[2024-01-24 10:47:06,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,600] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf5e1ad2-d35a-43b2-9805-2daffddbe1a7/dqc_reference
[2024-01-24 10:47:12,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,798] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,799] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f69fee1-37fd-4991-9c59-e69ed9186d36/GCF_004339675.1_ASM433967v1_genomic.fna.gz | prodigal -d GCF_004339675.1_ASM433967v1_genomic.fna/cds.fna -a GCF_004339675.1_ASM433967v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:23,579] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:23,580] [INFO] Task started: HMMsearch
[2024-01-24 10:47:23,580] [INFO] Running command: hmmsearch --tblout GCF_004339675.1_ASM433967v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf5e1ad2-d35a-43b2-9805-2daffddbe1a7/dqc_reference/reference_markers.hmm GCF_004339675.1_ASM433967v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:23,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:23,869] [INFO] Found 6/6 markers.
[2024-01-24 10:47:23,918] [INFO] Query marker FASTA was written to GCF_004339675.1_ASM433967v1_genomic.fna/markers.fasta
[2024-01-24 10:47:23,918] [INFO] Task started: Blastn
[2024-01-24 10:47:23,918] [INFO] Running command: blastn -query GCF_004339675.1_ASM433967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf5e1ad2-d35a-43b2-9805-2daffddbe1a7/dqc_reference/reference_markers.fasta -out GCF_004339675.1_ASM433967v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:24,980] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:24,984] [INFO] Selected 11 target genomes.
[2024-01-24 10:47:24,985] [INFO] Target genome list was writen to GCF_004339675.1_ASM433967v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,234] [INFO] Task started: fastANI
[2024-01-24 10:47:25,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f69fee1-37fd-4991-9c59-e69ed9186d36/GCF_004339675.1_ASM433967v1_genomic.fna.gz --refList GCF_004339675.1_ASM433967v1_genomic.fna/target_genomes.txt --output GCF_004339675.1_ASM433967v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:35,817] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:35,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf5e1ad2-d35a-43b2-9805-2daffddbe1a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:35,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf5e1ad2-d35a-43b2-9805-2daffddbe1a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:35,845] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:35,846] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:47:35,846] [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 steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	100.0	1180	1187	95	inconclusive
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	95.3272	959	1187	95	inconclusive
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	91.2494	923	1187	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	85.8867	866	1187	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	84.4174	847	1187	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	82.176	780	1187	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	81.6585	644	1187	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.2831	514	1187	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.7949	423	1187	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.7335	478	1187	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.7155	468	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:35,849] [INFO] DFAST Taxonomy check result was written to GCF_004339675.1_ASM433967v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:35,850] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:35,850] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:35,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf5e1ad2-d35a-43b2-9805-2daffddbe1a7/dqc_reference/checkm_data
[2024-01-24 10:47:35,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:35,892] [INFO] Task started: CheckM
[2024-01-24 10:47:35,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339675.1_ASM433967v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339675.1_ASM433967v1_genomic.fna/checkm_input GCF_004339675.1_ASM433967v1_genomic.fna/checkm_result
[2024-01-24 10:48:12,107] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:12,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:12,135] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:12,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:12,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339675.1_ASM433967v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:12,137] [INFO] Task started: Blastn
[2024-01-24 10:48:12,137] [INFO] Running command: blastn -query GCF_004339675.1_ASM433967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf5e1ad2-d35a-43b2-9805-2daffddbe1a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339675.1_ASM433967v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:14,156] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:14,161] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:14,162] [INFO] Target genome list was writen to GCF_004339675.1_ASM433967v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:14,204] [INFO] Task started: fastANI
[2024-01-24 10:48:14,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f69fee1-37fd-4991-9c59-e69ed9186d36/GCF_004339675.1_ASM433967v1_genomic.fna.gz --refList GCF_004339675.1_ASM433967v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339675.1_ASM433967v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:21,647] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:21,660] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:21,660] [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_004339675.1	s__Rhodovulum steppense	100.0	1180	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011048875.1	s__Rhodovulum sp011048875	93.3653	635	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	91.2379	923	1187	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	85.8834	867	1187	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	84.446	844	1187	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	83.0412	795	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002079305.1	s__Rhodovulum sp002079305	80.9079	680	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	80.8503	576	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:21,662] [INFO] GTDB search result was written to GCF_004339675.1_ASM433967v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:21,662] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:21,665] [INFO] DFAST_QC result json was written to GCF_004339675.1_ASM433967v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:21,665] [INFO] DFAST_QC completed!
[2024-01-24 10:48:21,666] [INFO] Total running time: 0h1m15s