[2024-01-25 19:59:50,425] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:50,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:50,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b44f7a3-aa40-46f2-8631-57c7b0d48236/dqc_reference
[2024-01-25 19:59:51,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:51,504] [INFO] Task started: Prodigal
[2024-01-25 19:59:51,504] [INFO] Running command: gunzip -c /var/lib/cwl/stgccf38f32-85a4-44e4-aad7-0baa21ec0a88/GCF_000227685.2_ASM22768v3_genomic.fna.gz | prodigal -d GCF_000227685.2_ASM22768v3_genomic.fna/cds.fna -a GCF_000227685.2_ASM22768v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:01,456] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:01,456] [INFO] Task started: HMMsearch
[2024-01-25 20:00:01,456] [INFO] Running command: hmmsearch --tblout GCF_000227685.2_ASM22768v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b44f7a3-aa40-46f2-8631-57c7b0d48236/dqc_reference/reference_markers.hmm GCF_000227685.2_ASM22768v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:01,658] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:01,659] [INFO] Found 6/6 markers.
[2024-01-25 20:00:01,687] [INFO] Query marker FASTA was written to GCF_000227685.2_ASM22768v3_genomic.fna/markers.fasta
[2024-01-25 20:00:01,687] [INFO] Task started: Blastn
[2024-01-25 20:00:01,687] [INFO] Running command: blastn -query GCF_000227685.2_ASM22768v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b44f7a3-aa40-46f2-8631-57c7b0d48236/dqc_reference/reference_markers.fasta -out GCF_000227685.2_ASM22768v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:02,497] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:02,499] [INFO] Selected 16 target genomes.
[2024-01-25 20:00:02,499] [INFO] Target genome list was writen to GCF_000227685.2_ASM22768v3_genomic.fna/target_genomes.txt
[2024-01-25 20:00:02,508] [INFO] Task started: fastANI
[2024-01-25 20:00:02,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgccf38f32-85a4-44e4-aad7-0baa21ec0a88/GCF_000227685.2_ASM22768v3_genomic.fna.gz --refList GCF_000227685.2_ASM22768v3_genomic.fna/target_genomes.txt --output GCF_000227685.2_ASM22768v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:14,235] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:14,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b44f7a3-aa40-46f2-8631-57c7b0d48236/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:14,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b44f7a3-aa40-46f2-8631-57c7b0d48236/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:14,245] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:14,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:14,246] [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
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	100.0	1252	1252	95	conclusive
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	89.7657	1005	1252	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	78.8248	314	1252	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	78.7438	317	1252	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	78.6292	314	1252	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	77.4668	133	1252	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	77.3323	128	1252	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.1963	138	1252	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	77.1094	119	1252	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	76.682	127	1252	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	76.5845	137	1252	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.3145	138	1252	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	76.2664	106	1252	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.1495	133	1252	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	76.0203	62	1252	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:14,247] [INFO] DFAST Taxonomy check result was written to GCF_000227685.2_ASM22768v3_genomic.fna/tc_result.tsv
[2024-01-25 20:00:14,247] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:14,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:14,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b44f7a3-aa40-46f2-8631-57c7b0d48236/dqc_reference/checkm_data
[2024-01-25 20:00:14,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:14,287] [INFO] Task started: CheckM
[2024-01-25 20:00:14,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000227685.2_ASM22768v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000227685.2_ASM22768v3_genomic.fna/checkm_input GCF_000227685.2_ASM22768v3_genomic.fna/checkm_result
[2024-01-25 20:00:55,066] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:55,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:55,088] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:55,089] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:55,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000227685.2_ASM22768v3_genomic.fna/markers.fasta)
[2024-01-25 20:00:55,089] [INFO] Task started: Blastn
[2024-01-25 20:00:55,089] [INFO] Running command: blastn -query GCF_000227685.2_ASM22768v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b44f7a3-aa40-46f2-8631-57c7b0d48236/dqc_reference/reference_markers_gtdb.fasta -out GCF_000227685.2_ASM22768v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:56,694] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:56,697] [INFO] Selected 11 target genomes.
[2024-01-25 20:00:56,697] [INFO] Target genome list was writen to GCF_000227685.2_ASM22768v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:56,715] [INFO] Task started: fastANI
[2024-01-25 20:00:56,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgccf38f32-85a4-44e4-aad7-0baa21ec0a88/GCF_000227685.2_ASM22768v3_genomic.fna.gz --refList GCF_000227685.2_ASM22768v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000227685.2_ASM22768v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:05,143] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:05,156] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:05,156] [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_000227685.2	s__Thioalkalivibrio_B paradoxus	100.0	1252	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000321415.2	s__Thioalkalivibrio_B nitratireducens	89.7813	1004	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003550945.1	s__Thioalkalivibrio_B sp003550945	80.5049	312	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692535.1	s__Thioalkalivibrio_B sp007692535	80.3393	489	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692435.1	s__Thioalkalivibrio_B sp007692435	80.1436	446	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003563455.1	s__Thioalkalivibrio_B sp003563455	80.0834	325	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	98.96	98.96	0.85	0.85	2	-
GCA_011389655.1	s__Thioalkalivibrio_B sp011389655	79.7968	457	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003555285.1	s__Thioalkalivibrio_B sp003555285	79.7338	407	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018224485.1	s__Thioalkalivibrio_B sp018224485	79.6963	349	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390565.1	s__Thioalkalivibrio_B paradoxus_A	79.6495	440	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133115.1	s__Thioalkalivibrio_B sp007133115	78.9312	234	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:05,163] [INFO] GTDB search result was written to GCF_000227685.2_ASM22768v3_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:05,164] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:05,167] [INFO] DFAST_QC result json was written to GCF_000227685.2_ASM22768v3_genomic.fna/dqc_result.json
[2024-01-25 20:01:05,167] [INFO] DFAST_QC completed!
[2024-01-25 20:01:05,167] [INFO] Total running time: 0h1m15s