[2024-01-25 18:40:21,105] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:21,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:21,107] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0f58472-84e4-4961-b5b9-e281df0079d1/dqc_reference
[2024-01-25 18:40:22,254] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:22,255] [INFO] Task started: Prodigal
[2024-01-25 18:40:22,255] [INFO] Running command: gunzip -c /var/lib/cwl/stg91ba548c-a57a-4117-96b6-f4b91cc29df7/GCF_003544895.1_ASM354489v1_genomic.fna.gz | prodigal -d GCF_003544895.1_ASM354489v1_genomic.fna/cds.fna -a GCF_003544895.1_ASM354489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:33,562] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:33,562] [INFO] Task started: HMMsearch
[2024-01-25 18:40:33,562] [INFO] Running command: hmmsearch --tblout GCF_003544895.1_ASM354489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0f58472-84e4-4961-b5b9-e281df0079d1/dqc_reference/reference_markers.hmm GCF_003544895.1_ASM354489v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:33,816] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:33,817] [INFO] Found 6/6 markers.
[2024-01-25 18:40:33,852] [INFO] Query marker FASTA was written to GCF_003544895.1_ASM354489v1_genomic.fna/markers.fasta
[2024-01-25 18:40:33,852] [INFO] Task started: Blastn
[2024-01-25 18:40:33,852] [INFO] Running command: blastn -query GCF_003544895.1_ASM354489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0f58472-84e4-4961-b5b9-e281df0079d1/dqc_reference/reference_markers.fasta -out GCF_003544895.1_ASM354489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:34,660] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:34,664] [INFO] Selected 27 target genomes.
[2024-01-25 18:40:34,664] [INFO] Target genome list was writen to GCF_003544895.1_ASM354489v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:34,676] [INFO] Task started: fastANI
[2024-01-25 18:40:34,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg91ba548c-a57a-4117-96b6-f4b91cc29df7/GCF_003544895.1_ASM354489v1_genomic.fna.gz --refList GCF_003544895.1_ASM354489v1_genomic.fna/target_genomes.txt --output GCF_003544895.1_ASM354489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:53,543] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:53,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0f58472-84e4-4961-b5b9-e281df0079d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:53,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0f58472-84e4-4961-b5b9-e281df0079d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:53,559] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:53,559] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:53,559] [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
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	100.0	1186	1186	95	conclusive
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	77.5104	260	1186	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	77.4815	264	1186	95	below_threshold
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	77.4594	227	1186	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.4205	321	1186	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.4128	356	1186	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.3914	306	1186	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.1817	300	1186	95	below_threshold
Qingshengfaniella alkalisoli	strain=LN3S51	GCA_007855645.1	2599296	2599296	type	True	77.1752	122	1186	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.1568	265	1186	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.0982	271	1186	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	77.0978	268	1186	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.0714	252	1186	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.9963	302	1186	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.9514	225	1186	95	below_threshold
Litorivita pollutaquae	strain=FSX-11	GCA_003205515.1	2200892	2200892	type	True	76.9066	204	1186	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.9056	226	1186	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	76.8919	262	1186	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	76.8843	257	1186	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.8436	211	1186	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	76.8053	265	1186	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.7355	250	1186	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	76.6374	131	1186	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.6347	224	1186	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.6341	224	1186	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.5881	255	1186	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.2369	174	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:53,561] [INFO] DFAST Taxonomy check result was written to GCF_003544895.1_ASM354489v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:53,562] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:53,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:53,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0f58472-84e4-4961-b5b9-e281df0079d1/dqc_reference/checkm_data
[2024-01-25 18:40:53,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:53,599] [INFO] Task started: CheckM
[2024-01-25 18:40:53,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003544895.1_ASM354489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003544895.1_ASM354489v1_genomic.fna/checkm_input GCF_003544895.1_ASM354489v1_genomic.fna/checkm_result
[2024-01-25 18:41:28,234] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:28,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:28,250] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:28,250] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:28,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003544895.1_ASM354489v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:28,251] [INFO] Task started: Blastn
[2024-01-25 18:41:28,251] [INFO] Running command: blastn -query GCF_003544895.1_ASM354489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0f58472-84e4-4961-b5b9-e281df0079d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003544895.1_ASM354489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:29,702] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:29,704] [INFO] Selected 11 target genomes.
[2024-01-25 18:41:29,704] [INFO] Target genome list was writen to GCF_003544895.1_ASM354489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:29,710] [INFO] Task started: fastANI
[2024-01-25 18:41:29,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg91ba548c-a57a-4117-96b6-f4b91cc29df7/GCF_003544895.1_ASM354489v1_genomic.fna.gz --refList GCF_003544895.1_ASM354489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003544895.1_ASM354489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:38,074] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:38,081] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:38,082] [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_003544895.1	s__Profundibacter amoris	100.0	1186	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015494385.1	s__Profundibacter sp015494385	90.4845	669	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488685.1	s__Profundibacter sp015488685	89.1298	915	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002732995.1	s__Profundibacter sp002732995	80.6667	555	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352425.1	s__Profundibacter sp002352425	78.6769	499	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748285.1	s__Profundibacter sp002748285	78.4796	396	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003535335.1	s__Profundibacter sp003535335	78.0182	241	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	77.7925	349	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	77.6135	355	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCA_017792425.1	s__Thalassobius sp017792425	77.3622	294	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	76.9082	260	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:38,083] [INFO] GTDB search result was written to GCF_003544895.1_ASM354489v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:38,084] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:38,087] [INFO] DFAST_QC result json was written to GCF_003544895.1_ASM354489v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:38,087] [INFO] DFAST_QC completed!
[2024-01-25 18:41:38,087] [INFO] Total running time: 0h1m17s