[2024-01-24 14:30:46,261] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:46,263] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:46,263] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbf9a4d4-a46f-4f43-9814-8a7651163832/dqc_reference
[2024-01-24 14:30:47,500] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:47,501] [INFO] Task started: Prodigal
[2024-01-24 14:30:47,501] [INFO] Running command: gunzip -c /var/lib/cwl/stga76148df-f217-4b56-adfd-f1594ae7bc48/GCF_003293745.1_ASM329374v1_genomic.fna.gz | prodigal -d GCF_003293745.1_ASM329374v1_genomic.fna/cds.fna -a GCF_003293745.1_ASM329374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:57,506] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:57,506] [INFO] Task started: HMMsearch
[2024-01-24 14:30:57,506] [INFO] Running command: hmmsearch --tblout GCF_003293745.1_ASM329374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbf9a4d4-a46f-4f43-9814-8a7651163832/dqc_reference/reference_markers.hmm GCF_003293745.1_ASM329374v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:57,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:57,794] [INFO] Found 6/6 markers.
[2024-01-24 14:30:57,823] [INFO] Query marker FASTA was written to GCF_003293745.1_ASM329374v1_genomic.fna/markers.fasta
[2024-01-24 14:30:57,824] [INFO] Task started: Blastn
[2024-01-24 14:30:57,824] [INFO] Running command: blastn -query GCF_003293745.1_ASM329374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbf9a4d4-a46f-4f43-9814-8a7651163832/dqc_reference/reference_markers.fasta -out GCF_003293745.1_ASM329374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:58,584] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:58,591] [INFO] Selected 19 target genomes.
[2024-01-24 14:30:58,592] [INFO] Target genome list was writen to GCF_003293745.1_ASM329374v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:58,606] [INFO] Task started: fastANI
[2024-01-24 14:30:58,606] [INFO] Running command: fastANI --query /var/lib/cwl/stga76148df-f217-4b56-adfd-f1594ae7bc48/GCF_003293745.1_ASM329374v1_genomic.fna.gz --refList GCF_003293745.1_ASM329374v1_genomic.fna/target_genomes.txt --output GCF_003293745.1_ASM329374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:14,829] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:14,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbf9a4d4-a46f-4f43-9814-8a7651163832/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:14,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbf9a4d4-a46f-4f43-9814-8a7651163832/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:14,844] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:14,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:14,845] [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
Herminiimonas fonticola	strain=S-94	GCA_003293745.1	303380	303380	type	True	100.0	1032	1032	95	conclusive
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	99.9989	1029	1032	95	conclusive
Herminiimonas arsenitoxidans	strain=AS8	GCA_900130075.1	1809410	1809410	type	True	81.8554	672	1032	95	below_threshold
Oxalicibacterium faecigallinarum	strain=CCM 2767	GCA_014635705.1	573741	573741	type	True	78.884	403	1032	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	78.6065	429	1032	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	78.2227	246	1032	95	below_threshold
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	78.0966	261	1032	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	77.8549	272	1032	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	77.8473	258	1032	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	77.8318	256	1032	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.7987	225	1032	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	77.6554	294	1032	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	77.4524	194	1032	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	77.3699	239	1032	95	below_threshold
Janthinobacterium lividum	strain=H-24	GCA_001758635.1	29581	29581	suspected-type	True	77.3227	184	1032	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	76.8483	168	1032	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	76.8338	172	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:14,849] [INFO] DFAST Taxonomy check result was written to GCF_003293745.1_ASM329374v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:14,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:14,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:14,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbf9a4d4-a46f-4f43-9814-8a7651163832/dqc_reference/checkm_data
[2024-01-24 14:31:14,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:14,894] [INFO] Task started: CheckM
[2024-01-24 14:31:14,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003293745.1_ASM329374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003293745.1_ASM329374v1_genomic.fna/checkm_input GCF_003293745.1_ASM329374v1_genomic.fna/checkm_result
[2024-01-24 14:31:50,494] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:50,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:50,516] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:50,516] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:50,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003293745.1_ASM329374v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:50,518] [INFO] Task started: Blastn
[2024-01-24 14:31:50,518] [INFO] Running command: blastn -query GCF_003293745.1_ASM329374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbf9a4d4-a46f-4f43-9814-8a7651163832/dqc_reference/reference_markers_gtdb.fasta -out GCF_003293745.1_ASM329374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:52,003] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:52,007] [INFO] Selected 6 target genomes.
[2024-01-24 14:31:52,007] [INFO] Target genome list was writen to GCF_003293745.1_ASM329374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:52,014] [INFO] Task started: fastANI
[2024-01-24 14:31:52,014] [INFO] Running command: fastANI --query /var/lib/cwl/stga76148df-f217-4b56-adfd-f1594ae7bc48/GCF_003293745.1_ASM329374v1_genomic.fna.gz --refList GCF_003293745.1_ASM329374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003293745.1_ASM329374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:58,254] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:58,262] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:58,263] [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_003293745.1	s__Herminiimonas fonticola	100.0	1032	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_001464355.1	s__Herminiimonas sp001464355	86.1437	803	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384815.1	s__Herminiimonas sp002384815	83.6814	652	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000026125.1	s__Herminiimonas arsenicoxydans	83.5594	717	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130075.1	s__Herminiimonas arsenitoxidans	81.8402	674	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013625.1	s__Herminiimonas sp000013625	81.0535	626	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:58,264] [INFO] GTDB search result was written to GCF_003293745.1_ASM329374v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:58,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:58,270] [INFO] DFAST_QC result json was written to GCF_003293745.1_ASM329374v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:58,271] [INFO] DFAST_QC completed!
[2024-01-24 14:31:58,271] [INFO] Total running time: 0h1m12s