[2024-01-24 13:27:56,561] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:56,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:56,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg691f2158-86bd-4826-b152-001fee0f04b6/dqc_reference
[2024-01-24 13:27:57,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:57,784] [INFO] Task started: Prodigal
[2024-01-24 13:27:57,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f604f2a-3093-4f89-8d0c-ef8204783da4/GCF_014650375.1_ASM1465037v1_genomic.fna.gz | prodigal -d GCF_014650375.1_ASM1465037v1_genomic.fna/cds.fna -a GCF_014650375.1_ASM1465037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:19,102] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:19,102] [INFO] Task started: HMMsearch
[2024-01-24 13:28:19,102] [INFO] Running command: hmmsearch --tblout GCF_014650375.1_ASM1465037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg691f2158-86bd-4826-b152-001fee0f04b6/dqc_reference/reference_markers.hmm GCF_014650375.1_ASM1465037v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:19,472] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:19,473] [INFO] Found 6/6 markers.
[2024-01-24 13:28:19,530] [INFO] Query marker FASTA was written to GCF_014650375.1_ASM1465037v1_genomic.fna/markers.fasta
[2024-01-24 13:28:19,531] [INFO] Task started: Blastn
[2024-01-24 13:28:19,531] [INFO] Running command: blastn -query GCF_014650375.1_ASM1465037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg691f2158-86bd-4826-b152-001fee0f04b6/dqc_reference/reference_markers.fasta -out GCF_014650375.1_ASM1465037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:20,834] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:20,836] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:20,837] [INFO] Target genome list was writen to GCF_014650375.1_ASM1465037v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:20,845] [INFO] Task started: fastANI
[2024-01-24 13:28:20,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f604f2a-3093-4f89-8d0c-ef8204783da4/GCF_014650375.1_ASM1465037v1_genomic.fna.gz --refList GCF_014650375.1_ASM1465037v1_genomic.fna/target_genomes.txt --output GCF_014650375.1_ASM1465037v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:52,014] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:52,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg691f2158-86bd-4826-b152-001fee0f04b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:52,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg691f2158-86bd-4826-b152-001fee0f04b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:52,029] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:52,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:52,029] [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 nitrosporeus	strain=JCM 4598	GCA_014650375.1	28894	28894	type	True	100.0	2576	2582	95	conclusive
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	99.996	2479	2582	95	conclusive
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	87.1861	1709	2582	95	below_threshold
Streptomyces clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	85.9999	1691	2582	95	below_threshold
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	85.9306	1703	2582	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	85.7667	1658	2582	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	84.5333	1268	2582	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	84.1882	1437	2582	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	84.1492	1494	2582	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	84.1448	1556	2582	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.1107	1406	2582	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.9367	1288	2582	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.6123	1055	2582	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	81.0437	1072	2582	95	below_threshold
Streptomyces thermoviolaceus subsp. apingens	strain=JCM 4312	GCA_014649255.1	66859	1952	type	True	81.0313	1104	2582	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	79.9326	941	2582	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	79.8283	1079	2582	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	79.5356	1050	2582	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:52,031] [INFO] DFAST Taxonomy check result was written to GCF_014650375.1_ASM1465037v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:52,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:52,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:52,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg691f2158-86bd-4826-b152-001fee0f04b6/dqc_reference/checkm_data
[2024-01-24 13:28:52,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:52,126] [INFO] Task started: CheckM
[2024-01-24 13:28:52,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650375.1_ASM1465037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650375.1_ASM1465037v1_genomic.fna/checkm_input GCF_014650375.1_ASM1465037v1_genomic.fna/checkm_result
[2024-01-24 13:30:37,717] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:37,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:37,739] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:37,739] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:37,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650375.1_ASM1465037v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:37,740] [INFO] Task started: Blastn
[2024-01-24 13:30:37,740] [INFO] Running command: blastn -query GCF_014650375.1_ASM1465037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg691f2158-86bd-4826-b152-001fee0f04b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650375.1_ASM1465037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:39,724] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:39,729] [INFO] Selected 21 target genomes.
[2024-01-24 13:30:39,729] [INFO] Target genome list was writen to GCF_014650375.1_ASM1465037v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:39,748] [INFO] Task started: fastANI
[2024-01-24 13:30:39,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f604f2a-3093-4f89-8d0c-ef8204783da4/GCF_014650375.1_ASM1465037v1_genomic.fna.gz --refList GCF_014650375.1_ASM1465037v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650375.1_ASM1465037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:16,554] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:16,575] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:16,575] [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_008704555.1	s__Streptomyces nitrosporeus	99.9867	2480	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCF_000177195.2	s__Streptomyces sp000177195	87.5581	1679	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.71	97.52	0.98	0.91	17	-
GCA_000720535.1	s__Streptomyces halstedii	87.2006	1712	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	96.54	0.92	0.83	17	-
GCF_001905505.1	s__Streptomyces sp001905505	85.9867	1735	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002711365.1	s__Streptomyces sp002711365	85.9822	1691	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	96.67	0.92	0.87	7	-
GCA_014651175.1	s__Streptomyces clavifer	85.9617	1698	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.32	0.96	0.94	5	-
GCF_001715295.1	s__Streptomyces griseus_G	85.8924	1528	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002941025.1	s__Streptomyces sp002941025	85.8352	1713	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829855.1	s__Streptomyces argenteolus	85.5744	1707	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717025.1	s__Streptomyces atroolivaceus	85.5507	1679	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007096885.1	s__Streptomyces sp007096885	84.2339	1456	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905735.1	s__Streptomyces sp001905735	84.0998	1521	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	95.22	0.92	0.85	6	-
GCF_000830005.1	s__Streptomyces vietnamensis	81.9285	1356	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865245.1	s__Streptomyces sp001865245	81.4708	1154	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.88	98.02	0.87	0.86	3	-
GCF_014203595.1	s__Streptomyces echinatus	80.8708	1268	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	80.8423	1307	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495685.1	s__Streptomyces sp014495685	80.6923	1197	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	79.8082	1084	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_900091855.1	s__Streptomyces sp900091855	79.7206	887	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013302895.1	s__Streptomyces chlorinus	79.5595	1078	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323715.1	s__Streptomyces diacarni	79.5547	1045	2582	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:16,577] [INFO] GTDB search result was written to GCF_014650375.1_ASM1465037v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:16,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:16,581] [INFO] DFAST_QC result json was written to GCF_014650375.1_ASM1465037v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:16,582] [INFO] DFAST_QC completed!
[2024-01-24 13:31:16,582] [INFO] Total running time: 0h3m20s