[2024-01-25 17:44:35,750] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:35,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:35,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg30e64ddc-d1e8-4cb4-bf9d-bc8d5c56ef9d/dqc_reference
[2024-01-25 17:44:36,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:36,897] [INFO] Task started: Prodigal
[2024-01-25 17:44:36,897] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfb84c70-3f65-4158-9890-08c291db43c8/GCF_003206495.1_ASM320649v1_genomic.fna.gz | prodigal -d GCF_003206495.1_ASM320649v1_genomic.fna/cds.fna -a GCF_003206495.1_ASM320649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:46,968] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:46,968] [INFO] Task started: HMMsearch
[2024-01-25 17:44:46,968] [INFO] Running command: hmmsearch --tblout GCF_003206495.1_ASM320649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30e64ddc-d1e8-4cb4-bf9d-bc8d5c56ef9d/dqc_reference/reference_markers.hmm GCF_003206495.1_ASM320649v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:47,165] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:47,166] [INFO] Found 6/6 markers.
[2024-01-25 17:44:47,195] [INFO] Query marker FASTA was written to GCF_003206495.1_ASM320649v1_genomic.fna/markers.fasta
[2024-01-25 17:44:47,195] [INFO] Task started: Blastn
[2024-01-25 17:44:47,195] [INFO] Running command: blastn -query GCF_003206495.1_ASM320649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30e64ddc-d1e8-4cb4-bf9d-bc8d5c56ef9d/dqc_reference/reference_markers.fasta -out GCF_003206495.1_ASM320649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:47,916] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:47,919] [INFO] Selected 16 target genomes.
[2024-01-25 17:44:47,920] [INFO] Target genome list was writen to GCF_003206495.1_ASM320649v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:47,925] [INFO] Task started: fastANI
[2024-01-25 17:44:47,925] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb84c70-3f65-4158-9890-08c291db43c8/GCF_003206495.1_ASM320649v1_genomic.fna.gz --refList GCF_003206495.1_ASM320649v1_genomic.fna/target_genomes.txt --output GCF_003206495.1_ASM320649v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:58,867] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:58,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30e64ddc-d1e8-4cb4-bf9d-bc8d5c56ef9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:58,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30e64ddc-d1e8-4cb4-bf9d-bc8d5c56ef9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:58,874] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:44:58,874] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:44:58,874] [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
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	92.5092	923	1127	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	92.4815	948	1127	95	below_threshold
Novacetimonas hansenii	strain=NBRC 14820	GCA_006539705.1	436	436	type	True	87.2568	782	1127	95	below_threshold
Novacetimonas hansenii	strain=JCM 7643	GCA_000964405.1	436	436	type	True	87.1558	765	1127	95	below_threshold
Novacetimonas pomaceti	strain=T5K1	GCA_003207955.1	2021998	2021998	type	True	86.3766	828	1127	95	below_threshold
Novacetimonas cocois	strain=WE7	GCA_003311635.1	1747507	1747507	type	True	86.3177	843	1127	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.6823	156	1127	95	below_threshold
Roseomonas arctica	strain=LMG 28251	GCA_018128965.1	1509237	1509237	type	True	76.6713	118	1127	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	75.907	63	1127	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:58,876] [INFO] DFAST Taxonomy check result was written to GCF_003206495.1_ASM320649v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:58,876] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:58,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:58,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30e64ddc-d1e8-4cb4-bf9d-bc8d5c56ef9d/dqc_reference/checkm_data
[2024-01-25 17:44:58,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:58,914] [INFO] Task started: CheckM
[2024-01-25 17:44:58,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003206495.1_ASM320649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003206495.1_ASM320649v1_genomic.fna/checkm_input GCF_003206495.1_ASM320649v1_genomic.fna/checkm_result
[2024-01-25 17:45:35,527] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:35,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:35,548] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:35,549] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:35,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003206495.1_ASM320649v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:35,549] [INFO] Task started: Blastn
[2024-01-25 17:45:35,549] [INFO] Running command: blastn -query GCF_003206495.1_ASM320649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30e64ddc-d1e8-4cb4-bf9d-bc8d5c56ef9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003206495.1_ASM320649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:36,931] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:36,934] [INFO] Selected 12 target genomes.
[2024-01-25 17:45:36,934] [INFO] Target genome list was writen to GCF_003206495.1_ASM320649v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:36,946] [INFO] Task started: fastANI
[2024-01-25 17:45:36,947] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb84c70-3f65-4158-9890-08c291db43c8/GCF_003206495.1_ASM320649v1_genomic.fna.gz --refList GCF_003206495.1_ASM320649v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003206495.1_ASM320649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:47,771] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:47,779] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:47,779] [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_003206495.1	s__Komagataeibacter entanii	100.0	1121	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.26	98.23	0.88	0.87	3	conclusive
GCF_002906255.1	s__Komagataeibacter maltaceti	92.5092	923	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.99	99.99	0.97	0.97	2	-
GCF_000964405.1	s__Komagataeibacter hansenii	87.1533	766	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.02	97.76	0.88	0.75	12	-
GCF_003311635.1	s__Komagataeibacter cocois	86.3092	844	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	95.20	95.16	0.89	0.89	4	-
GCF_003207895.1	s__Komagataeibacter swingsii	82.4126	641	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	-
GCF_014199155.1	s__Komagataeibacter kakiaceti	82.1412	607	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.94	99.94	1.00	1.00	2	-
GCF_000964425.1	s__Komagataeibacter intermedius	81.4578	590	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_003207855.1	s__Komagataeibacter rhaeticus	81.3531	611	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.08	98.72	0.93	0.91	8	-
GCF_003207825.1	s__Komagataeibacter saccharivorans	80.97	560	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.47	98.42	0.92	0.87	4	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	79.5815	479	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_018128965.1	s__Roseomonas_C arctica	76.6532	119	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:47,782] [INFO] GTDB search result was written to GCF_003206495.1_ASM320649v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:47,782] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:47,790] [INFO] DFAST_QC result json was written to GCF_003206495.1_ASM320649v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:47,790] [INFO] DFAST_QC completed!
[2024-01-25 17:45:47,790] [INFO] Total running time: 0h1m12s