[2024-01-25 19:47:35,591] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:35,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:35,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg136b01ae-5f4c-4836-8e1e-ff14eb590683/dqc_reference
[2024-01-25 19:47:36,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:36,731] [INFO] Task started: Prodigal
[2024-01-25 19:47:36,731] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5c95fff-c153-4961-802f-05f9f174834b/GCF_030814115.1_ASM3081411v1_genomic.fna.gz | prodigal -d GCF_030814115.1_ASM3081411v1_genomic.fna/cds.fna -a GCF_030814115.1_ASM3081411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:41,295] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:41,295] [INFO] Task started: HMMsearch
[2024-01-25 19:47:41,295] [INFO] Running command: hmmsearch --tblout GCF_030814115.1_ASM3081411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg136b01ae-5f4c-4836-8e1e-ff14eb590683/dqc_reference/reference_markers.hmm GCF_030814115.1_ASM3081411v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:41,506] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:41,507] [INFO] Found 6/6 markers.
[2024-01-25 19:47:41,531] [INFO] Query marker FASTA was written to GCF_030814115.1_ASM3081411v1_genomic.fna/markers.fasta
[2024-01-25 19:47:41,531] [INFO] Task started: Blastn
[2024-01-25 19:47:41,532] [INFO] Running command: blastn -query GCF_030814115.1_ASM3081411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg136b01ae-5f4c-4836-8e1e-ff14eb590683/dqc_reference/reference_markers.fasta -out GCF_030814115.1_ASM3081411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:42,090] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:42,093] [INFO] Selected 29 target genomes.
[2024-01-25 19:47:42,093] [INFO] Target genome list was writen to GCF_030814115.1_ASM3081411v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:42,174] [INFO] Task started: fastANI
[2024-01-25 19:47:42,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5c95fff-c153-4961-802f-05f9f174834b/GCF_030814115.1_ASM3081411v1_genomic.fna.gz --refList GCF_030814115.1_ASM3081411v1_genomic.fna/target_genomes.txt --output GCF_030814115.1_ASM3081411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:57,972] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:57,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg136b01ae-5f4c-4836-8e1e-ff14eb590683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:57,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg136b01ae-5f4c-4836-8e1e-ff14eb590683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:57,985] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:47:57,985] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:47:57,985] [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
Alkalibacillus haloalkaliphilus	strain=NBRC 103110	GCA_007991275.1	94136	94136	type	True	89.7312	791	891	95	below_threshold
Alkalibacillus aidingensis	strain=YIM 98829	GCA_014595945.1	2747607	2747607	type	True	78.2239	267	891	95	below_threshold
Alkalibacillus almallahensis	strain=CECT 8373	GCA_011761495.1	1379154	1379154	type	True	77.8626	230	891	95	below_threshold
Halalkalibacillus sediminis	strain=B3227	GCA_002844535.1	2018042	2018042	type	True	77.3479	99	891	95	below_threshold
Piscibacillus halophilus	strain=DSM 21633	GCA_900110685.1	571933	571933	type	True	77.2276	146	891	95	below_threshold
Pontibacillus marinus	strain=BH030004	GCA_000775605.1	273164	273164	type	True	76.8501	65	891	95	below_threshold
Pontibacillus marinus	strain=DSM 16465	GCA_000425225.1	273164	273164	type	True	76.81	65	891	95	below_threshold
Allobacillus halotolerans	strain=LMG 24826	GCA_018967645.1	570278	570278	type	True	76.5481	77	891	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	76.3538	66	891	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:57,986] [INFO] DFAST Taxonomy check result was written to GCF_030814115.1_ASM3081411v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:57,987] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:57,987] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:57,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg136b01ae-5f4c-4836-8e1e-ff14eb590683/dqc_reference/checkm_data
[2024-01-25 19:47:57,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:58,015] [INFO] Task started: CheckM
[2024-01-25 19:47:58,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814115.1_ASM3081411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814115.1_ASM3081411v1_genomic.fna/checkm_input GCF_030814115.1_ASM3081411v1_genomic.fna/checkm_result
[2024-01-25 19:48:17,646] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:17,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:17,662] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:17,662] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:17,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814115.1_ASM3081411v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:17,663] [INFO] Task started: Blastn
[2024-01-25 19:48:17,663] [INFO] Running command: blastn -query GCF_030814115.1_ASM3081411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg136b01ae-5f4c-4836-8e1e-ff14eb590683/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814115.1_ASM3081411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:18,452] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:18,456] [INFO] Selected 20 target genomes.
[2024-01-25 19:48:18,456] [INFO] Target genome list was writen to GCF_030814115.1_ASM3081411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:18,482] [INFO] Task started: fastANI
[2024-01-25 19:48:18,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5c95fff-c153-4961-802f-05f9f174834b/GCF_030814115.1_ASM3081411v1_genomic.fna.gz --refList GCF_030814115.1_ASM3081411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814115.1_ASM3081411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:30,160] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:30,167] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:48:30,167] [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_000269905.1	s__Alkalibacillus haloalkaliphilus_A	89.8408	671	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991275.1	s__Alkalibacillus haloalkaliphilus	89.7312	791	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595945.1	s__Alkalibacillus sp014595945	78.2244	267	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761495.1	s__Alkalibacillus almallahensis	77.874	230	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110685.1	s__Piscibacillus halophilus	77.2381	147	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Piscibacillus	95.0	99.37	99.37	0.93	0.93	2	-
GCF_009858175.1	s__Pontibacillus sp009858175	77.2276	59	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003843875.1	s__Aquisalibacillus elongatus	77.1601	158	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Aquisalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425225.1	s__Pontibacillus marinus	76.7773	66	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001368815.1	s__Paraliobacillus sp001368815	76.3519	56	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	76.2685	55	891	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:30,169] [INFO] GTDB search result was written to GCF_030814115.1_ASM3081411v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:30,169] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:30,173] [INFO] DFAST_QC result json was written to GCF_030814115.1_ASM3081411v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:30,174] [INFO] DFAST_QC completed!
[2024-01-25 19:48:30,174] [INFO] Total running time: 0h0m55s