[2024-01-24 11:13:49,476] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,478] [INFO] DQC Reference Directory: /var/lib/cwl/stgd41c271e-6640-44b2-85c7-d7c72b37cf16/dqc_reference
[2024-01-24 11:13:50,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,675] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg177ab76c-5b8f-4df1-93ad-ea611d5fe9a4/GCF_016863375.1_ASM1686337v1_genomic.fna.gz | prodigal -d GCF_016863375.1_ASM1686337v1_genomic.fna/cds.fna -a GCF_016863375.1_ASM1686337v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:14:16,210] [INFO] Task succeeded: Prodigal
[2024-01-24 11:14:16,210] [INFO] Task started: HMMsearch
[2024-01-24 11:14:16,210] [INFO] Running command: hmmsearch --tblout GCF_016863375.1_ASM1686337v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd41c271e-6640-44b2-85c7-d7c72b37cf16/dqc_reference/reference_markers.hmm GCF_016863375.1_ASM1686337v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:14:16,596] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:14:16,598] [INFO] Found 6/6 markers.
[2024-01-24 11:14:16,665] [INFO] Query marker FASTA was written to GCF_016863375.1_ASM1686337v1_genomic.fna/markers.fasta
[2024-01-24 11:14:16,665] [INFO] Task started: Blastn
[2024-01-24 11:14:16,665] [INFO] Running command: blastn -query GCF_016863375.1_ASM1686337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd41c271e-6640-44b2-85c7-d7c72b37cf16/dqc_reference/reference_markers.fasta -out GCF_016863375.1_ASM1686337v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:18,000] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:18,006] [INFO] Selected 16 target genomes.
[2024-01-24 11:14:18,006] [INFO] Target genome list was writen to GCF_016863375.1_ASM1686337v1_genomic.fna/target_genomes.txt
[2024-01-24 11:14:18,011] [INFO] Task started: fastANI
[2024-01-24 11:14:18,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg177ab76c-5b8f-4df1-93ad-ea611d5fe9a4/GCF_016863375.1_ASM1686337v1_genomic.fna.gz --refList GCF_016863375.1_ASM1686337v1_genomic.fna/target_genomes.txt --output GCF_016863375.1_ASM1686337v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:48,988] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:48,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd41c271e-6640-44b2-85c7-d7c72b37cf16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:48,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd41c271e-6640-44b2-85c7-d7c72b37cf16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:49,003] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:14:49,003] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:49,003] [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
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	99.9834	2794	2819	95	conclusive
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	83.1711	1653	2819	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	83.0265	1627	2819	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	82.8445	1503	2819	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	82.83	1510	2819	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	82.8163	1504	2819	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	82.8024	1497	2819	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	82.523	1553	2819	95	below_threshold
Sphaerisporangium rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	82.1713	1422	2819	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	80.1973	1204	2819	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	80.167	1286	2819	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	80.1377	1284	2819	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.8543	1335	2819	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.852	848	2819	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	79.6649	1183	2819	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.1058	1248	2819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:49,004] [INFO] DFAST Taxonomy check result was written to GCF_016863375.1_ASM1686337v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:49,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:49,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:49,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd41c271e-6640-44b2-85c7-d7c72b37cf16/dqc_reference/checkm_data
[2024-01-24 11:14:49,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:49,082] [INFO] Task started: CheckM
[2024-01-24 11:14:49,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863375.1_ASM1686337v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863375.1_ASM1686337v1_genomic.fna/checkm_input GCF_016863375.1_ASM1686337v1_genomic.fna/checkm_result
[2024-01-24 11:16:12,782] [INFO] Task succeeded: CheckM
[2024-01-24 11:16:12,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:16:12,804] [INFO] ===== Completeness check finished =====
[2024-01-24 11:16:12,805] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:16:12,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863375.1_ASM1686337v1_genomic.fna/markers.fasta)
[2024-01-24 11:16:12,805] [INFO] Task started: Blastn
[2024-01-24 11:16:12,806] [INFO] Running command: blastn -query GCF_016863375.1_ASM1686337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd41c271e-6640-44b2-85c7-d7c72b37cf16/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863375.1_ASM1686337v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:16:14,921] [INFO] Task succeeded: Blastn
[2024-01-24 11:16:14,924] [INFO] Selected 12 target genomes.
[2024-01-24 11:16:14,924] [INFO] Target genome list was writen to GCF_016863375.1_ASM1686337v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:16:14,953] [INFO] Task started: fastANI
[2024-01-24 11:16:14,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg177ab76c-5b8f-4df1-93ad-ea611d5fe9a4/GCF_016863375.1_ASM1686337v1_genomic.fna.gz --refList GCF_016863375.1_ASM1686337v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863375.1_ASM1686337v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:16:39,408] [INFO] Task succeeded: fastANI
[2024-01-24 11:16:39,425] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:16:39,425] [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_014646695.1	s__Sphaerisporangium melleum	99.9834	2794	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_018531465.1	s__Sphaerisporangium sp018531465	83.0946	1670	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323745.1	s__Sphaerisporangium album	83.0145	1628	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200435.1	s__Sphaerisporangium krabiense	82.8434	1508	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014205275.1	s__Sphaerisporangium siamense	82.7962	1498	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863395.1	s__Sphaerisporangium rufum	82.4748	1561	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207705.1	s__Sphaerisporangium rubeum	82.1492	1426	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711645.1	s__Planomonospora sp015711645	80.2756	1172	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017896165.1	s__Microbispora sp017896165	80.1792	1210	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	80.1559	1279	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	80.1433	1261	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_014203795.1	s__Streptosporangium album	79.6414	1188	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:16:39,427] [INFO] GTDB search result was written to GCF_016863375.1_ASM1686337v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:16:39,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:16:39,433] [INFO] DFAST_QC result json was written to GCF_016863375.1_ASM1686337v1_genomic.fna/dqc_result.json
[2024-01-24 11:16:39,433] [INFO] DFAST_QC completed!
[2024-01-24 11:16:39,433] [INFO] Total running time: 0h2m50s