[2024-01-25 20:11:20,432] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:20,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:20,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg0775620b-a197-4542-b25b-9af245dd4f0d/dqc_reference
[2024-01-25 20:11:21,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:21,542] [INFO] Task started: Prodigal
[2024-01-25 20:11:21,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b7e48fa-697a-4cdc-b0dc-9e71e54e8828/GCF_024648865.1_ASM2464886v1_genomic.fna.gz | prodigal -d GCF_024648865.1_ASM2464886v1_genomic.fna/cds.fna -a GCF_024648865.1_ASM2464886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:11:36,706] [INFO] Task succeeded: Prodigal
[2024-01-25 20:11:36,706] [INFO] Task started: HMMsearch
[2024-01-25 20:11:36,706] [INFO] Running command: hmmsearch --tblout GCF_024648865.1_ASM2464886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0775620b-a197-4542-b25b-9af245dd4f0d/dqc_reference/reference_markers.hmm GCF_024648865.1_ASM2464886v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:11:36,991] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:11:36,992] [INFO] Found 6/6 markers.
[2024-01-25 20:11:37,036] [INFO] Query marker FASTA was written to GCF_024648865.1_ASM2464886v1_genomic.fna/markers.fasta
[2024-01-25 20:11:37,036] [INFO] Task started: Blastn
[2024-01-25 20:11:37,037] [INFO] Running command: blastn -query GCF_024648865.1_ASM2464886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0775620b-a197-4542-b25b-9af245dd4f0d/dqc_reference/reference_markers.fasta -out GCF_024648865.1_ASM2464886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:11:38,303] [INFO] Task succeeded: Blastn
[2024-01-25 20:11:38,307] [INFO] Selected 12 target genomes.
[2024-01-25 20:11:38,308] [INFO] Target genome list was writen to GCF_024648865.1_ASM2464886v1_genomic.fna/target_genomes.txt
[2024-01-25 20:11:38,381] [INFO] Task started: fastANI
[2024-01-25 20:11:38,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b7e48fa-697a-4cdc-b0dc-9e71e54e8828/GCF_024648865.1_ASM2464886v1_genomic.fna.gz --refList GCF_024648865.1_ASM2464886v1_genomic.fna/target_genomes.txt --output GCF_024648865.1_ASM2464886v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:11:54,120] [INFO] Task succeeded: fastANI
[2024-01-25 20:11:54,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0775620b-a197-4542-b25b-9af245dd4f0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:11:54,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0775620b-a197-4542-b25b-9af245dd4f0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:11:54,129] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:11:54,129] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:11:54,129] [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
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	88.7478	1450	1876	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	88.63	1429	1876	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	83.9189	1289	1876	95	below_threshold
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	83.911	1266	1876	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	80.324	952	1876	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	80.2716	963	1876	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.2369	949	1876	95	below_threshold
Saccharomonospora piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	79.3508	699	1876	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.341	843	1876	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	79.3301	767	1876	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.6056	849	1876	95	below_threshold
Amycolatopsis pittospori	strain=PIP199	GCA_013870525.1	2749434	2749434	type	True	78.5318	714	1876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:11:54,130] [INFO] DFAST Taxonomy check result was written to GCF_024648865.1_ASM2464886v1_genomic.fna/tc_result.tsv
[2024-01-25 20:11:54,131] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:11:54,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:11:54,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0775620b-a197-4542-b25b-9af245dd4f0d/dqc_reference/checkm_data
[2024-01-25 20:11:54,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:11:54,183] [INFO] Task started: CheckM
[2024-01-25 20:11:54,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024648865.1_ASM2464886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024648865.1_ASM2464886v1_genomic.fna/checkm_input GCF_024648865.1_ASM2464886v1_genomic.fna/checkm_result
[2024-01-25 20:12:55,973] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:55,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:55,995] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:55,995] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:55,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024648865.1_ASM2464886v1_genomic.fna/markers.fasta)
[2024-01-25 20:12:55,996] [INFO] Task started: Blastn
[2024-01-25 20:12:55,996] [INFO] Running command: blastn -query GCF_024648865.1_ASM2464886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0775620b-a197-4542-b25b-9af245dd4f0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024648865.1_ASM2464886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:57,946] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:57,949] [INFO] Selected 11 target genomes.
[2024-01-25 20:12:57,949] [INFO] Target genome list was writen to GCF_024648865.1_ASM2464886v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:57,960] [INFO] Task started: fastANI
[2024-01-25 20:12:57,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b7e48fa-697a-4cdc-b0dc-9e71e54e8828/GCF_024648865.1_ASM2464886v1_genomic.fna.gz --refList GCF_024648865.1_ASM2464886v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024648865.1_ASM2464886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:12,985] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:12,993] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:12,993] [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_014195435.1	s__Saccharomonospora sediminis	99.3564	1718	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014191605.1	s__Saccharomonospora isguenensis	88.7478	1450	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719975.1	s__Saccharomonospora rugosa	83.8994	1267	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	-
GCF_001942305.1	s__Saccharomonospora sp001942305	83.5593	1132	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.3372	1033	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	80.2717	963	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016595675.1	s__Saccharomonospora sp016595675	80.2325	949	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	80.2006	1023	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_005862235.1	s__Saccharomonospora piscinae	79.3784	695	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	98.79	98.27	0.95	0.94	3	-
GCF_011758765.1	s__Amycolatopsis viridis	79.3178	769	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_013870525.1	s__Amycolatopsis pittospori	78.527	715	1876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:12,994] [INFO] GTDB search result was written to GCF_024648865.1_ASM2464886v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:12,995] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:12,998] [INFO] DFAST_QC result json was written to GCF_024648865.1_ASM2464886v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:12,998] [INFO] DFAST_QC completed!
[2024-01-25 20:13:12,998] [INFO] Total running time: 0h1m53s