[2024-01-24 13:49:55,702] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg120dce31-39fd-4068-b77f-ce631a91d110/dqc_reference
[2024-01-24 13:49:57,066] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:57,067] [INFO] Task started: Prodigal
[2024-01-24 13:49:57,067] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7a56fc6-dde5-48a5-b046-49b1247eec4c/GCF_009857745.1_ASM985774v1_genomic.fna.gz | prodigal -d GCF_009857745.1_ASM985774v1_genomic.fna/cds.fna -a GCF_009857745.1_ASM985774v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:09,555] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:09,556] [INFO] Task started: HMMsearch
[2024-01-24 13:50:09,556] [INFO] Running command: hmmsearch --tblout GCF_009857745.1_ASM985774v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg120dce31-39fd-4068-b77f-ce631a91d110/dqc_reference/reference_markers.hmm GCF_009857745.1_ASM985774v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:09,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:09,855] [INFO] Found 6/6 markers.
[2024-01-24 13:50:09,895] [INFO] Query marker FASTA was written to GCF_009857745.1_ASM985774v1_genomic.fna/markers.fasta
[2024-01-24 13:50:09,895] [INFO] Task started: Blastn
[2024-01-24 13:50:09,895] [INFO] Running command: blastn -query GCF_009857745.1_ASM985774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg120dce31-39fd-4068-b77f-ce631a91d110/dqc_reference/reference_markers.fasta -out GCF_009857745.1_ASM985774v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:10,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:10,847] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:10,847] [INFO] Target genome list was writen to GCF_009857745.1_ASM985774v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:10,853] [INFO] Task started: fastANI
[2024-01-24 13:50:10,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7a56fc6-dde5-48a5-b046-49b1247eec4c/GCF_009857745.1_ASM985774v1_genomic.fna.gz --refList GCF_009857745.1_ASM985774v1_genomic.fna/target_genomes.txt --output GCF_009857745.1_ASM985774v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:26,107] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:26,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg120dce31-39fd-4068-b77f-ce631a91d110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:26,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg120dce31-39fd-4068-b77f-ce631a91d110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:26,121] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:26,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:26,121] [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
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	100.0	1371	1372	95	conclusive
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	88.893	1058	1372	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	82.5144	888	1372	95	below_threshold
Thalassobius gelatinovorus	strain=CECT 4357	GCA_001458355.1	53501	53501	type	True	82.4177	883	1372	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.5479	564	1372	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.3792	535	1372	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	79.164	631	1372	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	79.066	525	1372	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	79.0458	523	1372	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.9958	490	1372	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.9694	574	1372	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.9354	625	1372	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.9067	567	1372	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.6555	532	1372	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.3302	463	1372	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.0274	390	1372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:26,123] [INFO] DFAST Taxonomy check result was written to GCF_009857745.1_ASM985774v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:26,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:26,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:26,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg120dce31-39fd-4068-b77f-ce631a91d110/dqc_reference/checkm_data
[2024-01-24 13:50:26,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:26,167] [INFO] Task started: CheckM
[2024-01-24 13:50:26,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009857745.1_ASM985774v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009857745.1_ASM985774v1_genomic.fna/checkm_input GCF_009857745.1_ASM985774v1_genomic.fna/checkm_result
[2024-01-24 13:51:04,820] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:04,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:04,839] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:04,839] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:04,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009857745.1_ASM985774v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:04,840] [INFO] Task started: Blastn
[2024-01-24 13:51:04,840] [INFO] Running command: blastn -query GCF_009857745.1_ASM985774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg120dce31-39fd-4068-b77f-ce631a91d110/dqc_reference/reference_markers_gtdb.fasta -out GCF_009857745.1_ASM985774v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:06,352] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:06,355] [INFO] Selected 14 target genomes.
[2024-01-24 13:51:06,355] [INFO] Target genome list was writen to GCF_009857745.1_ASM985774v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:06,375] [INFO] Task started: fastANI
[2024-01-24 13:51:06,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7a56fc6-dde5-48a5-b046-49b1247eec4c/GCF_009857745.1_ASM985774v1_genomic.fna.gz --refList GCF_009857745.1_ASM985774v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009857745.1_ASM985774v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:17,711] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:17,726] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:17,726] [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_009857745.1	s__Thalassobius mangrovi	100.0	1371	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018219815.1	s__Thalassobius aquimarinus	88.8907	1058	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458355.1	s__Thalassobius gelatinovorus	82.44	882	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	99.99	0.99	0.99	3	-
GCF_004799325.1	s__Thalassobius vesicularis	80.9368	730	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	80.7667	629	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	79.6376	594	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.5612	515	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900129345.1	s__Ruegeria intermedia	79.5479	564	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	79.5153	547	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	79.3794	535	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	79.1713	630	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	79.1227	587	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458435.1	s__Thalassobius mediterraneus	79.074	525	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.9438	407	1372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:17,728] [INFO] GTDB search result was written to GCF_009857745.1_ASM985774v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:17,729] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:17,732] [INFO] DFAST_QC result json was written to GCF_009857745.1_ASM985774v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:17,732] [INFO] DFAST_QC completed!
[2024-01-24 13:51:17,733] [INFO] Total running time: 0h1m22s