[2023-06-17 11:26:56,014] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:26:56,019] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:26:56,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg4779b7d9-da6d-4ce0-9ff4-704c857fb314/dqc_reference
[2023-06-17 11:26:57,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:26:57,399] [INFO] Task started: Prodigal
[2023-06-17 11:26:57,400] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d9c8c6a-a1a4-4f90-a5da-22a1288444b5/GCA_028287385.1_ASM2828738v1_genomic.fna.gz | prodigal -d GCA_028287385.1_ASM2828738v1_genomic.fna/cds.fna -a GCA_028287385.1_ASM2828738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:27:03,065] [INFO] Task succeeded: Prodigal
[2023-06-17 11:27:03,065] [INFO] Task started: HMMsearch
[2023-06-17 11:27:03,065] [INFO] Running command: hmmsearch --tblout GCA_028287385.1_ASM2828738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4779b7d9-da6d-4ce0-9ff4-704c857fb314/dqc_reference/reference_markers.hmm GCA_028287385.1_ASM2828738v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:27:03,277] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:27:03,278] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4d9c8c6a-a1a4-4f90-a5da-22a1288444b5/GCA_028287385.1_ASM2828738v1_genomic.fna.gz]
[2023-06-17 11:27:03,310] [INFO] Query marker FASTA was written to GCA_028287385.1_ASM2828738v1_genomic.fna/markers.fasta
[2023-06-17 11:27:03,310] [INFO] Task started: Blastn
[2023-06-17 11:27:03,311] [INFO] Running command: blastn -query GCA_028287385.1_ASM2828738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4779b7d9-da6d-4ce0-9ff4-704c857fb314/dqc_reference/reference_markers.fasta -out GCA_028287385.1_ASM2828738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:03,839] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:03,844] [INFO] Selected 10 target genomes.
[2023-06-17 11:27:03,845] [INFO] Target genome list was writen to GCA_028287385.1_ASM2828738v1_genomic.fna/target_genomes.txt
[2023-06-17 11:27:03,849] [INFO] Task started: fastANI
[2023-06-17 11:27:03,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d9c8c6a-a1a4-4f90-a5da-22a1288444b5/GCA_028287385.1_ASM2828738v1_genomic.fna.gz --refList GCA_028287385.1_ASM2828738v1_genomic.fna/target_genomes.txt --output GCA_028287385.1_ASM2828738v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:27:11,660] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:11,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4779b7d9-da6d-4ce0-9ff4-704c857fb314/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:27:11,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4779b7d9-da6d-4ce0-9ff4-704c857fb314/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:27:11,666] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:27:11,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:27:11,666] [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
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	74.6993	60	527	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	74.6267	69	527	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	74.5662	59	527	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:27:11,669] [INFO] DFAST Taxonomy check result was written to GCA_028287385.1_ASM2828738v1_genomic.fna/tc_result.tsv
[2023-06-17 11:27:11,669] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:27:11,669] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:27:11,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4779b7d9-da6d-4ce0-9ff4-704c857fb314/dqc_reference/checkm_data
[2023-06-17 11:27:11,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:27:11,702] [INFO] Task started: CheckM
[2023-06-17 11:27:11,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028287385.1_ASM2828738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028287385.1_ASM2828738v1_genomic.fna/checkm_input GCA_028287385.1_ASM2828738v1_genomic.fna/checkm_result
[2023-06-17 11:27:33,786] [INFO] Task succeeded: CheckM
[2023-06-17 11:27:33,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:27:33,809] [INFO] ===== Completeness check finished =====
[2023-06-17 11:27:33,809] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:27:33,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028287385.1_ASM2828738v1_genomic.fna/markers.fasta)
[2023-06-17 11:27:33,810] [INFO] Task started: Blastn
[2023-06-17 11:27:33,810] [INFO] Running command: blastn -query GCA_028287385.1_ASM2828738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4779b7d9-da6d-4ce0-9ff4-704c857fb314/dqc_reference/reference_markers_gtdb.fasta -out GCA_028287385.1_ASM2828738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:34,368] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:34,373] [INFO] Selected 10 target genomes.
[2023-06-17 11:27:34,373] [INFO] Target genome list was writen to GCA_028287385.1_ASM2828738v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:27:34,382] [INFO] Task started: fastANI
[2023-06-17 11:27:34,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d9c8c6a-a1a4-4f90-a5da-22a1288444b5/GCA_028287385.1_ASM2828738v1_genomic.fna.gz --refList GCA_028287385.1_ASM2828738v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028287385.1_ASM2828738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:27:40,801] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:40,813] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 11:27:40,813] [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_013361335.1	s__AG11 sp013361335	79.5525	252	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	99.60	99.48	0.90	0.83	7	-
GCA_003223455.1	s__AG11 sp003223455	78.2017	227	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002215645.1	s__AG11 sp002215645	77.3391	149	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378185.1	s__AG11 sp014378185	77.3078	122	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361935.1	s__JABFXC01 sp013361935	76.7989	140	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	99.88	99.88	0.94	0.92	3	-
GCA_013361745.1	s__JABFXC01 sp013361745	76.7965	96	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016194585.1	s__Fen-1231 sp016194585	76.5862	100	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	99.33	99.33	0.81	0.81	2	-
GCA_013820975.1	s__JACDHQ01 sp013820975	76.5848	64	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACDHQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825965.1	s__PNKF01 sp902825965	76.1403	79	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697785.1	s__FEN-1250 sp013697785	75.9205	65	527	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__FEN-1250	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:27:40,815] [INFO] GTDB search result was written to GCA_028287385.1_ASM2828738v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:27:40,816] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:27:40,819] [INFO] DFAST_QC result json was written to GCA_028287385.1_ASM2828738v1_genomic.fna/dqc_result.json
[2023-06-17 11:27:40,820] [INFO] DFAST_QC completed!
[2023-06-17 11:27:40,820] [INFO] Total running time: 0h0m45s