[2024-01-24 13:48:59,801] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg42fdd339-9930-4c83-96b5-3d8715a5d224/dqc_reference
[2024-01-24 13:49:01,091] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,092] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,092] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4062618-b718-49f6-9da7-877e98164031/GCF_031455225.1_ASM3145522v1_genomic.fna.gz | prodigal -d GCF_031455225.1_ASM3145522v1_genomic.fna/cds.fna -a GCF_031455225.1_ASM3145522v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:32,719] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:32,719] [INFO] Task started: HMMsearch
[2024-01-24 13:49:32,720] [INFO] Running command: hmmsearch --tblout GCF_031455225.1_ASM3145522v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42fdd339-9930-4c83-96b5-3d8715a5d224/dqc_reference/reference_markers.hmm GCF_031455225.1_ASM3145522v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:33,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:33,117] [INFO] Found 6/6 markers.
[2024-01-24 13:49:33,183] [INFO] Query marker FASTA was written to GCF_031455225.1_ASM3145522v1_genomic.fna/markers.fasta
[2024-01-24 13:49:33,184] [INFO] Task started: Blastn
[2024-01-24 13:49:33,184] [INFO] Running command: blastn -query GCF_031455225.1_ASM3145522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42fdd339-9930-4c83-96b5-3d8715a5d224/dqc_reference/reference_markers.fasta -out GCF_031455225.1_ASM3145522v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:34,695] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:34,698] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:34,699] [INFO] Target genome list was writen to GCF_031455225.1_ASM3145522v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:34,705] [INFO] Task started: fastANI
[2024-01-24 13:49:34,706] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4062618-b718-49f6-9da7-877e98164031/GCF_031455225.1_ASM3145522v1_genomic.fna.gz --refList GCF_031455225.1_ASM3145522v1_genomic.fna/target_genomes.txt --output GCF_031455225.1_ASM3145522v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:12,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:12,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42fdd339-9930-4c83-96b5-3d8715a5d224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:12,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42fdd339-9930-4c83-96b5-3d8715a5d224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:12,659] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:12,659] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:12,659] [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
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	85.8101	1956	2791	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	85.7099	1846	2791	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	85.6993	2006	2791	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	85.6924	1967	2791	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	85.5845	1910	2791	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	85.2565	1845	2791	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	84.8609	1801	2791	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	83.7137	1578	2791	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	83.5524	1575	2791	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	82.9722	1501	2791	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.5815	1304	2791	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	80.097	1331	2791	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	79.1391	1164	2791	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.1924	1217	2791	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.0944	939	2791	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:12,661] [INFO] DFAST Taxonomy check result was written to GCF_031455225.1_ASM3145522v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:12,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:12,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:12,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42fdd339-9930-4c83-96b5-3d8715a5d224/dqc_reference/checkm_data
[2024-01-24 13:50:12,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:12,744] [INFO] Task started: CheckM
[2024-01-24 13:50:12,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031455225.1_ASM3145522v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031455225.1_ASM3145522v1_genomic.fna/checkm_input GCF_031455225.1_ASM3145522v1_genomic.fna/checkm_result
[2024-01-24 13:53:28,909] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:28,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:28,945] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:28,945] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:28,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031455225.1_ASM3145522v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:28,946] [INFO] Task started: Blastn
[2024-01-24 13:53:28,946] [INFO] Running command: blastn -query GCF_031455225.1_ASM3145522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42fdd339-9930-4c83-96b5-3d8715a5d224/dqc_reference/reference_markers_gtdb.fasta -out GCF_031455225.1_ASM3145522v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:31,262] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:31,265] [INFO] Selected 11 target genomes.
[2024-01-24 13:53:31,265] [INFO] Target genome list was writen to GCF_031455225.1_ASM3145522v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:31,276] [INFO] Task started: fastANI
[2024-01-24 13:53:31,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4062618-b718-49f6-9da7-877e98164031/GCF_031455225.1_ASM3145522v1_genomic.fna.gz --refList GCF_031455225.1_ASM3145522v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031455225.1_ASM3145522v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:54:01,193] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:01,211] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:54:01,211] [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_003752005.1	s__Actinosynnema texasense	85.8087	1958	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_009498035.1	s__Actinosynnema syringae	85.7204	2000	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003014735.1	s__Actinosynnema carneum	85.6541	1855	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_006716745.1	s__Actinosynnema saharense	85.5835	1912	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	85.423	1944	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	85.2735	1844	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984175.1	s__Actinosynnema sp001984175	85.1164	1790	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716595.1	s__Actinosynnema sp000716595	85.0991	1799	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205015.1	s__Actinosynnema ecbatanense	84.8353	1807	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	83.5485	1574	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	79.1408	1164	2791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:54:01,213] [INFO] GTDB search result was written to GCF_031455225.1_ASM3145522v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:54:01,213] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:54:01,217] [INFO] DFAST_QC result json was written to GCF_031455225.1_ASM3145522v1_genomic.fna/dqc_result.json
[2024-01-24 13:54:01,217] [INFO] DFAST_QC completed!
[2024-01-24 13:54:01,217] [INFO] Total running time: 0h5m1s