[2024-01-24 11:06:04,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,663] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg218f31d0-5602-4a33-96ed-d82bc655187a/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bd1e10d-e7e1-4311-bef7-83a3a6fadc37/GCF_002154615.1_ASM215461v1_genomic.fna.gz | prodigal -d GCF_002154615.1_ASM215461v1_genomic.fna/cds.fna -a GCF_002154615.1_ASM215461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:21,523] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:21,524] [INFO] Task started: HMMsearch
[2024-01-24 11:06:21,524] [INFO] Running command: hmmsearch --tblout GCF_002154615.1_ASM215461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg218f31d0-5602-4a33-96ed-d82bc655187a/dqc_reference/reference_markers.hmm GCF_002154615.1_ASM215461v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:21,822] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:21,824] [INFO] Found 6/6 markers.
[2024-01-24 11:06:21,876] [INFO] Query marker FASTA was written to GCF_002154615.1_ASM215461v1_genomic.fna/markers.fasta
[2024-01-24 11:06:21,877] [INFO] Task started: Blastn
[2024-01-24 11:06:21,877] [INFO] Running command: blastn -query GCF_002154615.1_ASM215461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg218f31d0-5602-4a33-96ed-d82bc655187a/dqc_reference/reference_markers.fasta -out GCF_002154615.1_ASM215461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:23,203] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:23,206] [INFO] Selected 15 target genomes.
[2024-01-24 11:06:23,206] [INFO] Target genome list was writen to GCF_002154615.1_ASM215461v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:23,212] [INFO] Task started: fastANI
[2024-01-24 11:06:23,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd1e10d-e7e1-4311-bef7-83a3a6fadc37/GCF_002154615.1_ASM215461v1_genomic.fna.gz --refList GCF_002154615.1_ASM215461v1_genomic.fna/target_genomes.txt --output GCF_002154615.1_ASM215461v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:48,157] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:48,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg218f31d0-5602-4a33-96ed-d82bc655187a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:48,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg218f31d0-5602-4a33-96ed-d82bc655187a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:48,175] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:06:48,175] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:06:48,175] [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 recifensis	strain=NRRL B-3811	GCA_002154615.1	67355	67355	type	True	100.0	1611	1631	95	inconclusive
Streptomyces griseoluteus	strain=JCM 4765	GCA_014656035.1	29306	29306	type	True	96.5049	1436	1631	95	inconclusive
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	96.4914	1441	1631	95	inconclusive
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	95.3335	1388	1631	95	inconclusive
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	85.9049	1181	1631	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	85.6862	1156	1631	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	85.6451	1190	1631	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	85.521	1179	1631	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.9179	1093	1631	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.5027	999	1631	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	84.3701	1124	1631	95	below_threshold
Streptomyces triticisoli	strain=NEAU-DSCPA1-4-4	GCA_003270085.1	2182797	2182797	type	True	84.3451	1019	1631	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	84.2771	1123	1631	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.0607	1143	1631	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.7186	1040	1631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:48,177] [INFO] DFAST Taxonomy check result was written to GCF_002154615.1_ASM215461v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:48,177] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:48,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:48,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg218f31d0-5602-4a33-96ed-d82bc655187a/dqc_reference/checkm_data
[2024-01-24 11:06:48,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:48,237] [INFO] Task started: CheckM
[2024-01-24 11:06:48,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154615.1_ASM215461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154615.1_ASM215461v1_genomic.fna/checkm_input GCF_002154615.1_ASM215461v1_genomic.fna/checkm_result
[2024-01-24 11:07:35,661] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:35,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:35,683] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:35,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:35,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154615.1_ASM215461v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:35,684] [INFO] Task started: Blastn
[2024-01-24 11:07:35,684] [INFO] Running command: blastn -query GCF_002154615.1_ASM215461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg218f31d0-5602-4a33-96ed-d82bc655187a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154615.1_ASM215461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:37,852] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:37,855] [INFO] Selected 10 target genomes.
[2024-01-24 11:07:37,855] [INFO] Target genome list was writen to GCF_002154615.1_ASM215461v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:37,864] [INFO] Task started: fastANI
[2024-01-24 11:07:37,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd1e10d-e7e1-4311-bef7-83a3a6fadc37/GCF_002154615.1_ASM215461v1_genomic.fna.gz --refList GCF_002154615.1_ASM215461v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154615.1_ASM215461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:53,821] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:53,834] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:53,834] [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_004784465.1	s__Streptomyces griseoluteus	96.4914	1441	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	conclusive
GCF_004784475.1	s__Streptomyces bauhiniae	95.3769	1385	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	95.70	95.47	0.88	0.84	6	-
GCF_019090105.1	s__Streptomyces sp019090105	92.6613	1341	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373625.1	s__Streptomyces sp000373625	88.0955	1236	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009863025.1	s__Streptomyces sp009863025	87.8562	1119	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016482685.1	s__Streptomyces sp016482685	87.6931	1262	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813405.1	s__Streptomyces sp002813405	86.3584	1200	1631	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	85.6435	1159	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004124325.1	s__Streptomyces sp004124325	85.5586	1154	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	84.3464	1133	1631	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 11:07:53,835] [INFO] GTDB search result was written to GCF_002154615.1_ASM215461v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:53,836] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:53,839] [INFO] DFAST_QC result json was written to GCF_002154615.1_ASM215461v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:53,839] [INFO] DFAST_QC completed!
[2024-01-24 11:07:53,839] [INFO] Total running time: 0h1m49s