[2024-01-25 19:50:05,475] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:05,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:05,477] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d7ff169-bae1-4ce6-9f3e-12fbf0fb1a96/dqc_reference
[2024-01-25 19:50:06,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:06,573] [INFO] Task started: Prodigal
[2024-01-25 19:50:06,573] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbc05e25-97d5-4c04-9cb6-6437f4908df5/GCF_000821245.2_ASM82124v2_genomic.fna.gz | prodigal -d GCF_000821245.2_ASM82124v2_genomic.fna/cds.fna -a GCF_000821245.2_ASM82124v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:15,409] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:15,409] [INFO] Task started: HMMsearch
[2024-01-25 19:50:15,409] [INFO] Running command: hmmsearch --tblout GCF_000821245.2_ASM82124v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d7ff169-bae1-4ce6-9f3e-12fbf0fb1a96/dqc_reference/reference_markers.hmm GCF_000821245.2_ASM82124v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:15,654] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:15,655] [INFO] Found 6/6 markers.
[2024-01-25 19:50:15,686] [INFO] Query marker FASTA was written to GCF_000821245.2_ASM82124v2_genomic.fna/markers.fasta
[2024-01-25 19:50:15,686] [INFO] Task started: Blastn
[2024-01-25 19:50:15,686] [INFO] Running command: blastn -query GCF_000821245.2_ASM82124v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d7ff169-bae1-4ce6-9f3e-12fbf0fb1a96/dqc_reference/reference_markers.fasta -out GCF_000821245.2_ASM82124v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:16,237] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:16,240] [INFO] Selected 25 target genomes.
[2024-01-25 19:50:16,240] [INFO] Target genome list was writen to GCF_000821245.2_ASM82124v2_genomic.fna/target_genomes.txt
[2024-01-25 19:50:16,269] [INFO] Task started: fastANI
[2024-01-25 19:50:16,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc05e25-97d5-4c04-9cb6-6437f4908df5/GCF_000821245.2_ASM82124v2_genomic.fna.gz --refList GCF_000821245.2_ASM82124v2_genomic.fna/target_genomes.txt --output GCF_000821245.2_ASM82124v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:32,943] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:32,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d7ff169-bae1-4ce6-9f3e-12fbf0fb1a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:32,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d7ff169-bae1-4ce6-9f3e-12fbf0fb1a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:32,952] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:50:32,952] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:50:32,952] [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
Sediminibacillus dalangtanensis	strain=DP4-553-S	GCA_017792025.1	2729421	2729421	type	True	82.3031	876	1304	95	below_threshold
Sediminibacillus terrae	strain=JSM 102062	GCA_009602435.1	1562106	1562106	type	True	82.0356	810	1304	95	below_threshold
Sediminibacillus halophilus	strain=CGMCC 1.6199	GCA_900103695.1	482461	482461	type	True	81.8641	847	1304	95	below_threshold
Sediminibacillus albus	strain=CGMCC 1.6502	GCA_900101125.1	407036	407036	type	True	78.7433	377	1304	95	below_threshold
Halobacillus massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	78.0856	76	1304	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.4971	67	1304	95	below_threshold
Thalassobacillus pellis	strain=DSM 22784	GCA_016908295.1	748008	748008	type	True	77.3521	88	1304	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	77.2706	104	1304	95	below_threshold
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	77.0536	75	1304	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.0374	109	1304	95	below_threshold
Gracilibacillus halophilus	strain=YIM-C55.5	GCA_000359605.1	470864	470864	type	True	76.0117	55	1304	95	below_threshold
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	75.9302	71	1304	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	75.5582	51	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:32,954] [INFO] DFAST Taxonomy check result was written to GCF_000821245.2_ASM82124v2_genomic.fna/tc_result.tsv
[2024-01-25 19:50:32,954] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:32,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:32,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d7ff169-bae1-4ce6-9f3e-12fbf0fb1a96/dqc_reference/checkm_data
[2024-01-25 19:50:32,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:32,995] [INFO] Task started: CheckM
[2024-01-25 19:50:32,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000821245.2_ASM82124v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000821245.2_ASM82124v2_genomic.fna/checkm_input GCF_000821245.2_ASM82124v2_genomic.fna/checkm_result
[2024-01-25 19:51:02,200] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:02,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:02,218] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:02,218] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:02,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000821245.2_ASM82124v2_genomic.fna/markers.fasta)
[2024-01-25 19:51:02,218] [INFO] Task started: Blastn
[2024-01-25 19:51:02,218] [INFO] Running command: blastn -query GCF_000821245.2_ASM82124v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d7ff169-bae1-4ce6-9f3e-12fbf0fb1a96/dqc_reference/reference_markers_gtdb.fasta -out GCF_000821245.2_ASM82124v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:02,950] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:02,953] [INFO] Selected 14 target genomes.
[2024-01-25 19:51:02,953] [INFO] Target genome list was writen to GCF_000821245.2_ASM82124v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:02,970] [INFO] Task started: fastANI
[2024-01-25 19:51:02,970] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc05e25-97d5-4c04-9cb6-6437f4908df5/GCF_000821245.2_ASM82124v2_genomic.fna.gz --refList GCF_000821245.2_ASM82124v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000821245.2_ASM82124v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:13,929] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:13,936] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:13,936] [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_000821245.2	s__Sediminibacillus senegalensis	99.9999	1299	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017792025.1	s__Sediminibacillus sp017792025	82.3202	876	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009602435.1	s__Sediminibacillus terrae	82.0277	812	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	99.15	99.14	0.93	0.93	3	-
GCF_900103695.1	s__Sediminibacillus halophilus	81.875	846	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101125.1	s__Sediminibacillus albus	78.6958	380	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156915.1	s__Sediminibacillus_A massiliensis	78.0442	242	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	77.4574	68	1304	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_008304605.1	s__Oceanobacillus polygoni	76.3554	79	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000359605.1	s__Gracilibacillus halophilus	75.9669	53	1304	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_001591625.1	s__Metabacillus fastidiosus	75.6048	50	1304	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:13,937] [INFO] GTDB search result was written to GCF_000821245.2_ASM82124v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:13,938] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:13,940] [INFO] DFAST_QC result json was written to GCF_000821245.2_ASM82124v2_genomic.fna/dqc_result.json
[2024-01-25 19:51:13,941] [INFO] DFAST_QC completed!
[2024-01-25 19:51:13,941] [INFO] Total running time: 0h1m8s