[2024-01-24 12:06:10,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:10,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:10,395] [INFO] DQC Reference Directory: /var/lib/cwl/stgf25e4d8a-0b1a-4d25-9776-9bedb78bbd6e/dqc_reference
[2024-01-24 12:06:13,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,248] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg52a41e4c-5ac6-455b-b181-34d4f8442568/GCF_001456895.1_ASM145689v1_genomic.fna.gz | prodigal -d GCF_001456895.1_ASM145689v1_genomic.fna/cds.fna -a GCF_001456895.1_ASM145689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:21,922] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:21,922] [INFO] Task started: HMMsearch
[2024-01-24 12:06:21,922] [INFO] Running command: hmmsearch --tblout GCF_001456895.1_ASM145689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf25e4d8a-0b1a-4d25-9776-9bedb78bbd6e/dqc_reference/reference_markers.hmm GCF_001456895.1_ASM145689v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:22,231] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:22,233] [INFO] Found 6/6 markers.
[2024-01-24 12:06:22,266] [INFO] Query marker FASTA was written to GCF_001456895.1_ASM145689v1_genomic.fna/markers.fasta
[2024-01-24 12:06:22,267] [INFO] Task started: Blastn
[2024-01-24 12:06:22,267] [INFO] Running command: blastn -query GCF_001456895.1_ASM145689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf25e4d8a-0b1a-4d25-9776-9bedb78bbd6e/dqc_reference/reference_markers.fasta -out GCF_001456895.1_ASM145689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:22,889] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:22,892] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:22,893] [INFO] Target genome list was writen to GCF_001456895.1_ASM145689v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:22,911] [INFO] Task started: fastANI
[2024-01-24 12:06:22,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg52a41e4c-5ac6-455b-b181-34d4f8442568/GCF_001456895.1_ASM145689v1_genomic.fna.gz --refList GCF_001456895.1_ASM145689v1_genomic.fna/target_genomes.txt --output GCF_001456895.1_ASM145689v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:32,747] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:32,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf25e4d8a-0b1a-4d25-9776-9bedb78bbd6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:32,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf25e4d8a-0b1a-4d25-9776-9bedb78bbd6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:32,757] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:06:32,757] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:06:32,757] [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
Exiguobacterium enclense	strain=NIO-1109	GCA_900096925.1	1017277	1017277	type	True	100.0	1078	1079	95	inconclusive
Exiguobacterium enclense	strain=NIO-1109	GCA_001456895.1	1017277	1017277	type	True	100.0	1078	1079	95	inconclusive
Exiguobacterium indicum	strain=HHS 31	GCA_001939065.1	296995	296995	type	True	97.8851	1021	1079	95	inconclusive
Exiguobacterium acetylicum	strain=DSM 20416	GCA_000702605.1	41170	41170	suspected-type	True	94.0386	960	1079	95	below_threshold
Exiguobacterium oxidotolerans	strain=JCM 12280	GCA_000702625.1	223958	223958	type	True	81.2239	558	1079	95	below_threshold
Exiguobacterium undae	strain=DSM 14481	GCA_000620805.1	169177	169177	type	True	81.1092	583	1079	95	below_threshold
Exiguobacterium artemiae	strain=9AN	GCA_025234645.1	340145	340145	type	True	80.8876	540	1079	95	below_threshold
Exiguobacterium flavidum	strain=HF60	GCA_003344535.1	2184695	2184695	type	True	79.1215	309	1079	95	below_threshold
Exiguobacterium aestuarii	strain=TF_16	GCA_025234735.1	273527	273527	type	True	77.3577	137	1079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:32,759] [INFO] DFAST Taxonomy check result was written to GCF_001456895.1_ASM145689v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:32,762] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:32,762] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:32,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf25e4d8a-0b1a-4d25-9776-9bedb78bbd6e/dqc_reference/checkm_data
[2024-01-24 12:06:32,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:32,812] [INFO] Task started: CheckM
[2024-01-24 12:06:32,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001456895.1_ASM145689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001456895.1_ASM145689v1_genomic.fna/checkm_input GCF_001456895.1_ASM145689v1_genomic.fna/checkm_result
[2024-01-24 12:07:05,897] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:05,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:05,931] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:05,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:05,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001456895.1_ASM145689v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:05,933] [INFO] Task started: Blastn
[2024-01-24 12:07:05,933] [INFO] Running command: blastn -query GCF_001456895.1_ASM145689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf25e4d8a-0b1a-4d25-9776-9bedb78bbd6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001456895.1_ASM145689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:06,724] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:06,727] [INFO] Selected 9 target genomes.
[2024-01-24 12:07:06,727] [INFO] Target genome list was writen to GCF_001456895.1_ASM145689v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:06,749] [INFO] Task started: fastANI
[2024-01-24 12:07:06,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg52a41e4c-5ac6-455b-b181-34d4f8442568/GCF_001456895.1_ASM145689v1_genomic.fna.gz --refList GCF_001456895.1_ASM145689v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001456895.1_ASM145689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:13,568] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:13,584] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:13,584] [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_001939065.1	s__Exiguobacterium_A indicum	97.8851	1021	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	96.62	95.33	0.92	0.89	22	conclusive
GCF_000702605.1	s__Exiguobacterium_A acetylicum	94.0386	960	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	97.66	95.06	0.95	0.91	10	-
GCF_001423965.1	s__Exiguobacterium_A sp001423965	90.8088	891	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	97.21	96.36	0.96	0.93	17	-
GCF_001275385.1	s__Exiguobacterium_A sp001275385	90.6334	976	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702625.1	s__Exiguobacterium_A oxidotolerans	81.2171	559	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	95.91	95.68	0.90	0.87	15	-
GCF_018618755.1	s__Exiguobacterium_A sp018618755	81.199	587	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620805.1	s__Exiguobacterium_A undae	81.0621	589	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	97.90	97.06	0.95	0.92	5	-
GCF_000620865.1	s__Exiguobacterium_A sibiricum_A	80.8828	547	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019905.1	s__Exiguobacterium_A sibiricum	80.8029	552	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	96.48	95.46	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:13,586] [INFO] GTDB search result was written to GCF_001456895.1_ASM145689v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:13,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:13,591] [INFO] DFAST_QC result json was written to GCF_001456895.1_ASM145689v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:13,592] [INFO] DFAST_QC completed!
[2024-01-24 12:07:13,592] [INFO] Total running time: 0h1m3s