[2023-06-28 06:48:26,700] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:48:26,703] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:48:26,703] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf1c2712-7397-4172-aba9-43593e156904/dqc_reference
[2023-06-28 06:48:28,005] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:48:28,006] [INFO] Task started: Prodigal
[2023-06-28 06:48:28,006] [INFO] Running command: gunzip -c /var/lib/cwl/stg641eaa9e-15a6-4403-ae56-a61efb1040e3/GCA_019689655.1_ASM1968965v1_genomic.fna.gz | prodigal -d GCA_019689655.1_ASM1968965v1_genomic.fna/cds.fna -a GCA_019689655.1_ASM1968965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:48:42,856] [INFO] Task succeeded: Prodigal
[2023-06-28 06:48:42,856] [INFO] Task started: HMMsearch
[2023-06-28 06:48:42,857] [INFO] Running command: hmmsearch --tblout GCA_019689655.1_ASM1968965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf1c2712-7397-4172-aba9-43593e156904/dqc_reference/reference_markers.hmm GCA_019689655.1_ASM1968965v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:48:43,202] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:48:43,204] [INFO] Found 6/6 markers.
[2023-06-28 06:48:43,256] [INFO] Query marker FASTA was written to GCA_019689655.1_ASM1968965v1_genomic.fna/markers.fasta
[2023-06-28 06:48:43,257] [INFO] Task started: Blastn
[2023-06-28 06:48:43,257] [INFO] Running command: blastn -query GCA_019689655.1_ASM1968965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf1c2712-7397-4172-aba9-43593e156904/dqc_reference/reference_markers.fasta -out GCA_019689655.1_ASM1968965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:48:44,585] [INFO] Task succeeded: Blastn
[2023-06-28 06:48:44,594] [INFO] Selected 15 target genomes.
[2023-06-28 06:48:44,595] [INFO] Target genome list was writen to GCA_019689655.1_ASM1968965v1_genomic.fna/target_genomes.txt
[2023-06-28 06:48:44,598] [INFO] Task started: fastANI
[2023-06-28 06:48:44,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg641eaa9e-15a6-4403-ae56-a61efb1040e3/GCA_019689655.1_ASM1968965v1_genomic.fna.gz --refList GCA_019689655.1_ASM1968965v1_genomic.fna/target_genomes.txt --output GCA_019689655.1_ASM1968965v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:49:11,445] [INFO] Task succeeded: fastANI
[2023-06-28 06:49:11,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf1c2712-7397-4172-aba9-43593e156904/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:49:11,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf1c2712-7397-4172-aba9-43593e156904/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:49:11,461] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:49:11,462] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:49:11,462] [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
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	91.2593	1359	1719	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	91.2136	1358	1719	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	90.6362	1371	1719	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	90.6324	1387	1719	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	90.5964	1375	1719	95	below_threshold
Microbispora rosea	strain=ATCC 12950	GCA_900156315.1	58117	58117	type	True	90.0889	1353	1719	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	90.0871	1380	1719	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	90.0798	1354	1719	95	below_threshold
Microbispora bryophytorum	strain=NEAU-TX2-2	GCA_014712735.1	1460882	1460882	type	True	89.9972	1323	1719	95	below_threshold
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	89.9696	1328	1719	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	83.1028	1044	1719	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.5275	906	1719	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.1949	948	1719	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.9608	654	1719	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.4498	919	1719	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:49:11,464] [INFO] DFAST Taxonomy check result was written to GCA_019689655.1_ASM1968965v1_genomic.fna/tc_result.tsv
[2023-06-28 06:49:11,465] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:49:11,465] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:49:11,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf1c2712-7397-4172-aba9-43593e156904/dqc_reference/checkm_data
[2023-06-28 06:49:11,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:49:11,529] [INFO] Task started: CheckM
[2023-06-28 06:49:11,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019689655.1_ASM1968965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019689655.1_ASM1968965v1_genomic.fna/checkm_input GCA_019689655.1_ASM1968965v1_genomic.fna/checkm_result
[2023-06-28 06:49:57,991] [INFO] Task succeeded: CheckM
[2023-06-28 06:49:57,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:49:58,017] [INFO] ===== Completeness check finished =====
[2023-06-28 06:49:58,017] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:49:58,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019689655.1_ASM1968965v1_genomic.fna/markers.fasta)
[2023-06-28 06:49:58,018] [INFO] Task started: Blastn
[2023-06-28 06:49:58,018] [INFO] Running command: blastn -query GCA_019689655.1_ASM1968965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf1c2712-7397-4172-aba9-43593e156904/dqc_reference/reference_markers_gtdb.fasta -out GCA_019689655.1_ASM1968965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:50:00,021] [INFO] Task succeeded: Blastn
[2023-06-28 06:50:00,026] [INFO] Selected 8 target genomes.
[2023-06-28 06:50:00,026] [INFO] Target genome list was writen to GCA_019689655.1_ASM1968965v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:50:00,030] [INFO] Task started: fastANI
[2023-06-28 06:50:00,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg641eaa9e-15a6-4403-ae56-a61efb1040e3/GCA_019689655.1_ASM1968965v1_genomic.fna.gz --refList GCA_019689655.1_ASM1968965v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019689655.1_ASM1968965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:50:14,400] [INFO] Task succeeded: fastANI
[2023-06-28 06:50:14,414] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 06:50:14,414] [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_014647835.1	s__Microbispora aerata	91.2484	1360	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863095.1	s__Microbispora siamensis	90.6507	1371	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_006334915.2	s__Microbispora catharanthi	90.6284	1386	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_900156315.1	s__Microbispora rosea	90.1082	1351	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
GCF_006874475.1	s__Microbispora hainanensis	90.1048	1379	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_014161445.1	s__Microbispora sp014161445	90.045	1349	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_006874465.1	s__Microbispora bryophytorum	89.9563	1329	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCA_003260025.2	s__Microbispora triticiradicis	87.0454	1165	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
--------------------------------------------------------------------------------
[2023-06-28 06:50:14,416] [INFO] GTDB search result was written to GCA_019689655.1_ASM1968965v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:50:14,417] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:50:14,420] [INFO] DFAST_QC result json was written to GCA_019689655.1_ASM1968965v1_genomic.fna/dqc_result.json
[2023-06-28 06:50:14,420] [INFO] DFAST_QC completed!
[2023-06-28 06:50:14,420] [INFO] Total running time: 0h1m48s