[2024-01-24 15:02:16,441] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:16,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:16,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg101f49e8-08a2-4808-9ea7-f8048aefd8b6/dqc_reference
[2024-01-24 15:02:17,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:17,707] [INFO] Task started: Prodigal
[2024-01-24 15:02:17,708] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd9296f3-3de6-41dd-a452-768b4e6d44a5/GCF_014206945.1_ASM1420694v1_genomic.fna.gz | prodigal -d GCF_014206945.1_ASM1420694v1_genomic.fna/cds.fna -a GCF_014206945.1_ASM1420694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:24,109] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:24,110] [INFO] Task started: HMMsearch
[2024-01-24 15:02:24,110] [INFO] Running command: hmmsearch --tblout GCF_014206945.1_ASM1420694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg101f49e8-08a2-4808-9ea7-f8048aefd8b6/dqc_reference/reference_markers.hmm GCF_014206945.1_ASM1420694v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:24,412] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:24,413] [INFO] Found 6/6 markers.
[2024-01-24 15:02:24,456] [INFO] Query marker FASTA was written to GCF_014206945.1_ASM1420694v1_genomic.fna/markers.fasta
[2024-01-24 15:02:24,457] [INFO] Task started: Blastn
[2024-01-24 15:02:24,457] [INFO] Running command: blastn -query GCF_014206945.1_ASM1420694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg101f49e8-08a2-4808-9ea7-f8048aefd8b6/dqc_reference/reference_markers.fasta -out GCF_014206945.1_ASM1420694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:25,090] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:25,095] [INFO] Selected 24 target genomes.
[2024-01-24 15:02:25,096] [INFO] Target genome list was writen to GCF_014206945.1_ASM1420694v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:25,106] [INFO] Task started: fastANI
[2024-01-24 15:02:25,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd9296f3-3de6-41dd-a452-768b4e6d44a5/GCF_014206945.1_ASM1420694v1_genomic.fna.gz --refList GCF_014206945.1_ASM1420694v1_genomic.fna/target_genomes.txt --output GCF_014206945.1_ASM1420694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:40,284] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:40,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg101f49e8-08a2-4808-9ea7-f8048aefd8b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:40,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg101f49e8-08a2-4808-9ea7-f8048aefd8b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:40,300] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:40,300] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:40,300] [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
Gracilibacillus halotolerans	strain=DSM 11805	GCA_014206945.1	74386	74386	type	True	100.0	1099	1103	95	conclusive
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	77.5276	55	1103	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.1366	59	1103	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	77.1364	162	1103	95	below_threshold
Gracilibacillus massiliensis	strain=Awa-1	GCA_001458115.1	1564956	1564956	type	True	77.1103	137	1103	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.0806	66	1103	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	77.006	159	1103	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	76.9683	153	1103	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	76.9605	62	1103	95	below_threshold
Radiobacillus deserti	strain=TKL69	GCA_007301515.1	2594883	2594883	type	True	76.9337	68	1103	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	76.9174	161	1103	95	below_threshold
Gracilibacillus kekensis	strain=CGMCC 1.10681	GCA_900143085.1	1027249	1027249	type	True	76.8803	148	1103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:40,302] [INFO] DFAST Taxonomy check result was written to GCF_014206945.1_ASM1420694v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:40,303] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:40,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:40,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg101f49e8-08a2-4808-9ea7-f8048aefd8b6/dqc_reference/checkm_data
[2024-01-24 15:02:40,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:40,339] [INFO] Task started: CheckM
[2024-01-24 15:02:40,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014206945.1_ASM1420694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014206945.1_ASM1420694v1_genomic.fna/checkm_input GCF_014206945.1_ASM1420694v1_genomic.fna/checkm_result
[2024-01-24 15:03:06,599] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:06,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:06,621] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:06,621] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:06,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014206945.1_ASM1420694v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:06,622] [INFO] Task started: Blastn
[2024-01-24 15:03:06,623] [INFO] Running command: blastn -query GCF_014206945.1_ASM1420694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg101f49e8-08a2-4808-9ea7-f8048aefd8b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014206945.1_ASM1420694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:07,472] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:07,477] [INFO] Selected 27 target genomes.
[2024-01-24 15:03:07,477] [INFO] Target genome list was writen to GCF_014206945.1_ASM1420694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:07,500] [INFO] Task started: fastANI
[2024-01-24 15:03:07,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd9296f3-3de6-41dd-a452-768b4e6d44a5/GCF_014206945.1_ASM1420694v1_genomic.fna.gz --refList GCF_014206945.1_ASM1420694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014206945.1_ASM1420694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:24,713] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:24,732] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:24,732] [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_014206945.1	s__Gracilibacillus halotolerans	100.0	1099	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003628445.1	s__Oceanobacillus bengalensis	77.1643	60	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521485.1	s__Gracilibacillus boraciitolerans	77.0993	125	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458115.1	s__Gracilibacillus massiliensis	77.0915	138	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005870085.1	s__BH258 sp005870085	77.0806	66	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650095.1	s__Gracilibacillus sp002797295	76.9683	153	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	76.9605	62	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_000377765.1	s__Gracilibacillus lacisalsi	76.9193	160	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCF_900143085.1	s__Gracilibacillus kekensis	76.8803	148	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993965.1	s__Gracilibacillus sp010993965	76.8225	115	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	76.7812	72	1103	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_001659985.1	s__Oceanobacillus sp001659985	76.6186	62	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919725.1	s__Virgibacillus sp016919725	76.5816	55	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_016908155.1	s__Oceanobacillus caeni	76.5543	59	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:24,734] [INFO] GTDB search result was written to GCF_014206945.1_ASM1420694v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:24,735] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:24,739] [INFO] DFAST_QC result json was written to GCF_014206945.1_ASM1420694v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:24,739] [INFO] DFAST_QC completed!
[2024-01-24 15:03:24,739] [INFO] Total running time: 0h1m8s