[2024-01-24 10:47:06,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg1681977c-ce8d-4792-9a44-8207b84ede70/dqc_reference
[2024-01-24 10:47:12,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,799] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,800] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a54025d-ab23-40d1-b2ce-7f80b9b090d3/GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna.gz | prodigal -d GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/cds.fna -a GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,968] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,968] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,968] [INFO] Running command: hmmsearch --tblout GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1681977c-ce8d-4792-9a44-8207b84ede70/dqc_reference/reference_markers.hmm GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,242] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,243] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,284] [INFO] Query marker FASTA was written to GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/markers.fasta
[2024-01-24 10:47:22,284] [INFO] Task started: Blastn
[2024-01-24 10:47:22,284] [INFO] Running command: blastn -query GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/markers.fasta -db /var/lib/cwl/stg1681977c-ce8d-4792-9a44-8207b84ede70/dqc_reference/reference_markers.fasta -out GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:23,038] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:23,043] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:23,043] [INFO] Target genome list was writen to GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/target_genomes.txt
[2024-01-24 10:47:24,297] [INFO] Task started: fastANI
[2024-01-24 10:47:24,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a54025d-ab23-40d1-b2ce-7f80b9b090d3/GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna.gz --refList GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/target_genomes.txt --output GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:37,448] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:37,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1681977c-ce8d-4792-9a44-8207b84ede70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:37,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1681977c-ce8d-4792-9a44-8207b84ede70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:37,465] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:47:37,466] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:37,466] [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
Nereida ignava	strain=CECT 5292	GCA_001404155.1	282199	282199	type	True	100.0	925	929	95	conclusive
Nereida ignava	strain=CECT 5292	GCA_001049735.1	282199	282199	type	True	99.9998	925	929	95	conclusive
Nereida ignava	strain=DSM 16309	GCA_900114125.1	282199	282199	type	True	99.976	912	929	95	conclusive
Thalassobacter stenotrophicus	strain=DSM 16310	GCA_900141945.1	266809	266809	type	True	82.1295	133	929	95	below_threshold
Thalassobacter stenotrophicus	strain=CECT 5294	GCA_001458315.1	266809	266809	type	True	82.0858	136	929	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	78.7571	107	929	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	77.3843	107	929	95	below_threshold
Cochlodiniinecator piscidefendens	strain=M26A2M	GCA_011326755.1	2715756	2715756	type	True	77.3277	72	929	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.1039	100	929	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.0083	98	929	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	76.9049	51	929	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.8992	93	929	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.6044	88	929	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	76.5987	121	929	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.1397	50	929	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	76.1202	60	929	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	75.6964	59	929	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:37,467] [INFO] DFAST Taxonomy check result was written to GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/tc_result.tsv
[2024-01-24 10:47:37,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:37,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:37,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1681977c-ce8d-4792-9a44-8207b84ede70/dqc_reference/checkm_data
[2024-01-24 10:47:37,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:37,498] [INFO] Task started: CheckM
[2024-01-24 10:47:37,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/checkm_input GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/checkm_result
[2024-01-24 10:48:09,811] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:09,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,833] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:09,833] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:09,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/markers.fasta)
[2024-01-24 10:48:09,834] [INFO] Task started: Blastn
[2024-01-24 10:48:09,834] [INFO] Running command: blastn -query GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/markers.fasta -db /var/lib/cwl/stg1681977c-ce8d-4792-9a44-8207b84ede70/dqc_reference/reference_markers_gtdb.fasta -out GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:11,125] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:11,130] [INFO] Selected 27 target genomes.
[2024-01-24 10:48:11,130] [INFO] Target genome list was writen to GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:11,167] [INFO] Task started: fastANI
[2024-01-24 10:48:11,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a54025d-ab23-40d1-b2ce-7f80b9b090d3/GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna.gz --refList GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/target_genomes_gtdb.txt --output GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:27,968] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:27,995] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:27,996] [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_001049735.1	s__Nereida ignava	99.9998	925	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nereida	95.0	99.99	99.98	0.99	0.99	3	conclusive
GCF_001458315.1	s__Thalassobacter stenotrophicus	82.1417	135	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobacter	95.0	98.03	96.21	0.91	0.88	5	-
GCF_001458255.1	s__Thalassobius autumnalis	78.7571	107	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001890925.1	s__Planktotalea frisia	77.5106	113	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.35	98.99	0.94	0.89	4	-
GCF_900143545.1	s__Yoonia sp900143545	77.468	99	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	77.4023	80	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326755.1	s__Halocynthiibacter sp011326755	77.2552	73	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850435.1	s__Marivivens zhoushanense	77.1847	84	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	77.1106	119	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003003285.1	s__Yoonia maritima	77.1039	100	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161835.1	s__R2A62 sp000161835	77.0369	137	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__R2A62	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622325.1	s__Sulfitobacter geojensis	76.9374	97	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_900111875.1	s__Poseidonocella pacifica	76.9048	51	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	76.7526	69	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115105.1	s__Yoonia tamlensis	76.6305	121	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	76.6299	87	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	76.621	73	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCA_000472185.1	s__HIMB11 sp000472185	76.427	63	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923355.1	s__Phaeobacter_A marinintestinus	76.4225	91	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771405.1	s__Parasedimentitalea marina_A	76.4213	72	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	97.09	97.09	0.92	0.92	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	76.2711	93	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854855.1	s__Sulfitobacter sp017854855	76.172	78	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129875.1	s__Marivita hallyeonensis	76.1202	60	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214665.1	s__JABSSA01 sp013214665	75.9746	70	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854675.1	s__Sulfitobacter sp017854675	75.9515	66	929	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:27,997] [INFO] GTDB search result was written to GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:27,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:28,002] [INFO] DFAST_QC result json was written to GCF_001404155.1_N.ignavaCECT5292_PROKKA_genomic.fna/dqc_result.json
[2024-01-24 10:48:28,003] [INFO] DFAST_QC completed!
[2024-01-24 10:48:28,003] [INFO] Total running time: 0h1m21s