[2024-01-24 12:06:14,277] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,289] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,289] [INFO] DQC Reference Directory: /var/lib/cwl/stgedca43f7-9f11-4cfe-b9a2-c4f1044a7f71/dqc_reference
[2024-01-24 12:06:15,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,647] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg5808bf4d-e18a-4476-a412-43e9c6988e53/GCF_024128855.1_ASM2412885v1_genomic.fna.gz | prodigal -d GCF_024128855.1_ASM2412885v1_genomic.fna/cds.fna -a GCF_024128855.1_ASM2412885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:25,881] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:25,881] [INFO] Task started: HMMsearch
[2024-01-24 12:06:25,881] [INFO] Running command: hmmsearch --tblout GCF_024128855.1_ASM2412885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedca43f7-9f11-4cfe-b9a2-c4f1044a7f71/dqc_reference/reference_markers.hmm GCF_024128855.1_ASM2412885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:26,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:26,160] [INFO] Found 6/6 markers.
[2024-01-24 12:06:26,192] [INFO] Query marker FASTA was written to GCF_024128855.1_ASM2412885v1_genomic.fna/markers.fasta
[2024-01-24 12:06:26,193] [INFO] Task started: Blastn
[2024-01-24 12:06:26,193] [INFO] Running command: blastn -query GCF_024128855.1_ASM2412885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedca43f7-9f11-4cfe-b9a2-c4f1044a7f71/dqc_reference/reference_markers.fasta -out GCF_024128855.1_ASM2412885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:27,320] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:27,324] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:27,325] [INFO] Target genome list was writen to GCF_024128855.1_ASM2412885v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:27,329] [INFO] Task started: fastANI
[2024-01-24 12:06:27,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg5808bf4d-e18a-4476-a412-43e9c6988e53/GCF_024128855.1_ASM2412885v1_genomic.fna.gz --refList GCF_024128855.1_ASM2412885v1_genomic.fna/target_genomes.txt --output GCF_024128855.1_ASM2412885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:37,957] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:37,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedca43f7-9f11-4cfe-b9a2-c4f1044a7f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:37,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedca43f7-9f11-4cfe-b9a2-c4f1044a7f71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:37,978] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:37,978] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:06:37,979] [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
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	100.0	1141	1142	95	inconclusive
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	95.0634	980	1142	95	inconclusive
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	90.1293	919	1142	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	85.7551	881	1142	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	84.8442	849	1142	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	82.1591	768	1142	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	81.7105	642	1142	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.4234	515	1142	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.723	484	1142	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	78.71	486	1142	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.6353	474	1142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:37,981] [INFO] DFAST Taxonomy check result was written to GCF_024128855.1_ASM2412885v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:37,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:37,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:37,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedca43f7-9f11-4cfe-b9a2-c4f1044a7f71/dqc_reference/checkm_data
[2024-01-24 12:06:37,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:38,022] [INFO] Task started: CheckM
[2024-01-24 12:06:38,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024128855.1_ASM2412885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024128855.1_ASM2412885v1_genomic.fna/checkm_input GCF_024128855.1_ASM2412885v1_genomic.fna/checkm_result
[2024-01-24 12:07:14,937] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:14,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:14,966] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:14,966] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:14,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024128855.1_ASM2412885v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:14,967] [INFO] Task started: Blastn
[2024-01-24 12:07:14,967] [INFO] Running command: blastn -query GCF_024128855.1_ASM2412885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedca43f7-9f11-4cfe-b9a2-c4f1044a7f71/dqc_reference/reference_markers_gtdb.fasta -out GCF_024128855.1_ASM2412885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:17,103] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:17,107] [INFO] Selected 8 target genomes.
[2024-01-24 12:07:17,107] [INFO] Target genome list was writen to GCF_024128855.1_ASM2412885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:17,130] [INFO] Task started: fastANI
[2024-01-24 12:07:17,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg5808bf4d-e18a-4476-a412-43e9c6988e53/GCF_024128855.1_ASM2412885v1_genomic.fna.gz --refList GCF_024128855.1_ASM2412885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024128855.1_ASM2412885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:24,421] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:24,429] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:07:24,429] [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
GCA_011048875.1	s__Rhodovulum sp011048875	95.601	666	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_004339675.1	s__Rhodovulum steppense	95.0634	980	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_009649175.1	s__Rhodovulum strictum	90.1185	920	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	85.7551	881	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	84.8566	848	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142935.1	s__Rhodovulum sp900142935	83.1118	793	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	82.1888	754	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_002079305.1	s__Rhodovulum sp002079305	80.9433	681	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:24,431] [INFO] GTDB search result was written to GCF_024128855.1_ASM2412885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:24,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:24,436] [INFO] DFAST_QC result json was written to GCF_024128855.1_ASM2412885v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:24,436] [INFO] DFAST_QC completed!
[2024-01-24 12:07:24,436] [INFO] Total running time: 0h1m10s