[2024-01-25 17:43:50,773] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:50,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:50,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg094b7d7e-050f-437b-9df1-544c668bc29d/dqc_reference
[2024-01-25 17:43:51,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:51,886] [INFO] Task started: Prodigal
[2024-01-25 17:43:51,887] [INFO] Running command: gunzip -c /var/lib/cwl/stg06239bef-c485-42a8-af5d-162f942beaa9/GCF_000717315.1_ASM71731v1_genomic.fna.gz | prodigal -d GCF_000717315.1_ASM71731v1_genomic.fna/cds.fna -a GCF_000717315.1_ASM71731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:10,354] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:10,354] [INFO] Task started: HMMsearch
[2024-01-25 17:44:10,354] [INFO] Running command: hmmsearch --tblout GCF_000717315.1_ASM71731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg094b7d7e-050f-437b-9df1-544c668bc29d/dqc_reference/reference_markers.hmm GCF_000717315.1_ASM71731v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:10,661] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:10,663] [INFO] Found 6/6 markers.
[2024-01-25 17:44:10,724] [INFO] Query marker FASTA was written to GCF_000717315.1_ASM71731v1_genomic.fna/markers.fasta
[2024-01-25 17:44:10,724] [INFO] Task started: Blastn
[2024-01-25 17:44:10,724] [INFO] Running command: blastn -query GCF_000717315.1_ASM71731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg094b7d7e-050f-437b-9df1-544c668bc29d/dqc_reference/reference_markers.fasta -out GCF_000717315.1_ASM71731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:12,007] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:12,010] [INFO] Selected 20 target genomes.
[2024-01-25 17:44:12,010] [INFO] Target genome list was writen to GCF_000717315.1_ASM71731v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:12,030] [INFO] Task started: fastANI
[2024-01-25 17:44:12,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg06239bef-c485-42a8-af5d-162f942beaa9/GCF_000717315.1_ASM71731v1_genomic.fna.gz --refList GCF_000717315.1_ASM71731v1_genomic.fna/target_genomes.txt --output GCF_000717315.1_ASM71731v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:52,940] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:52,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg094b7d7e-050f-437b-9df1-544c668bc29d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:52,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg094b7d7e-050f-437b-9df1-544c668bc29d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:52,952] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:44:52,952] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:44:52,952] [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 malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	88.0565	1846	2402	95	below_threshold
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	87.8918	1828	2402	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	87.8582	1807	2402	95	below_threshold
Streptomyces pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	87.8391	1833	2402	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	87.8186	1819	2402	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	87.7426	1832	2402	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	87.7042	1836	2402	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	87.482	1817	2402	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	87.4067	1829	2402	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	87.1023	1465	2402	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.6124	1667	2402	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.4704	1701	2402	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.3845	1698	2402	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.2947	1542	2402	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.2828	1410	2402	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	85.2012	1667	2402	95	below_threshold
Streptomyces mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	85.1814	1628	2402	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.1224	1358	2402	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.0717	1655	2402	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	84.8501	1700	2402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:52,954] [INFO] DFAST Taxonomy check result was written to GCF_000717315.1_ASM71731v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:52,955] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:52,955] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:52,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg094b7d7e-050f-437b-9df1-544c668bc29d/dqc_reference/checkm_data
[2024-01-25 17:44:52,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:53,023] [INFO] Task started: CheckM
[2024-01-25 17:44:53,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000717315.1_ASM71731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000717315.1_ASM71731v1_genomic.fna/checkm_input GCF_000717315.1_ASM71731v1_genomic.fna/checkm_result
[2024-01-25 17:46:37,714] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:37,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:37,736] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:37,736] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:37,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000717315.1_ASM71731v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:37,737] [INFO] Task started: Blastn
[2024-01-25 17:46:37,737] [INFO] Running command: blastn -query GCF_000717315.1_ASM71731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg094b7d7e-050f-437b-9df1-544c668bc29d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000717315.1_ASM71731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:40,020] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:40,022] [INFO] Selected 9 target genomes.
[2024-01-25 17:46:40,023] [INFO] Target genome list was writen to GCF_000717315.1_ASM71731v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:40,043] [INFO] Task started: fastANI
[2024-01-25 17:46:40,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg06239bef-c485-42a8-af5d-162f942beaa9/GCF_000717315.1_ASM71731v1_genomic.fna.gz --refList GCF_000717315.1_ASM71731v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000717315.1_ASM71731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:59,387] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:59,394] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:59,394] [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
GCA_014649355.1	s__Streptomyces althioticus	99.2167	2306	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.43	96.72	0.91	0.83	9	conclusive
GCA_014649575.1	s__Streptomyces griseoincarnatus	95.3202	2079	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.24	97.52	0.91	0.85	21	-
GCA_014656175.1	s__Streptomyces werraensis	94.649	2066	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014655195.1	s__Streptomyces cellulosae	94.3129	2052	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.87	0.87	0.85	11	-
GCA_014650475.1	s__Streptomyces albogriseolus	94.0294	2042	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.59	97.23	0.93	0.90	7	-
GCA_002154585.1	s__Streptomyces pseudogriseolus	93.0054	1641	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.58	96.58	0.90	0.87	9	-
GCF_002899455.1	s__Streptomyces sp002899455	92.5149	1894	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650055.1	s__Streptomyces malachitofuscus	88.0383	1849	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715605.1	s__Streptomyces speibonae	87.4638	1809	2402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.03	99.02	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:59,396] [INFO] GTDB search result was written to GCF_000717315.1_ASM71731v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:59,396] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:59,400] [INFO] DFAST_QC result json was written to GCF_000717315.1_ASM71731v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:59,401] [INFO] DFAST_QC completed!
[2024-01-25 17:46:59,401] [INFO] Total running time: 0h3m9s