[2024-01-24 10:57:26,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,755] [INFO] DQC Reference Directory: /var/lib/cwl/stga8a53f53-bdff-4bc1-858f-a5581a45a729/dqc_reference
[2024-01-24 10:57:28,163] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,164] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ba9ecab-8442-4201-8e38-81877f8cf538/GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/cds.fna -a GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:39,959] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:39,959] [INFO] Task started: HMMsearch
[2024-01-24 10:57:39,959] [INFO] Running command: hmmsearch --tblout GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8a53f53-bdff-4bc1-858f-a5581a45a729/dqc_reference/reference_markers.hmm GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:40,238] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:40,239] [INFO] Found 6/6 markers.
[2024-01-24 10:57:40,276] [INFO] Query marker FASTA was written to GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:57:40,276] [INFO] Task started: Blastn
[2024-01-24 10:57:40,276] [INFO] Running command: blastn -query GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga8a53f53-bdff-4bc1-858f-a5581a45a729/dqc_reference/reference_markers.fasta -out GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:41,019] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:41,022] [INFO] Selected 30 target genomes.
[2024-01-24 10:57:41,023] [INFO] Target genome list was writen to GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:57:41,054] [INFO] Task started: fastANI
[2024-01-24 10:57:41,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba9ecab-8442-4201-8e38-81877f8cf538/GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna.gz --refList GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:04,981] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:04,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8a53f53-bdff-4bc1-858f-a5581a45a729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:04,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8a53f53-bdff-4bc1-858f-a5581a45a729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:05,003] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:05,003] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:05,004] [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
Arboricoccus pini	strain=B29T1	GCA_900187945.1	1963835	1963835	type	True	100.0	1342	1343	95	conclusive
Geminicoccus roseus	strain=DSM 18922	GCA_000427665.1	404900	404900	type	True	76.4818	180	1343	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.3321	97	1343	95	below_threshold
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	76.1953	89	1343	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	75.9974	98	1343	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.9471	111	1343	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	75.884	54	1343	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	75.8747	56	1343	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.8726	120	1343	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.8632	126	1343	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.8618	63	1343	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.8136	106	1343	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.7673	75	1343	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	75.7633	103	1343	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_003201475.1	28210	28210	type	True	75.7463	87	1343	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_018398275.1	28210	28210	type	True	75.7341	85	1343	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	75.7138	112	1343	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.6813	84	1343	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.6798	115	1343	95	below_threshold
Paracoccus contaminans	strain=RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	GCA_002105555.1	1945662	1945662	type	True	75.6285	54	1343	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.6141	82	1343	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.6126	137	1343	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.557	138	1343	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	75.4716	69	1343	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	75.446	106	1343	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	75.3835	101	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:05,005] [INFO] DFAST Taxonomy check result was written to GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:58:05,006] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:05,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:05,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8a53f53-bdff-4bc1-858f-a5581a45a729/dqc_reference/checkm_data
[2024-01-24 10:58:05,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:05,051] [INFO] Task started: CheckM
[2024-01-24 10:58:05,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/checkm_input GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:58:42,345] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:42,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:42,365] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:42,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:42,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:58:42,366] [INFO] Task started: Blastn
[2024-01-24 10:58:42,366] [INFO] Running command: blastn -query GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga8a53f53-bdff-4bc1-858f-a5581a45a729/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:43,450] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:43,453] [INFO] Selected 26 target genomes.
[2024-01-24 10:58:43,453] [INFO] Target genome list was writen to GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:43,488] [INFO] Task started: fastANI
[2024-01-24 10:58:43,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba9ecab-8442-4201-8e38-81877f8cf538/GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna.gz --refList GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:01,743] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:01,762] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:01,762] [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_900187945.1	s__Arboricoccus pini	100.0	1342	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Arboricoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007131045.1	s__SLRI01 sp007131045	76.5078	114	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427665.1	s__Geminicoccus roseus	76.4702	181	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Geminicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390475.1	s__SLRI01 sp011390475	76.2892	125	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363955.1	s__Enterovirga rhinocerotis	76.1953	89	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	76.1725	74	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104485.1	s__Bauldia litoralis	75.9678	100	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971455.1	s__REEB85 sp018971455	75.929	60	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908425.1	s__JAAAPF01 sp009908425	75.9206	94	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__JAAAPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826935.1	s__CADEGR01 sp902826935	75.8626	155	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__CADEGR01	95.0	98.81	98.69	0.93	0.92	4	-
GCA_002898275.1	s__HRBIN40 sp002898275	75.7981	87	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__HRBIN40	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	75.7688	101	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201475.1	s__Chelatococcus asaccharovorans	75.7309	88	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014640615.1	s__Paramesorhizobium endophyticum	75.6966	73	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142875.1	s__Paracoccus solventivorans	75.6812	66	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.61	95.99	0.87	0.87	3	-
GCF_001509835.1	s__Bosea sp001509835	75.6688	123	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003012705.1	s__Pseudaminobacter soli	75.667	87	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105555.1	s__Paracoccus contaminans	75.6285	54	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	75.6151	104	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	75.5955	154	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970625.1	s__CAJCJG01 sp903970625	75.5704	77	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAJCJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222815.1	s__Roseomonas_A sp005222815	75.5238	99	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	75.4804	61	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	75.446	106	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:01,764] [INFO] GTDB search result was written to GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:01,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:01,769] [INFO] DFAST_QC result json was written to GCF_900187945.1_IMG-taxon_2693429500_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:59:01,769] [INFO] DFAST_QC completed!
[2024-01-24 10:59:01,769] [INFO] Total running time: 0h1m35s