[2024-01-24 13:28:11,437] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg7407737f-a079-4781-9b88-17574e2626a8/dqc_reference
[2024-01-24 13:28:12,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:12,646] [INFO] Task started: Prodigal
[2024-01-24 13:28:12,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg55343d1f-4a4f-4d69-95eb-6800fa9c17ed/GCF_000377765.1_ASM37776v1_genomic.fna.gz | prodigal -d GCF_000377765.1_ASM37776v1_genomic.fna/cds.fna -a GCF_000377765.1_ASM37776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:21,577] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:21,578] [INFO] Task started: HMMsearch
[2024-01-24 13:28:21,578] [INFO] Running command: hmmsearch --tblout GCF_000377765.1_ASM37776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7407737f-a079-4781-9b88-17574e2626a8/dqc_reference/reference_markers.hmm GCF_000377765.1_ASM37776v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:21,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:21,877] [INFO] Found 6/6 markers.
[2024-01-24 13:28:21,917] [INFO] Query marker FASTA was written to GCF_000377765.1_ASM37776v1_genomic.fna/markers.fasta
[2024-01-24 13:28:21,918] [INFO] Task started: Blastn
[2024-01-24 13:28:21,918] [INFO] Running command: blastn -query GCF_000377765.1_ASM37776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7407737f-a079-4781-9b88-17574e2626a8/dqc_reference/reference_markers.fasta -out GCF_000377765.1_ASM37776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:22,516] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:22,520] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:22,521] [INFO] Target genome list was writen to GCF_000377765.1_ASM37776v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:22,527] [INFO] Task started: fastANI
[2024-01-24 13:28:22,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg55343d1f-4a4f-4d69-95eb-6800fa9c17ed/GCF_000377765.1_ASM37776v1_genomic.fna.gz --refList GCF_000377765.1_ASM37776v1_genomic.fna/target_genomes.txt --output GCF_000377765.1_ASM37776v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:33,087] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:33,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7407737f-a079-4781-9b88-17574e2626a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:33,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7407737f-a079-4781-9b88-17574e2626a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:33,094] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:28:33,094] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:28:33,094] [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 lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	100.0	1443	1449	95	inconclusive
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	96.0619	1145	1449	95	inconclusive
Gracilibacillus thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	96.04	1158	1449	95	inconclusive
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	95.3285	1177	1449	95	inconclusive
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	91.2238	1166	1449	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	85.4936	1116	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:33,096] [INFO] DFAST Taxonomy check result was written to GCF_000377765.1_ASM37776v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:33,096] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:33,096] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:33,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7407737f-a079-4781-9b88-17574e2626a8/dqc_reference/checkm_data
[2024-01-24 13:28:33,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:33,143] [INFO] Task started: CheckM
[2024-01-24 13:28:33,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000377765.1_ASM37776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000377765.1_ASM37776v1_genomic.fna/checkm_input GCF_000377765.1_ASM37776v1_genomic.fna/checkm_result
[2024-01-24 13:29:04,736] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:04,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:04,759] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:04,759] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:04,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000377765.1_ASM37776v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:04,760] [INFO] Task started: Blastn
[2024-01-24 13:29:04,760] [INFO] Running command: blastn -query GCF_000377765.1_ASM37776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7407737f-a079-4781-9b88-17574e2626a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000377765.1_ASM37776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:05,502] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:05,510] [INFO] Selected 9 target genomes.
[2024-01-24 13:29:05,511] [INFO] Target genome list was writen to GCF_000377765.1_ASM37776v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:05,572] [INFO] Task started: fastANI
[2024-01-24 13:29:05,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg55343d1f-4a4f-4d69-95eb-6800fa9c17ed/GCF_000377765.1_ASM37776v1_genomic.fna.gz --refList GCF_000377765.1_ASM37776v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000377765.1_ASM37776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:15,408] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:15,422] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:15,423] [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_000377765.1	s__Gracilibacillus lacisalsi	100.0	1443	1449	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	conclusive
GCF_017599345.1	s__Gracilibacillus sp017599345	91.2456	1164	1449	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_009650095.1	s__Gracilibacillus sp002797295	85.4996	1115	1449	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_900114645.1	s__Gracilibacillus orientalis	83.8421	1027	1449	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	79.1411	491	1449	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_900143085.1	s__Gracilibacillus kekensis	79.0623	469	1449	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	78.2533	266	1449	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_007301515.1	s__Radiobacillus deserti	77.2077	101	1449	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:15,424] [INFO] GTDB search result was written to GCF_000377765.1_ASM37776v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:15,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:15,428] [INFO] DFAST_QC result json was written to GCF_000377765.1_ASM37776v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:15,428] [INFO] DFAST_QC completed!
[2024-01-24 13:29:15,428] [INFO] Total running time: 0h1m4s