[2024-01-25 18:16:35,652] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:35,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:35,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg2153b19d-1520-46a3-b415-6b3fee5893e9/dqc_reference
[2024-01-25 18:16:36,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:36,737] [INFO] Task started: Prodigal
[2024-01-25 18:16:36,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg945ddfea-0254-455b-8eab-d7aafc27748b/GCF_014648075.1_ASM1464807v1_genomic.fna.gz | prodigal -d GCF_014648075.1_ASM1464807v1_genomic.fna/cds.fna -a GCF_014648075.1_ASM1464807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:59,761] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:59,762] [INFO] Task started: HMMsearch
[2024-01-25 18:16:59,762] [INFO] Running command: hmmsearch --tblout GCF_014648075.1_ASM1464807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2153b19d-1520-46a3-b415-6b3fee5893e9/dqc_reference/reference_markers.hmm GCF_014648075.1_ASM1464807v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:17:00,083] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:17:00,084] [INFO] Found 6/6 markers.
[2024-01-25 18:17:00,139] [INFO] Query marker FASTA was written to GCF_014648075.1_ASM1464807v1_genomic.fna/markers.fasta
[2024-01-25 18:17:00,140] [INFO] Task started: Blastn
[2024-01-25 18:17:00,140] [INFO] Running command: blastn -query GCF_014648075.1_ASM1464807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2153b19d-1520-46a3-b415-6b3fee5893e9/dqc_reference/reference_markers.fasta -out GCF_014648075.1_ASM1464807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:01,397] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:01,405] [INFO] Selected 27 target genomes.
[2024-01-25 18:17:01,405] [INFO] Target genome list was writen to GCF_014648075.1_ASM1464807v1_genomic.fna/target_genomes.txt
[2024-01-25 18:17:01,428] [INFO] Task started: fastANI
[2024-01-25 18:17:01,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg945ddfea-0254-455b-8eab-d7aafc27748b/GCF_014648075.1_ASM1464807v1_genomic.fna.gz --refList GCF_014648075.1_ASM1464807v1_genomic.fna/target_genomes.txt --output GCF_014648075.1_ASM1464807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:51,080] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:51,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2153b19d-1520-46a3-b415-6b3fee5893e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:51,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2153b19d-1520-46a3-b415-6b3fee5893e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:51,097] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:17:51,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:17:51,097] [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 ruber	strain=JCM 3131	GCA_014648075.1	83378	83378	type	True	100.0	2595	2596	95	conclusive
Streptomyces poonensis	strain=JCM 4815	GCA_014650915.1	68255	68255	type	True	89.4236	1840	2596	95	below_threshold
Streptomyces bluensis	strain=JCM 4729	GCA_014650715.1	33897	33897	type	True	85.299	1632	2596	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	85.09	1425	2596	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	84.2962	1619	2596	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	84.2483	1624	2596	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.1617	1593	2596	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.1402	1400	2596	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.124	1614	2596	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	84.1028	1562	2596	95	below_threshold
Streptomyces triticisoli	strain=NEAU-DSCPA1-4-4	GCA_003270085.1	2182797	2182797	type	True	83.9743	1291	2596	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	83.9322	1564	2596	95	below_threshold
Streptomyces neyagawaensis	strain=NRRL B-3092	GCA_001418645.1	42238	42238	type	True	83.896	1222	2596	95	below_threshold
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	83.7713	1354	2596	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	83.6725	1493	2596	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	83.6661	1518	2596	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	83.6498	1397	2596	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.6079	1458	2596	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	83.543	1620	2596	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	83.4941	1592	2596	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	83.0807	1304	2596	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=JCM 4843	GCA_014650975.1	66860	1952	type	True	83.0517	1305	2596	95	below_threshold
Streptomyces toxytricini	strain=JCM 4421	GCA_014649915.1	67369	67369	type	True	80.9794	1193	2596	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	80.2044	1071	2596	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.1233	806	2596	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	80.013	852	2596	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	79.5763	1141	2596	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:51,099] [INFO] DFAST Taxonomy check result was written to GCF_014648075.1_ASM1464807v1_genomic.fna/tc_result.tsv
[2024-01-25 18:17:51,099] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:51,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:51,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2153b19d-1520-46a3-b415-6b3fee5893e9/dqc_reference/checkm_data
[2024-01-25 18:17:51,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:51,172] [INFO] Task started: CheckM
[2024-01-25 18:17:51,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648075.1_ASM1464807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648075.1_ASM1464807v1_genomic.fna/checkm_input GCF_014648075.1_ASM1464807v1_genomic.fna/checkm_result
[2024-01-25 18:20:00,877] [INFO] Task succeeded: CheckM
[2024-01-25 18:20:00,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:20:00,901] [INFO] ===== Completeness check finished =====
[2024-01-25 18:20:00,901] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:20:00,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648075.1_ASM1464807v1_genomic.fna/markers.fasta)
[2024-01-25 18:20:00,902] [INFO] Task started: Blastn
[2024-01-25 18:20:00,902] [INFO] Running command: blastn -query GCF_014648075.1_ASM1464807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2153b19d-1520-46a3-b415-6b3fee5893e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648075.1_ASM1464807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:03,007] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:03,010] [INFO] Selected 19 target genomes.
[2024-01-25 18:20:03,010] [INFO] Target genome list was writen to GCF_014648075.1_ASM1464807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:20:03,046] [INFO] Task started: fastANI
[2024-01-25 18:20:03,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg945ddfea-0254-455b-8eab-d7aafc27748b/GCF_014648075.1_ASM1464807v1_genomic.fna.gz --refList GCF_014648075.1_ASM1464807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648075.1_ASM1464807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:20:41,013] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:41,025] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:20:41,025] [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_014648075.1	s__Streptomyces ruber	100.0	2595	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000719105.1	s__Streptomyces sclerotialus_B	89.7859	1668	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650915.1	s__Streptomyces poonensis	89.4195	1841	2596	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	85.0184	1433	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	84.5394	1646	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006782915.1	s__Streptomyces calvus	84.2109	1638	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_014534645.1	s__Streptomyces sp014534645	84.1774	1591	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003270085.1	s__Streptomyces triticisoli	83.9876	1290	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	83.9759	1562	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317595.1	s__Streptomyces ipomoeae	83.8743	1452	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
GCF_001418475.1	s__Streptomyces ossamyceticus	83.7881	1353	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6547	98.97	98.97	0.90	0.90	2	-
GCF_018070565.1	s__Streptomyces sp018070565	83.7696	1537	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649995.1	s__Streptomyces griseoflavus	83.7035	1488	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	83.5312	1623	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636945.1	s__Streptomyces sp001636945	83.4684	1436	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001298555.1	s__Streptomyces sp001298555	80.765	1179	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097205.2	s__Streptomyces alkaliterrae	79.9857	859	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.63	99.32	0.91	0.86	3	-
GCF_900110255.1	s__Streptomyces rubidus	79.5833	1141	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091855.1	s__Streptomyces sp900091855	79.507	972	2596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:20:41,026] [INFO] GTDB search result was written to GCF_014648075.1_ASM1464807v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:20:41,027] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:20:41,031] [INFO] DFAST_QC result json was written to GCF_014648075.1_ASM1464807v1_genomic.fna/dqc_result.json
[2024-01-25 18:20:41,031] [INFO] DFAST_QC completed!
[2024-01-25 18:20:41,031] [INFO] Total running time: 0h4m5s