[2024-01-24 10:57:12,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:12,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:12,616] [INFO] DQC Reference Directory: /var/lib/cwl/stge94a9ad2-e769-4b93-aaaa-0bf9c608664d/dqc_reference
[2024-01-24 10:57:14,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,180] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,180] [INFO] Running command: gunzip -c /var/lib/cwl/stg9956b503-417a-4095-9746-65eab247e0f8/GCF_003265965.1_ASM326596v1_genomic.fna.gz | prodigal -d GCF_003265965.1_ASM326596v1_genomic.fna/cds.fna -a GCF_003265965.1_ASM326596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:26,515] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:26,515] [INFO] Task started: HMMsearch
[2024-01-24 10:57:26,515] [INFO] Running command: hmmsearch --tblout GCF_003265965.1_ASM326596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge94a9ad2-e769-4b93-aaaa-0bf9c608664d/dqc_reference/reference_markers.hmm GCF_003265965.1_ASM326596v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:26,848] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:26,849] [INFO] Found 6/6 markers.
[2024-01-24 10:57:26,891] [INFO] Query marker FASTA was written to GCF_003265965.1_ASM326596v1_genomic.fna/markers.fasta
[2024-01-24 10:57:26,891] [INFO] Task started: Blastn
[2024-01-24 10:57:26,891] [INFO] Running command: blastn -query GCF_003265965.1_ASM326596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge94a9ad2-e769-4b93-aaaa-0bf9c608664d/dqc_reference/reference_markers.fasta -out GCF_003265965.1_ASM326596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:28,095] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:28,098] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:28,099] [INFO] Target genome list was writen to GCF_003265965.1_ASM326596v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:28,101] [INFO] Task started: fastANI
[2024-01-24 10:57:28,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg9956b503-417a-4095-9746-65eab247e0f8/GCF_003265965.1_ASM326596v1_genomic.fna.gz --refList GCF_003265965.1_ASM326596v1_genomic.fna/target_genomes.txt --output GCF_003265965.1_ASM326596v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:41,240] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:41,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge94a9ad2-e769-4b93-aaaa-0bf9c608664d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:41,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge94a9ad2-e769-4b93-aaaa-0bf9c608664d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:41,256] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:41,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:41,257] [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 visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	94.4823	1238	1433	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	88.5837	1070	1433	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	88.5328	1073	1433	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	82.1805	751	1433	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	82.1327	744	1433	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	82.1128	737	1433	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	81.937	807	1433	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	81.8353	796	1433	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	80.8469	643	1433	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	80.7307	645	1433	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.1085	544	1433	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.2877	453	1433	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.9596	394	1433	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.92	396	1433	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7868	387	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:41,258] [INFO] DFAST Taxonomy check result was written to GCF_003265965.1_ASM326596v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:41,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:41,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:41,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge94a9ad2-e769-4b93-aaaa-0bf9c608664d/dqc_reference/checkm_data
[2024-01-24 10:57:41,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:41,309] [INFO] Task started: CheckM
[2024-01-24 10:57:41,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003265965.1_ASM326596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003265965.1_ASM326596v1_genomic.fna/checkm_input GCF_003265965.1_ASM326596v1_genomic.fna/checkm_result
[2024-01-24 10:58:23,654] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:23,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:23,679] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:23,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:23,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003265965.1_ASM326596v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:23,680] [INFO] Task started: Blastn
[2024-01-24 10:58:23,680] [INFO] Running command: blastn -query GCF_003265965.1_ASM326596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge94a9ad2-e769-4b93-aaaa-0bf9c608664d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003265965.1_ASM326596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:25,770] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:25,774] [INFO] Selected 8 target genomes.
[2024-01-24 10:58:25,774] [INFO] Target genome list was writen to GCF_003265965.1_ASM326596v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:25,778] [INFO] Task started: fastANI
[2024-01-24 10:58:25,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg9956b503-417a-4095-9746-65eab247e0f8/GCF_003265965.1_ASM326596v1_genomic.fna.gz --refList GCF_003265965.1_ASM326596v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003265965.1_ASM326596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:33,957] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:33,964] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:33,965] [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_003053725.1	s__Rhodovulum kholense	98.2497	1380	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	conclusive
GCF_004365965.1	s__Rhodovulum visakhapatnamense	94.4948	1237	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	88.5241	1074	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_002073975.1	s__Rhodovulum sp002073975	88.5099	1057	1433	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	82.0703	742	1433	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	81.9433	806	1433	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	81.8347	795	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	80.8073	647	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:33,966] [INFO] GTDB search result was written to GCF_003265965.1_ASM326596v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:33,967] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:33,970] [INFO] DFAST_QC result json was written to GCF_003265965.1_ASM326596v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:33,970] [INFO] DFAST_QC completed!
[2024-01-24 10:58:33,971] [INFO] Total running time: 0h1m21s