[2024-01-24 13:37:15,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:15,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:15,353] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd32dc34-5c6c-4ce9-bce6-034de4c082b0/dqc_reference
[2024-01-24 13:37:18,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:18,469] [INFO] Task started: Prodigal
[2024-01-24 13:37:18,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg36ab0ecb-a49a-4011-8951-ce2b59819e16/GCF_021474405.1_ASM2147440v1_genomic.fna.gz | prodigal -d GCF_021474405.1_ASM2147440v1_genomic.fna/cds.fna -a GCF_021474405.1_ASM2147440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:38,961] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:38,962] [INFO] Task started: HMMsearch
[2024-01-24 13:37:38,962] [INFO] Running command: hmmsearch --tblout GCF_021474405.1_ASM2147440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd32dc34-5c6c-4ce9-bce6-034de4c082b0/dqc_reference/reference_markers.hmm GCF_021474405.1_ASM2147440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:39,356] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:39,357] [INFO] Found 6/6 markers.
[2024-01-24 13:37:39,440] [INFO] Query marker FASTA was written to GCF_021474405.1_ASM2147440v1_genomic.fna/markers.fasta
[2024-01-24 13:37:39,443] [INFO] Task started: Blastn
[2024-01-24 13:37:39,443] [INFO] Running command: blastn -query GCF_021474405.1_ASM2147440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd32dc34-5c6c-4ce9-bce6-034de4c082b0/dqc_reference/reference_markers.fasta -out GCF_021474405.1_ASM2147440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:40,830] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:40,836] [INFO] Selected 11 target genomes.
[2024-01-24 13:37:40,836] [INFO] Target genome list was writen to GCF_021474405.1_ASM2147440v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:40,844] [INFO] Task started: fastANI
[2024-01-24 13:37:40,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg36ab0ecb-a49a-4011-8951-ce2b59819e16/GCF_021474405.1_ASM2147440v1_genomic.fna.gz --refList GCF_021474405.1_ASM2147440v1_genomic.fna/target_genomes.txt --output GCF_021474405.1_ASM2147440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:05,009] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:05,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd32dc34-5c6c-4ce9-bce6-034de4c082b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:05,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd32dc34-5c6c-4ce9-bce6-034de4c082b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:05,023] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:05,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:05,023] [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 indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	100.0	2444	2457	95	conclusive
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	92.8288	2029	2457	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	92.8277	2030	2457	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	92.2338	2054	2457	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	92.2038	1951	2457	95	below_threshold
Streptomyces luteogriseus	strain=DSM 40483	GCA_014205055.1	68233	68233	type	True	92.1514	2035	2457	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	91.9834	1981	2457	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	91.3243	1668	2457	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	90.39	1909	2457	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.1904	1920	2457	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.3516	1403	2457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:05,025] [INFO] DFAST Taxonomy check result was written to GCF_021474405.1_ASM2147440v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:05,025] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:05,025] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:05,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd32dc34-5c6c-4ce9-bce6-034de4c082b0/dqc_reference/checkm_data
[2024-01-24 13:38:05,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:05,103] [INFO] Task started: CheckM
[2024-01-24 13:38:05,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021474405.1_ASM2147440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021474405.1_ASM2147440v1_genomic.fna/checkm_input GCF_021474405.1_ASM2147440v1_genomic.fna/checkm_result
[2024-01-24 13:39:41,152] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:41,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:41,182] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:41,182] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:41,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021474405.1_ASM2147440v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:41,183] [INFO] Task started: Blastn
[2024-01-24 13:39:41,183] [INFO] Running command: blastn -query GCF_021474405.1_ASM2147440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd32dc34-5c6c-4ce9-bce6-034de4c082b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_021474405.1_ASM2147440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:43,466] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:43,472] [INFO] Selected 11 target genomes.
[2024-01-24 13:39:43,472] [INFO] Target genome list was writen to GCF_021474405.1_ASM2147440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:43,481] [INFO] Task started: fastANI
[2024-01-24 13:39:43,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg36ab0ecb-a49a-4011-8951-ce2b59819e16/GCF_021474405.1_ASM2147440v1_genomic.fna.gz --refList GCF_021474405.1_ASM2147440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021474405.1_ASM2147440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:07,200] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:07,217] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:40:07,218] [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_007655005.1	s__Streptomyces tibetensis	92.838	2028	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001280065.1	s__Streptomyces sp001280065	92.5102	1966	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648995.1	s__Streptomyces massasporeus	92.2072	2058	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCF_014205055.1	s__Streptomyces luteogriseus	92.1449	2035	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCF_014202475.1	s__Streptomyces paradoxus	92.0727	2044	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803895.1	s__Streptomyces hawaiiensis	92.0158	1955	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
GCA_014204745.1	s__Streptomyces collinus	92.0021	2042	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_000717055.1	s__Streptomyces iakyrus	91.9748	1982	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_001611795.1	s__Streptomyces qaidamensis	91.7665	1997	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_003330845.1	s__Streptomyces sp003330845	90.3313	1909	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900236475.1	s__Streptomyces chartreusis_D	90.1339	1923	2457	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:07,219] [INFO] GTDB search result was written to GCF_021474405.1_ASM2147440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:07,220] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:07,223] [INFO] DFAST_QC result json was written to GCF_021474405.1_ASM2147440v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:07,223] [INFO] DFAST_QC completed!
[2024-01-24 13:40:07,223] [INFO] Total running time: 0h2m52s