[2024-01-25 19:48:50,994] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:50,995] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:50,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg50c17e29-1103-4d33-b871-625442c4709c/dqc_reference
[2024-01-25 19:48:52,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:52,114] [INFO] Task started: Prodigal
[2024-01-25 19:48:52,114] [INFO] Running command: gunzip -c /var/lib/cwl/stg40ccd1db-cf9e-4568-9a04-7e44cf395855/GCF_904424705.1_Genoma_EAR8_genomic.fna.gz | prodigal -d GCF_904424705.1_Genoma_EAR8_genomic.fna/cds.fna -a GCF_904424705.1_Genoma_EAR8_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:01,969] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:01,969] [INFO] Task started: HMMsearch
[2024-01-25 19:49:01,969] [INFO] Running command: hmmsearch --tblout GCF_904424705.1_Genoma_EAR8_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50c17e29-1103-4d33-b871-625442c4709c/dqc_reference/reference_markers.hmm GCF_904424705.1_Genoma_EAR8_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:02,243] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:02,244] [INFO] Found 6/6 markers.
[2024-01-25 19:49:02,281] [INFO] Query marker FASTA was written to GCF_904424705.1_Genoma_EAR8_genomic.fna/markers.fasta
[2024-01-25 19:49:02,282] [INFO] Task started: Blastn
[2024-01-25 19:49:02,282] [INFO] Running command: blastn -query GCF_904424705.1_Genoma_EAR8_genomic.fna/markers.fasta -db /var/lib/cwl/stg50c17e29-1103-4d33-b871-625442c4709c/dqc_reference/reference_markers.fasta -out GCF_904424705.1_Genoma_EAR8_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:02,828] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:02,836] [INFO] Selected 12 target genomes.
[2024-01-25 19:49:02,836] [INFO] Target genome list was writen to GCF_904424705.1_Genoma_EAR8_genomic.fna/target_genomes.txt
[2024-01-25 19:49:02,846] [INFO] Task started: fastANI
[2024-01-25 19:49:02,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg40ccd1db-cf9e-4568-9a04-7e44cf395855/GCF_904424705.1_Genoma_EAR8_genomic.fna.gz --refList GCF_904424705.1_Genoma_EAR8_genomic.fna/target_genomes.txt --output GCF_904424705.1_Genoma_EAR8_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:11,977] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:11,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50c17e29-1103-4d33-b871-625442c4709c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:11,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50c17e29-1103-4d33-b871-625442c4709c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:11,983] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:49:11,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:11,983] [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
Rossellomorea arthrocnemi	strain=EAR8	GCA_904424705.1	2769542	2769542	type	True	100.0	1554	1559	95	conclusive
Rossellomorea vietnamensis	strain=NBRC 101237	GCA_001591825.1	218284	218284	suspected-type	True	84.8876	1061	1559	95	below_threshold
Rossellomorea aquimaris	strain=TF12	GCA_001648555.1	189382	189382	suspected-type	True	79.9712	519	1559	95	below_threshold
Bacillus enclensis	strain=SGD-1123	GCA_900094975.1	1402860	1402860	type	True	79.1482	468	1559	95	below_threshold
Bacillus enclensis	strain=SGD-1123	GCA_001456935.1	1402860	1402860	type	True	79.1358	469	1559	95	below_threshold
Rossellomorea marisflavi	strain=JCM 11544	GCA_001274775.1	189381	189381	suspected-type	True	78.3953	287	1559	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.2571	78	1559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:11,985] [INFO] DFAST Taxonomy check result was written to GCF_904424705.1_Genoma_EAR8_genomic.fna/tc_result.tsv
[2024-01-25 19:49:11,985] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:11,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:11,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50c17e29-1103-4d33-b871-625442c4709c/dqc_reference/checkm_data
[2024-01-25 19:49:11,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:12,032] [INFO] Task started: CheckM
[2024-01-25 19:49:12,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_904424705.1_Genoma_EAR8_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_904424705.1_Genoma_EAR8_genomic.fna/checkm_input GCF_904424705.1_Genoma_EAR8_genomic.fna/checkm_result
[2024-01-25 19:49:45,441] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:45,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:45,458] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:45,458] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:45,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_904424705.1_Genoma_EAR8_genomic.fna/markers.fasta)
[2024-01-25 19:49:45,458] [INFO] Task started: Blastn
[2024-01-25 19:49:45,458] [INFO] Running command: blastn -query GCF_904424705.1_Genoma_EAR8_genomic.fna/markers.fasta -db /var/lib/cwl/stg50c17e29-1103-4d33-b871-625442c4709c/dqc_reference/reference_markers_gtdb.fasta -out GCF_904424705.1_Genoma_EAR8_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:46,224] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:46,227] [INFO] Selected 9 target genomes.
[2024-01-25 19:49:46,227] [INFO] Target genome list was writen to GCF_904424705.1_Genoma_EAR8_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:46,230] [INFO] Task started: fastANI
[2024-01-25 19:49:46,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg40ccd1db-cf9e-4568-9a04-7e44cf395855/GCF_904424705.1_Genoma_EAR8_genomic.fna.gz --refList GCF_904424705.1_Genoma_EAR8_genomic.fna/target_genomes_gtdb.txt --output GCF_904424705.1_Genoma_EAR8_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:56,289] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:56,295] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:56,295] [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_904424705.1	s__Rossellomorea sp904424705	100.0	1554	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002563655.1	s__Rossellomorea sp002563655	85.4618	1133	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305855.1	s__Rossellomorea vietnamensis_A	85.4217	1089	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002561455.1	s__Rossellomorea sp002561455	85.3589	1038	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591825.1	s__Rossellomorea vietnamensis	84.865	1063	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	97.54	97.34	0.88	0.87	6	-
GCF_017303375.1	s__Rossellomorea sp017303375	84.159	1015	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180865.1	s__Rossellomorea aquimaris_D	83.4773	1020	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	97.97	97.96	0.89	0.89	3	-
GCF_003315075.1	s__Rossellomorea aquimaris_C	83.2662	932	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935355.1	s__Rossellomorea aquimaris_B	82.9617	925	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:56,297] [INFO] GTDB search result was written to GCF_904424705.1_Genoma_EAR8_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:56,297] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:56,299] [INFO] DFAST_QC result json was written to GCF_904424705.1_Genoma_EAR8_genomic.fna/dqc_result.json
[2024-01-25 19:49:56,300] [INFO] DFAST_QC completed!
[2024-01-25 19:49:56,300] [INFO] Total running time: 0h1m5s