[2024-01-25 20:00:05,632] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:05,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:05,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg546b94fa-c84c-4fa5-af66-719a9940eb69/dqc_reference
[2024-01-25 20:00:06,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:06,858] [INFO] Task started: Prodigal
[2024-01-25 20:00:06,858] [INFO] Running command: gunzip -c /var/lib/cwl/stgbeb4533b-027a-4314-a29a-7ec47f0638ef/GCF_025234645.1_ASM2523464v1_genomic.fna.gz | prodigal -d GCF_025234645.1_ASM2523464v1_genomic.fna/cds.fna -a GCF_025234645.1_ASM2523464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:13,222] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:13,223] [INFO] Task started: HMMsearch
[2024-01-25 20:00:13,223] [INFO] Running command: hmmsearch --tblout GCF_025234645.1_ASM2523464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg546b94fa-c84c-4fa5-af66-719a9940eb69/dqc_reference/reference_markers.hmm GCF_025234645.1_ASM2523464v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:13,455] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:13,456] [INFO] Found 6/6 markers.
[2024-01-25 20:00:13,485] [INFO] Query marker FASTA was written to GCF_025234645.1_ASM2523464v1_genomic.fna/markers.fasta
[2024-01-25 20:00:13,486] [INFO] Task started: Blastn
[2024-01-25 20:00:13,486] [INFO] Running command: blastn -query GCF_025234645.1_ASM2523464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg546b94fa-c84c-4fa5-af66-719a9940eb69/dqc_reference/reference_markers.fasta -out GCF_025234645.1_ASM2523464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:14,026] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:14,029] [INFO] Selected 9 target genomes.
[2024-01-25 20:00:14,029] [INFO] Target genome list was writen to GCF_025234645.1_ASM2523464v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:14,039] [INFO] Task started: fastANI
[2024-01-25 20:00:14,039] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeb4533b-027a-4314-a29a-7ec47f0638ef/GCF_025234645.1_ASM2523464v1_genomic.fna.gz --refList GCF_025234645.1_ASM2523464v1_genomic.fna/target_genomes.txt --output GCF_025234645.1_ASM2523464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:19,767] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:19,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg546b94fa-c84c-4fa5-af66-719a9940eb69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:19,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg546b94fa-c84c-4fa5-af66-719a9940eb69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:19,773] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:00:19,774] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:00:19,774] [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 artemiae	strain=9AN	GCA_025234645.1	340145	340145	type	True	100.0	901	914	95	inconclusive
Exiguobacterium sibiricum	strain=255-15	GCA_000019905.1	332410	332410	type	True	96.9	827	914	95	inconclusive
Exiguobacterium undae	strain=DSM 14481	GCA_000620805.1	169177	169177	type	True	86.1838	781	914	95	below_threshold
Exiguobacterium oxidotolerans	strain=JCM 12280	GCA_000702625.1	223958	223958	type	True	82.1417	614	914	95	below_threshold
Exiguobacterium indicum	strain=HHS 31	GCA_001939065.1	296995	296995	type	True	80.9514	523	914	95	below_threshold
Exiguobacterium enclense	strain=NIO-1109	GCA_001456895.1	1017277	1017277	type	True	80.7716	529	914	95	below_threshold
Exiguobacterium flavidum	strain=HF60	GCA_003344535.1	2184695	2184695	type	True	79.0449	267	914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:19,775] [INFO] DFAST Taxonomy check result was written to GCF_025234645.1_ASM2523464v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:19,775] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:19,776] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:19,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg546b94fa-c84c-4fa5-af66-719a9940eb69/dqc_reference/checkm_data
[2024-01-25 20:00:19,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:19,811] [INFO] Task started: CheckM
[2024-01-25 20:00:19,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025234645.1_ASM2523464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025234645.1_ASM2523464v1_genomic.fna/checkm_input GCF_025234645.1_ASM2523464v1_genomic.fna/checkm_result
[2024-01-25 20:00:44,439] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:44,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:44,460] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:44,461] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:44,461] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025234645.1_ASM2523464v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:44,461] [INFO] Task started: Blastn
[2024-01-25 20:00:44,462] [INFO] Running command: blastn -query GCF_025234645.1_ASM2523464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg546b94fa-c84c-4fa5-af66-719a9940eb69/dqc_reference/reference_markers_gtdb.fasta -out GCF_025234645.1_ASM2523464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:45,260] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:45,265] [INFO] Selected 6 target genomes.
[2024-01-25 20:00:45,265] [INFO] Target genome list was writen to GCF_025234645.1_ASM2523464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:45,274] [INFO] Task started: fastANI
[2024-01-25 20:00:45,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeb4533b-027a-4314-a29a-7ec47f0638ef/GCF_025234645.1_ASM2523464v1_genomic.fna.gz --refList GCF_025234645.1_ASM2523464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025234645.1_ASM2523464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:49,952] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:49,957] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:49,957] [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_000019905.1	s__Exiguobacterium_A sibiricum	96.9	827	914	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	96.48	95.46	0.93	0.90	4	conclusive
GCF_003339585.1	s__Exiguobacterium_A sp003339585	91.4456	832	914	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_014524545.1	s__Exiguobacterium_A sp004339505	90.9048	810	914	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	98.54	98.54	0.96	0.96	3	-
GCF_000620865.1	s__Exiguobacterium_A sibiricum_A	90.175	817	914	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363455.1	s__Exiguobacterium_A sp902363455	86.2697	762	914	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	86.1838	781	914	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	97.90	97.06	0.95	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:49,958] [INFO] GTDB search result was written to GCF_025234645.1_ASM2523464v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:49,959] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:49,961] [INFO] DFAST_QC result json was written to GCF_025234645.1_ASM2523464v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:49,961] [INFO] DFAST_QC completed!
[2024-01-25 20:00:49,961] [INFO] Total running time: 0h0m44s