[2024-01-25 19:46:50,557] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:50,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:50,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg100baae1-74a5-4e0b-a7ff-cfd80316cedd/dqc_reference
[2024-01-25 19:46:51,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:51,701] [INFO] Task started: Prodigal
[2024-01-25 19:46:51,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg8edcbdec-da30-4ba0-a610-7d14cca16dd5/GCF_000754095.2_ASM75409v2_genomic.fna.gz | prodigal -d GCF_000754095.2_ASM75409v2_genomic.fna/cds.fna -a GCF_000754095.2_ASM75409v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:00,717] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:00,717] [INFO] Task started: HMMsearch
[2024-01-25 19:47:00,717] [INFO] Running command: hmmsearch --tblout GCF_000754095.2_ASM75409v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg100baae1-74a5-4e0b-a7ff-cfd80316cedd/dqc_reference/reference_markers.hmm GCF_000754095.2_ASM75409v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:00,910] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:00,911] [INFO] Found 6/6 markers.
[2024-01-25 19:47:00,936] [INFO] Query marker FASTA was written to GCF_000754095.2_ASM75409v2_genomic.fna/markers.fasta
[2024-01-25 19:47:00,936] [INFO] Task started: Blastn
[2024-01-25 19:47:00,936] [INFO] Running command: blastn -query GCF_000754095.2_ASM75409v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg100baae1-74a5-4e0b-a7ff-cfd80316cedd/dqc_reference/reference_markers.fasta -out GCF_000754095.2_ASM75409v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:01,735] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:01,738] [INFO] Selected 24 target genomes.
[2024-01-25 19:47:01,738] [INFO] Target genome list was writen to GCF_000754095.2_ASM75409v2_genomic.fna/target_genomes.txt
[2024-01-25 19:47:01,753] [INFO] Task started: fastANI
[2024-01-25 19:47:01,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg8edcbdec-da30-4ba0-a610-7d14cca16dd5/GCF_000754095.2_ASM75409v2_genomic.fna.gz --refList GCF_000754095.2_ASM75409v2_genomic.fna/target_genomes.txt --output GCF_000754095.2_ASM75409v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:18,137] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:18,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg100baae1-74a5-4e0b-a7ff-cfd80316cedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:18,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg100baae1-74a5-4e0b-a7ff-cfd80316cedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:18,151] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:18,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:18,151] [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
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	100.0	1111	1116	95	conclusive
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	85.6267	677	1116	95	below_threshold
Acidihalobacter yilgarnensis	strain=F5	GCA_001753245.1	2819280	2819280	type	True	81.6043	731	1116	95	below_threshold
Acidihalobacter ferrooxydans	strain=V8	GCA_001975725.1	1765967	1765967	type	True	78.5686	316	1116	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.8654	209	1116	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	77.6378	158	1116	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.1018	190	1116	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	77.0182	164	1116	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.9134	135	1116	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.9072	163	1116	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.8746	217	1116	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.8577	124	1116	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.8147	163	1116	95	below_threshold
Wenzhouxiangella sediminis	strain=XDB06	GCA_003410055.1	1792836	1792836	type	True	76.6673	101	1116	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.6499	159	1116	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	76.586	120	1116	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	76.5736	172	1116	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	76.4924	143	1116	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.3501	171	1116	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.2831	173	1116	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	76.2003	106	1116	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	76.179	96	1116	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	75.9714	133	1116	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	75.9272	120	1116	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:18,153] [INFO] DFAST Taxonomy check result was written to GCF_000754095.2_ASM75409v2_genomic.fna/tc_result.tsv
[2024-01-25 19:47:18,153] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:18,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:18,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg100baae1-74a5-4e0b-a7ff-cfd80316cedd/dqc_reference/checkm_data
[2024-01-25 19:47:18,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:18,187] [INFO] Task started: CheckM
[2024-01-25 19:47:18,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000754095.2_ASM75409v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000754095.2_ASM75409v2_genomic.fna/checkm_input GCF_000754095.2_ASM75409v2_genomic.fna/checkm_result
[2024-01-25 19:47:47,852] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:47,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:47,874] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:47,874] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:47,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000754095.2_ASM75409v2_genomic.fna/markers.fasta)
[2024-01-25 19:47:47,875] [INFO] Task started: Blastn
[2024-01-25 19:47:47,875] [INFO] Running command: blastn -query GCF_000754095.2_ASM75409v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg100baae1-74a5-4e0b-a7ff-cfd80316cedd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000754095.2_ASM75409v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:49,344] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:49,347] [INFO] Selected 19 target genomes.
[2024-01-25 19:47:49,347] [INFO] Target genome list was writen to GCF_000754095.2_ASM75409v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:49,365] [INFO] Task started: fastANI
[2024-01-25 19:47:49,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg8edcbdec-da30-4ba0-a610-7d14cca16dd5/GCF_000754095.2_ASM75409v2_genomic.fna.gz --refList GCF_000754095.2_ASM75409v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000754095.2_ASM75409v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:59,861] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:59,873] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:59,873] [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_000754095.2	s__Acidihalobacter prosperus	100.0	1111	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001753165.1	s__Acidihalobacter aeolianus	85.6265	677	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001753245.1	s__Acidihalobacter yilgarnenesis	81.604	729	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975725.1	s__Acidihalobacter_A ferrooxydans	78.5691	317	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.9069	251	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	77.8614	210	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696465.1	s__J044 sp003696465	77.3125	113	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J044;f__J044;g__J044	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025545.1	s__Thioalkalivibrio sp000025545	77.0698	144	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.34	97.34	0.93	0.93	2	-
GCF_000633935.1	s__Ectothiorhodospira haloalkaliphila	77.0529	105	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	99.86	99.86	0.97	0.97	2	-
GCF_001632845.1	s__Ectothiorhodospira sp001632845	76.963	113	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	99.06	99.06	0.98	0.98	2	-
GCA_011321775.1	s__Thiogranum sp011321775	76.8796	149	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695825.1	s__J048 sp003695825	76.8551	122	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	76.673	139	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	76.669	148	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.6373	186	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_016182805.1	s__JACPFV01 sp016182805	76.4964	106	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__JACPFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001872285.1	s__CG2-30-68-42 sp001872285	76.0824	98	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CG2-30-68-42	95.0	99.75	99.70	0.94	0.93	3	-
GCA_012523465.1	s__JAAYIK01 sp012523465	76.0687	134	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__JAAYIK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344355.1	s__Pseudofulvimonas sp002344355	75.8867	138	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__UBA2363;g__Pseudofulvimonas	95.0	99.95	99.95	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:59,874] [INFO] GTDB search result was written to GCF_000754095.2_ASM75409v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:59,875] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:59,878] [INFO] DFAST_QC result json was written to GCF_000754095.2_ASM75409v2_genomic.fna/dqc_result.json
[2024-01-25 19:47:59,879] [INFO] DFAST_QC completed!
[2024-01-25 19:47:59,879] [INFO] Total running time: 0h1m9s