[2024-01-24 13:19:26,639] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:26,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:26,642] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb5f0efa-e054-4a46-95ae-1d2ed2e6e02e/dqc_reference
[2024-01-24 13:19:27,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:27,857] [INFO] Task started: Prodigal
[2024-01-24 13:19:27,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg70b50237-826b-4755-89c5-bed6bfb79b6f/GCF_014656035.1_ASM1465603v1_genomic.fna.gz | prodigal -d GCF_014656035.1_ASM1465603v1_genomic.fna/cds.fna -a GCF_014656035.1_ASM1465603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:46,577] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:46,577] [INFO] Task started: HMMsearch
[2024-01-24 13:19:46,577] [INFO] Running command: hmmsearch --tblout GCF_014656035.1_ASM1465603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb5f0efa-e054-4a46-95ae-1d2ed2e6e02e/dqc_reference/reference_markers.hmm GCF_014656035.1_ASM1465603v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:46,949] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:46,950] [INFO] Found 6/6 markers.
[2024-01-24 13:19:47,006] [INFO] Query marker FASTA was written to GCF_014656035.1_ASM1465603v1_genomic.fna/markers.fasta
[2024-01-24 13:19:47,006] [INFO] Task started: Blastn
[2024-01-24 13:19:47,007] [INFO] Running command: blastn -query GCF_014656035.1_ASM1465603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb5f0efa-e054-4a46-95ae-1d2ed2e6e02e/dqc_reference/reference_markers.fasta -out GCF_014656035.1_ASM1465603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:48,326] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:48,330] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:48,330] [INFO] Target genome list was writen to GCF_014656035.1_ASM1465603v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:48,921] [INFO] Task started: fastANI
[2024-01-24 13:19:48,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg70b50237-826b-4755-89c5-bed6bfb79b6f/GCF_014656035.1_ASM1465603v1_genomic.fna.gz --refList GCF_014656035.1_ASM1465603v1_genomic.fna/target_genomes.txt --output GCF_014656035.1_ASM1465603v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:16,427] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:16,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb5f0efa-e054-4a46-95ae-1d2ed2e6e02e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:16,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb5f0efa-e054-4a46-95ae-1d2ed2e6e02e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:16,448] [INFO] Found 14 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:20:16,449] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:20:16,449] [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 griseoluteus	strain=JCM 4765	GCA_014656035.1	29306	29306	type	True	100.0	2208	2209	95	inconclusive
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	99.9964	2206	2209	95	inconclusive
Streptomyces recifensis	strain=NRRL B-3811	GCA_002154615.1	67355	67355	type	True	96.2314	1416	2209	95	inconclusive
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	95.3859	1850	2209	95	inconclusive
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	85.5331	1603	2209	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	85.4638	1529	2209	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	85.4535	1541	2209	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	85.3327	1574	2209	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	85.245	1533	2209	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	84.2204	1435	2209	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.1513	1515	2209	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.1466	1262	2209	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.8686	1482	2209	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.3851	1342	2209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:16,451] [INFO] DFAST Taxonomy check result was written to GCF_014656035.1_ASM1465603v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:16,451] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:16,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:16,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb5f0efa-e054-4a46-95ae-1d2ed2e6e02e/dqc_reference/checkm_data
[2024-01-24 13:20:16,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:16,520] [INFO] Task started: CheckM
[2024-01-24 13:20:16,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656035.1_ASM1465603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656035.1_ASM1465603v1_genomic.fna/checkm_input GCF_014656035.1_ASM1465603v1_genomic.fna/checkm_result
[2024-01-24 13:21:22,315] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:22,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:22,341] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:22,341] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:22,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656035.1_ASM1465603v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:22,342] [INFO] Task started: Blastn
[2024-01-24 13:21:22,342] [INFO] Running command: blastn -query GCF_014656035.1_ASM1465603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb5f0efa-e054-4a46-95ae-1d2ed2e6e02e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656035.1_ASM1465603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:24,455] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:24,458] [INFO] Selected 10 target genomes.
[2024-01-24 13:21:24,458] [INFO] Target genome list was writen to GCF_014656035.1_ASM1465603v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:24,530] [INFO] Task started: fastANI
[2024-01-24 13:21:24,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg70b50237-826b-4755-89c5-bed6bfb79b6f/GCF_014656035.1_ASM1465603v1_genomic.fna.gz --refList GCF_014656035.1_ASM1465603v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656035.1_ASM1465603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:43,042] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:43,051] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:43,051] [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	99.9964	2206	2209	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	95.3648	1852	2209	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	92.622	1776	2209	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	87.7469	1645	2209	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	87.6367	1407	2209	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	87.4886	1670	2209	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	86.2531	1601	2209	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	85.4512	1517	2209	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	85.346	1525	2209	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	84.1791	1451	2209	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 13:21:43,053] [INFO] GTDB search result was written to GCF_014656035.1_ASM1465603v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:43,054] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:43,057] [INFO] DFAST_QC result json was written to GCF_014656035.1_ASM1465603v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:43,057] [INFO] DFAST_QC completed!
[2024-01-24 13:21:43,057] [INFO] Total running time: 0h2m16s