[2024-01-24 10:47:40,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,963] [INFO] DQC Reference Directory: /var/lib/cwl/stg34fb77b5-ba99-49da-9ac0-7faabfc6d264/dqc_reference
[2024-01-24 10:47:44,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,790] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,791] [INFO] Running command: gunzip -c /var/lib/cwl/stge15a45f9-f806-4601-bde6-6fb7e9e2111e/GCF_023276435.1_ASM2327643v1_genomic.fna.gz | prodigal -d GCF_023276435.1_ASM2327643v1_genomic.fna/cds.fna -a GCF_023276435.1_ASM2327643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:10,654] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:10,655] [INFO] Task started: HMMsearch
[2024-01-24 10:48:10,655] [INFO] Running command: hmmsearch --tblout GCF_023276435.1_ASM2327643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34fb77b5-ba99-49da-9ac0-7faabfc6d264/dqc_reference/reference_markers.hmm GCF_023276435.1_ASM2327643v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:11,060] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:11,063] [INFO] Found 6/6 markers.
[2024-01-24 10:48:11,158] [INFO] Query marker FASTA was written to GCF_023276435.1_ASM2327643v1_genomic.fna/markers.fasta
[2024-01-24 10:48:11,159] [INFO] Task started: Blastn
[2024-01-24 10:48:11,159] [INFO] Running command: blastn -query GCF_023276435.1_ASM2327643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34fb77b5-ba99-49da-9ac0-7faabfc6d264/dqc_reference/reference_markers.fasta -out GCF_023276435.1_ASM2327643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:12,542] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:12,545] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:12,546] [INFO] Target genome list was writen to GCF_023276435.1_ASM2327643v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:12,559] [INFO] Task started: fastANI
[2024-01-24 10:48:12,559] [INFO] Running command: fastANI --query /var/lib/cwl/stge15a45f9-f806-4601-bde6-6fb7e9e2111e/GCF_023276435.1_ASM2327643v1_genomic.fna.gz --refList GCF_023276435.1_ASM2327643v1_genomic.fna/target_genomes.txt --output GCF_023276435.1_ASM2327643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:46,313] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:46,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34fb77b5-ba99-49da-9ac0-7faabfc6d264/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:46,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34fb77b5-ba99-49da-9ac0-7faabfc6d264/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:46,330] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:46,331] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:46,331] [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 corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	85.045	1842	3043	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	84.8155	1730	3043	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	83.9178	1739	3043	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	83.143	1538	3043	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	83.0988	1570	3043	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	82.9787	1600	3043	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	82.9347	1583	3043	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	82.2953	1455	3043	95	below_threshold
Sphaerisporangium rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	81.8057	1386	3043	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	80.275	1276	3043	95	below_threshold
Microtetraspora fusca	strain=NBRC 13915	GCA_001570365.1	1997	1997	type	True	80.0887	1291	3043	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	79.9873	1240	3043	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	79.968	1247	3043	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	79.7856	962	3043	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.7028	918	3043	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	79.5862	1256	3043	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.4667	1368	3043	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.9045	1318	3043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:46,332] [INFO] DFAST Taxonomy check result was written to GCF_023276435.1_ASM2327643v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:46,333] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:46,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:46,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34fb77b5-ba99-49da-9ac0-7faabfc6d264/dqc_reference/checkm_data
[2024-01-24 10:48:46,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:46,417] [INFO] Task started: CheckM
[2024-01-24 10:48:46,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023276435.1_ASM2327643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023276435.1_ASM2327643v1_genomic.fna/checkm_input GCF_023276435.1_ASM2327643v1_genomic.fna/checkm_result
[2024-01-24 10:50:02,781] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:02,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.75%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:02,807] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:02,808] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:02,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023276435.1_ASM2327643v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:02,809] [INFO] Task started: Blastn
[2024-01-24 10:50:02,809] [INFO] Running command: blastn -query GCF_023276435.1_ASM2327643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34fb77b5-ba99-49da-9ac0-7faabfc6d264/dqc_reference/reference_markers_gtdb.fasta -out GCF_023276435.1_ASM2327643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:04,914] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:04,919] [INFO] Selected 12 target genomes.
[2024-01-24 10:50:04,919] [INFO] Target genome list was writen to GCF_023276435.1_ASM2327643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:04,946] [INFO] Task started: fastANI
[2024-01-24 10:50:04,946] [INFO] Running command: fastANI --query /var/lib/cwl/stge15a45f9-f806-4601-bde6-6fb7e9e2111e/GCF_023276435.1_ASM2327643v1_genomic.fna.gz --refList GCF_023276435.1_ASM2327643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023276435.1_ASM2327643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:28,758] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:28,773] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:50:28,774] [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	84.7735	1738	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_018531465.1	s__Sphaerisporangium sp018531465	84.0654	1818	3043	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	83.9323	1736	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205275.1	s__Sphaerisporangium siamense	83.1011	1569	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014200435.1	s__Sphaerisporangium krabiense	82.9618	1606	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016863395.1	s__Sphaerisporangium rufum	82.2733	1462	3043	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	81.781	1392	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	80.4068	1298	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409935.1	s__Streptosporangium sandarakinum	80.2352	1286	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_001570365.1	s__Microtetraspora fusca	80.0139	1311	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863015.1	s__Microbispora amethystogenes	79.9468	1253	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_003236395.1	s__Nonomuraea sp003236395	79.5659	1261	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:28,775] [INFO] GTDB search result was written to GCF_023276435.1_ASM2327643v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:28,776] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:28,779] [INFO] DFAST_QC result json was written to GCF_023276435.1_ASM2327643v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:28,779] [INFO] DFAST_QC completed!
[2024-01-24 10:50:28,779] [INFO] Total running time: 0h2m48s