCA_018822775.1_ASM1882277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f4849b0-d2bd-4dde-b9ae-dcaadb3e0f57/dqc_reference/reference_markers.fasta -out GCA_018822775.1_ASM1882277v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:01:33,044] [INFO] Task succeeded: Blastn
[2023-06-19 15:01:33,051] [INFO] Selected 20 target genomes.
[2023-06-19 15:01:33,051] [INFO] Target genome list was writen to GCA_018822775.1_ASM1882277v1_genomic.fna/target_genomes.txt
[2023-06-19 15:01:33,056] [INFO] Task started: fastANI
[2023-06-19 15:01:33,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ad7e7bb-2280-4931-a631-d6b53ed128d8/GCA_018822775.1_ASM1882277v1_genomic.fna.gz --refList GCA_018822775.1_ASM1882277v1_genomic.fna/target_genomes.txt --output GCA_018822775.1_ASM1882277v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 15:01:47,297] [INFO] Task succeeded: fastANI
[2023-06-19 15:01:47,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f4849b0-d2bd-4dde-b9ae-dcaadb3e0f57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 15:01:47,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f4849b0-d2bd-4dde-b9ae-dcaadb3e0f57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 15:01:47,309] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 15:01:47,309] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 15:01:47,309] [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
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	75.3533	61	1260	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	75.3531	59	1260	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	75.1769	97	1260	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	75.1358	74	1260	95	below_threshold
Sciscionella marina	strain=DSM 45152	GCA_000379465.1	508770	508770	type	True	75.0656	56	1260	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	75.0654	99	1260	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	74.8986	94	1260	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	74.754	66	1260	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 15:01:47,313] [INFO] DFAST Taxonomy check result was written to GCA_018822775.1_ASM1882277v1_genomic.fna/tc_result.tsv
[2023-06-19 15:01:47,314] [INFO] ===== Taxonomy check completed =====
[2023-06-19 15:01:47,314] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 15:01:47,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f4849b0-d2bd-4dde-b9ae-dcaadb3e0f57/dqc_reference/checkm_data
[2023-06-19 15:01:47,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 15:01:47,358] [INFO] Task started: CheckM
[2023-06-19 15:01:47,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018822775.1_ASM1882277v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018822775.1_ASM1882277v1_genomic.fna/checkm_input GCA_018822775.1_ASM1882277v1_genomic.fna/checkm_result
[2023-06-19 15:02:20,853] [INFO] Task succeeded: CheckM
[2023-06-19 15:02:20,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 15:02:20,885] [INFO] ===== Completeness check finished =====
[2023-06-19 15:02:20,885] [INFO] ===== Start GTDB Search =====
[2023-06-19 15:02:20,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018822775.1_ASM1882277v1_genomic.fna/markers.fasta)
[2023-06-19 15:02:20,886] [INFO] Task started: Blastn
[2023-06-19 15:02:20,886] [INFO] Running command: blastn -query GCA_018822775.1_ASM1882277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f4849b0-d2bd-4dde-b9ae-dcaadb3e0f57/dqc_reference/reference_markers_gtdb.fasta -out GCA_018822775.1_ASM1882277v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:02:21,807] [INFO] Task succeeded: Blastn
[2023-06-19 15:02:21,813] [INFO] Selected 20 target genomes.
[2023-06-19 15:02:21,813] [INFO] Target genome list was writen to GCA_018822775.1_ASM1882277v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 15:02:21,824] [INFO] Task started: fastANI
[2023-06-19 15:02:21,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ad7e7bb-2280-4931-a631-d6b53ed128d8/GCA_018822775.1_ASM1882277v1_genomic.fna.gz --refList GCA_018822775.1_ASM1882277v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018822775.1_ASM1882277v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 15:02:33,754] [INFO] Task succeeded: fastANI
[2023-06-19 15:02:33,770] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 15:02:33,771] [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_018831265.1	s__JAHJCO01 sp018831265	99.9713	1239	1260	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Fen-727;f__Anoxymicrobiaceae;g__JAHJCO01	95.0	99.97	99.97	0.99	0.98	3	conclusive
GCA_003157385.1	s__FEN-680 sp003157385	77.5649	315	1260	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Fen-727;f__Anoxymicrobiaceae;g__FEN-680	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843005.1	s__Anoxymicrobium japonicum	76.6426	77	1260	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Fen-727;f__Anoxymicrobiaceae;g__Anoxymicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014360655.1	s__JACIXC01 sp014360655	76.4416	94	1260	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Geothermincolales;f__RBG-13-55-18;g__JACIXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649525.1	s__JAENXM01 sp016649525	76.3443	122	1260	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Fen-727;f__Anoxymicrobiaceae;g__JAENXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013178005.1	s__Solincola_B sp013178005	75.8836	108	1260	d__Bacteria;p__Actinobacteriota;c__Geothermincolia;o__Geothermincolales;f__RBG-13-55-18;g__Solincola_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	75.1358	74	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200435.1	s__Sphaerisporangium krabiense	75.0713	98	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-19 15:02:33,776] [INFO] GTDB search result was written to GCA_018822775.1_ASM1882277v1_genomic.fna/result_gtdb.tsv
[2023-06-19 15:02:33,777] [INFO] ===== GTDB Search completed =====
[2023-06-19 15:02:33,781] [INFO] DFAST_QC result json was written to GCA_018822775.1_ASM1882277v1_genomic.fna/dqc_result.json
[2023-06-19 15:02:33,782] [INFO] DFAST_QC completed!
[2023-06-19 15:02:33,782] [INFO] Total running time: 0h1m13s