[2024-01-25 18:06:05,487] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:05,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:05,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg8993e466-8a39-4cd9-be9f-a4cab4ac518c/dqc_reference
[2024-01-25 18:06:06,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:06,599] [INFO] Task started: Prodigal
[2024-01-25 18:06:06,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b4df7b2-d73d-40da-a012-562eda9968ee/GCF_003270085.1_ASM327008v1_genomic.fna.gz | prodigal -d GCF_003270085.1_ASM327008v1_genomic.fna/cds.fna -a GCF_003270085.1_ASM327008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:23,173] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:23,173] [INFO] Task started: HMMsearch
[2024-01-25 18:06:23,173] [INFO] Running command: hmmsearch --tblout GCF_003270085.1_ASM327008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8993e466-8a39-4cd9-be9f-a4cab4ac518c/dqc_reference/reference_markers.hmm GCF_003270085.1_ASM327008v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:23,486] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:23,487] [INFO] Found 6/6 markers.
[2024-01-25 18:06:23,539] [INFO] Query marker FASTA was written to GCF_003270085.1_ASM327008v1_genomic.fna/markers.fasta
[2024-01-25 18:06:23,539] [INFO] Task started: Blastn
[2024-01-25 18:06:23,539] [INFO] Running command: blastn -query GCF_003270085.1_ASM327008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8993e466-8a39-4cd9-be9f-a4cab4ac518c/dqc_reference/reference_markers.fasta -out GCF_003270085.1_ASM327008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:24,933] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:24,935] [INFO] Selected 26 target genomes.
[2024-01-25 18:06:24,936] [INFO] Target genome list was writen to GCF_003270085.1_ASM327008v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:24,982] [INFO] Task started: fastANI
[2024-01-25 18:06:24,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b4df7b2-d73d-40da-a012-562eda9968ee/GCF_003270085.1_ASM327008v1_genomic.fna.gz --refList GCF_003270085.1_ASM327008v1_genomic.fna/target_genomes.txt --output GCF_003270085.1_ASM327008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:11,277] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:11,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8993e466-8a39-4cd9-be9f-a4cab4ac518c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:11,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8993e466-8a39-4cd9-be9f-a4cab4ac518c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:11,294] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:11,294] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:11,294] [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
Streptomyces triticisoli	strain=NEAU-DSCPA1-4-4	GCA_003270085.1	2182797	2182797	type	True	100.0	2115	2131	95	conclusive
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	93.555	1694	2131	95	below_threshold
Streptomyces thermovulgaris	strain=NRRL B-12375	GCA_002155915.1	1934	1934	type	True	90.6306	1279	2131	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	87.8088	1506	2131	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	87.6614	1380	2131	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	87.6378	1474	2131	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	87.0781	1350	2131	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	85.8344	1289	2131	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	85.7006	1229	2131	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.4062	1421	2131	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.3849	1386	2131	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.3586	1411	2131	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	85.0435	1400	2131	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	85.0167	1385	2131	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.8883	1394	2131	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	84.8468	1378	2131	95	below_threshold
Streptomyces misionensis	strain=DSM 40306	GCA_900104815.1	67331	67331	type	True	84.7756	1355	2131	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.6828	1407	2131	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.6099	1326	2131	95	below_threshold
Streptomyces ruber	strain=JCM 3131	GCA_014648075.1	83378	83378	type	True	83.9863	1321	2131	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	83.8002	1221	2131	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	81.0617	975	2131	95	below_threshold
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	79.7489	945	2131	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.736	789	2131	95	below_threshold
Actinospica durhamensis	strain=CSCA 57	GCA_018139695.1	1508375	1508375	type	True	77.1718	578	2131	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	76.3955	338	2131	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:11,296] [INFO] DFAST Taxonomy check result was written to GCF_003270085.1_ASM327008v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:11,296] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:11,297] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:11,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8993e466-8a39-4cd9-be9f-a4cab4ac518c/dqc_reference/checkm_data
[2024-01-25 18:07:11,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:11,362] [INFO] Task started: CheckM
[2024-01-25 18:07:11,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003270085.1_ASM327008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003270085.1_ASM327008v1_genomic.fna/checkm_input GCF_003270085.1_ASM327008v1_genomic.fna/checkm_result
[2024-01-25 18:08:42,170] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:42,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:42,191] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:42,191] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:42,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003270085.1_ASM327008v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:42,192] [INFO] Task started: Blastn
[2024-01-25 18:08:42,192] [INFO] Running command: blastn -query GCF_003270085.1_ASM327008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8993e466-8a39-4cd9-be9f-a4cab4ac518c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003270085.1_ASM327008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:44,547] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:44,553] [INFO] Selected 16 target genomes.
[2024-01-25 18:08:44,553] [INFO] Target genome list was writen to GCF_003270085.1_ASM327008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:44,569] [INFO] Task started: fastANI
[2024-01-25 18:08:44,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b4df7b2-d73d-40da-a012-562eda9968ee/GCF_003270085.1_ASM327008v1_genomic.fna.gz --refList GCF_003270085.1_ASM327008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003270085.1_ASM327008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:16,401] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:16,412] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:16,412] [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_003270085.1	s__Streptomyces triticisoli	100.0	2115	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001906585.1	s__Streptomyces kebangsaanensis	93.5519	1695	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155915.1	s__Streptomyces thermovulgaris	90.6241	1279	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.61	99.61	0.95	0.95	2	-
GCF_006540305.1	s__Streptomyces sp006540305	89.1969	1589	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803075.1	s__Streptomyces sp002803075	88.9594	1542	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654675.1	s__Streptomyces spiralis	87.8302	1503	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_002154505.1	s__Streptomyces carpinensis	87.661	1381	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506575.1	s__Streptomyces mexicanus	86.9915	1426	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_013364255.1	s__Streptomyces seoulensis_A	86.9212	1454	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704515.1	s__Streptomyces viridosporus	85.8776	1409	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	-
GCF_014534645.1	s__Streptomyces sp014534645	85.4379	1416	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	84.8536	1376	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_014648075.1	s__Streptomyces ruber	83.9894	1321	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612545.1	s__Streptomyces sp016612545	83.8372	1316	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377205.1	s__Streptomyces phyllanthi	83.8011	1223	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	81.4766	1163	2131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:16,414] [INFO] GTDB search result was written to GCF_003270085.1_ASM327008v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:16,414] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:16,418] [INFO] DFAST_QC result json was written to GCF_003270085.1_ASM327008v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:16,418] [INFO] DFAST_QC completed!
[2024-01-25 18:09:16,418] [INFO] Total running time: 0h3m11s