[2024-01-25 17:38:50,778] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:50,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:50,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg47a8b836-7100-4ebd-9c34-5d8042a2220d/dqc_reference
[2024-01-25 17:38:51,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:51,961] [INFO] Task started: Prodigal
[2024-01-25 17:38:51,961] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fe43db6-7f33-43a5-b97d-cad8a1bf5ccc/GCF_002085925.2_ASM208592v2_genomic.fna.gz | prodigal -d GCF_002085925.2_ASM208592v2_genomic.fna/cds.fna -a GCF_002085925.2_ASM208592v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:04,608] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:04,609] [INFO] Task started: HMMsearch
[2024-01-25 17:39:04,609] [INFO] Running command: hmmsearch --tblout GCF_002085925.2_ASM208592v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47a8b836-7100-4ebd-9c34-5d8042a2220d/dqc_reference/reference_markers.hmm GCF_002085925.2_ASM208592v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:04,875] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:04,877] [INFO] Found 6/6 markers.
[2024-01-25 17:39:04,920] [INFO] Query marker FASTA was written to GCF_002085925.2_ASM208592v2_genomic.fna/markers.fasta
[2024-01-25 17:39:04,920] [INFO] Task started: Blastn
[2024-01-25 17:39:04,921] [INFO] Running command: blastn -query GCF_002085925.2_ASM208592v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg47a8b836-7100-4ebd-9c34-5d8042a2220d/dqc_reference/reference_markers.fasta -out GCF_002085925.2_ASM208592v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:05,824] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:05,828] [INFO] Selected 10 target genomes.
[2024-01-25 17:39:05,829] [INFO] Target genome list was writen to GCF_002085925.2_ASM208592v2_genomic.fna/target_genomes.txt
[2024-01-25 17:39:05,833] [INFO] Task started: fastANI
[2024-01-25 17:39:05,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe43db6-7f33-43a5-b97d-cad8a1bf5ccc/GCF_002085925.2_ASM208592v2_genomic.fna.gz --refList GCF_002085925.2_ASM208592v2_genomic.fna/target_genomes.txt --output GCF_002085925.2_ASM208592v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:15,304] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:15,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47a8b836-7100-4ebd-9c34-5d8042a2220d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:15,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47a8b836-7100-4ebd-9c34-5d8042a2220d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:15,313] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:39:15,313] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:39:15,313] [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
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	100.0	1464	1464	95	inconclusive
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	96.2391	1267	1464	95	inconclusive
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	91.4244	1164	1464	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	85.2396	899	1464	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	85.133	915	1464	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.082	365	1464	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.7639	305	1464	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.6623	355	1464	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	77.6332	390	1464	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.5952	345	1464	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:15,315] [INFO] DFAST Taxonomy check result was written to GCF_002085925.2_ASM208592v2_genomic.fna/tc_result.tsv
[2024-01-25 17:39:15,316] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:15,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:15,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47a8b836-7100-4ebd-9c34-5d8042a2220d/dqc_reference/checkm_data
[2024-01-25 17:39:15,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:15,359] [INFO] Task started: CheckM
[2024-01-25 17:39:15,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002085925.2_ASM208592v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002085925.2_ASM208592v2_genomic.fna/checkm_input GCF_002085925.2_ASM208592v2_genomic.fna/checkm_result
[2024-01-25 17:39:55,467] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:55,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:55,488] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:55,488] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:55,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002085925.2_ASM208592v2_genomic.fna/markers.fasta)
[2024-01-25 17:39:55,488] [INFO] Task started: Blastn
[2024-01-25 17:39:55,488] [INFO] Running command: blastn -query GCF_002085925.2_ASM208592v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg47a8b836-7100-4ebd-9c34-5d8042a2220d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002085925.2_ASM208592v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:57,266] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:57,269] [INFO] Selected 5 target genomes.
[2024-01-25 17:39:57,269] [INFO] Target genome list was writen to GCF_002085925.2_ASM208592v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:57,276] [INFO] Task started: fastANI
[2024-01-25 17:39:57,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe43db6-7f33-43a5-b97d-cad8a1bf5ccc/GCF_002085925.2_ASM208592v2_genomic.fna.gz --refList GCF_002085925.2_ASM208592v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002085925.2_ASM208592v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:02,996] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:03,001] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:03,001] [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_002085925.2	s__Thioclava electrotropha	100.0	1464	1464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	N/A	N/A	N/A	N/A	1	conclusive
GCF_009296265.1	s__Thioclava sp009296265	96.2474	1285	1464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2474	N/A	N/A	N/A	N/A	1	conclusive
GCF_002020355.1	s__Thioclava sediminum	96.2391	1267	1464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	-
GCF_002563775.1	s__Thioclava sp002563775	94.9136	1174	1464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
GCF_001940525.2	s__Thioclava nitratireducens	91.4198	1162	1464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.60	98.50	0.92	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:03,003] [INFO] GTDB search result was written to GCF_002085925.2_ASM208592v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:03,005] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:03,007] [INFO] DFAST_QC result json was written to GCF_002085925.2_ASM208592v2_genomic.fna/dqc_result.json
[2024-01-25 17:40:03,007] [INFO] DFAST_QC completed!
[2024-01-25 17:40:03,007] [INFO] Total running time: 0h1m12s