[2024-01-24 11:05:27,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg9671fd7f-73e9-4805-a69c-93981a736ac6/dqc_reference
[2024-01-24 11:05:29,498] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,500] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,500] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf680371-595c-44f4-8b15-d9fe1d0ac5f0/GCF_016862595.1_ASM1686259v1_genomic.fna.gz | prodigal -d GCF_016862595.1_ASM1686259v1_genomic.fna/cds.fna -a GCF_016862595.1_ASM1686259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:57,754] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:57,754] [INFO] Task started: HMMsearch
[2024-01-24 11:05:57,754] [INFO] Running command: hmmsearch --tblout GCF_016862595.1_ASM1686259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9671fd7f-73e9-4805-a69c-93981a736ac6/dqc_reference/reference_markers.hmm GCF_016862595.1_ASM1686259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:58,231] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:58,233] [INFO] Found 6/6 markers.
[2024-01-24 11:05:58,304] [INFO] Query marker FASTA was written to GCF_016862595.1_ASM1686259v1_genomic.fna/markers.fasta
[2024-01-24 11:05:58,304] [INFO] Task started: Blastn
[2024-01-24 11:05:58,304] [INFO] Running command: blastn -query GCF_016862595.1_ASM1686259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9671fd7f-73e9-4805-a69c-93981a736ac6/dqc_reference/reference_markers.fasta -out GCF_016862595.1_ASM1686259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:59,668] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:59,671] [INFO] Selected 7 target genomes.
[2024-01-24 11:05:59,671] [INFO] Target genome list was writen to GCF_016862595.1_ASM1686259v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:59,673] [INFO] Task started: fastANI
[2024-01-24 11:05:59,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf680371-595c-44f4-8b15-d9fe1d0ac5f0/GCF_016862595.1_ASM1686259v1_genomic.fna.gz --refList GCF_016862595.1_ASM1686259v1_genomic.fna/target_genomes.txt --output GCF_016862595.1_ASM1686259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:20,137] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:20,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9671fd7f-73e9-4805-a69c-93981a736ac6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:20,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9671fd7f-73e9-4805-a69c-93981a736ac6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:20,150] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:20,150] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:06:20,150] [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
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	99.9965	2983	3003	95	inconclusive
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	96.0261	2523	3003	95	inconclusive
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	94.411	2394	3003	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	92.1421	2282	3003	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	91.3828	2200	3003	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	90.6223	2045	3003	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	90.5459	2044	3003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:20,152] [INFO] DFAST Taxonomy check result was written to GCF_016862595.1_ASM1686259v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:20,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:20,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:20,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9671fd7f-73e9-4805-a69c-93981a736ac6/dqc_reference/checkm_data
[2024-01-24 11:06:20,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:20,239] [INFO] Task started: CheckM
[2024-01-24 11:06:20,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862595.1_ASM1686259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862595.1_ASM1686259v1_genomic.fna/checkm_input GCF_016862595.1_ASM1686259v1_genomic.fna/checkm_result
[2024-01-24 11:07:48,834] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:48,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:48,868] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:48,868] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:48,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862595.1_ASM1686259v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:48,869] [INFO] Task started: Blastn
[2024-01-24 11:07:48,869] [INFO] Running command: blastn -query GCF_016862595.1_ASM1686259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9671fd7f-73e9-4805-a69c-93981a736ac6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862595.1_ASM1686259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:50,949] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:50,953] [INFO] Selected 7 target genomes.
[2024-01-24 11:07:50,953] [INFO] Target genome list was writen to GCF_016862595.1_ASM1686259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:50,956] [INFO] Task started: fastANI
[2024-01-24 11:07:50,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf680371-595c-44f4-8b15-d9fe1d0ac5f0/GCF_016862595.1_ASM1686259v1_genomic.fna.gz --refList GCF_016862595.1_ASM1686259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862595.1_ASM1686259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:10,000] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:10,010] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:10,010] [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_003610235.1	s__Catellatospora citrea	96.0641	2500	3003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	conclusive
GCF_009720365.1	s__Catellatospora paridis	94.4444	2390	3003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007483665.1	s__Catellatospora sichuanensis	92.133	2283	3003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720385.1	s__Catellatospora vulcania	91.376	2201	3003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862635.1	s__Catellatospora coxensis	91.0583	2210	3003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011297335.1	s__Catellatospora methionotrophica	90.5585	2042	3003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862575.1	s__Catellatospora bangladeshensis	86.7046	1962	3003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:10,012] [INFO] GTDB search result was written to GCF_016862595.1_ASM1686259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:10,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:10,015] [INFO] DFAST_QC result json was written to GCF_016862595.1_ASM1686259v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:10,015] [INFO] DFAST_QC completed!
[2024-01-24 11:08:10,015] [INFO] Total running time: 0h2m42s