[2024-01-24 11:12:36,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,242] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,242] [INFO] DQC Reference Directory: /var/lib/cwl/stg4818bb3c-549e-4254-bfd8-f9fd172347b0/dqc_reference
[2024-01-24 11:12:38,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,660] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,661] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4f43a50-73fa-4073-8315-6081253b4efd/GCF_002216775.1_ASM221677v1_genomic.fna.gz | prodigal -d GCF_002216775.1_ASM221677v1_genomic.fna/cds.fna -a GCF_002216775.1_ASM221677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:47,741] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:47,741] [INFO] Task started: HMMsearch
[2024-01-24 11:12:47,741] [INFO] Running command: hmmsearch --tblout GCF_002216775.1_ASM221677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4818bb3c-549e-4254-bfd8-f9fd172347b0/dqc_reference/reference_markers.hmm GCF_002216775.1_ASM221677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:47,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:47,977] [INFO] Found 6/6 markers.
[2024-01-24 11:12:48,013] [INFO] Query marker FASTA was written to GCF_002216775.1_ASM221677v1_genomic.fna/markers.fasta
[2024-01-24 11:12:48,013] [INFO] Task started: Blastn
[2024-01-24 11:12:48,013] [INFO] Running command: blastn -query GCF_002216775.1_ASM221677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4818bb3c-549e-4254-bfd8-f9fd172347b0/dqc_reference/reference_markers.fasta -out GCF_002216775.1_ASM221677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:48,618] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:48,624] [INFO] Selected 20 target genomes.
[2024-01-24 11:12:48,625] [INFO] Target genome list was writen to GCF_002216775.1_ASM221677v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:48,732] [INFO] Task started: fastANI
[2024-01-24 11:12:48,732] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f43a50-73fa-4073-8315-6081253b4efd/GCF_002216775.1_ASM221677v1_genomic.fna.gz --refList GCF_002216775.1_ASM221677v1_genomic.fna/target_genomes.txt --output GCF_002216775.1_ASM221677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:03,562] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:03,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4818bb3c-549e-4254-bfd8-f9fd172347b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:03,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4818bb3c-549e-4254-bfd8-f9fd172347b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:03,574] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:03,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:03,574] [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
Virgibacillus phasianinus	strain=LM2416	GCA_002216775.1	2017483	2017483	type	True	100.0	1356	1357	95	conclusive
Virgibacillus necropolis	strain=LMG 19488	GCA_002224365.1	163877	163877	type	True	79.7857	595	1357	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	79.4037	65	1357	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	78.6216	72	1357	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	78.1311	203	1357	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	77.7229	121	1357	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.4536	71	1357	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	77.4298	164	1357	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.3316	173	1357	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	77.2376	99	1357	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	77.2336	109	1357	95	below_threshold
Salinibacillus xinjiangensis	strain=J4	GCA_009649735.1	1229268	1229268	type	True	77.1186	53	1357	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	76.8735	120	1357	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	76.6118	122	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:03,576] [INFO] DFAST Taxonomy check result was written to GCF_002216775.1_ASM221677v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:03,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:03,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:03,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4818bb3c-549e-4254-bfd8-f9fd172347b0/dqc_reference/checkm_data
[2024-01-24 11:13:03,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:03,618] [INFO] Task started: CheckM
[2024-01-24 11:13:03,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002216775.1_ASM221677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002216775.1_ASM221677v1_genomic.fna/checkm_input GCF_002216775.1_ASM221677v1_genomic.fna/checkm_result
[2024-01-24 11:13:34,207] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:34,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:34,227] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:34,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:34,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002216775.1_ASM221677v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:34,228] [INFO] Task started: Blastn
[2024-01-24 11:13:34,228] [INFO] Running command: blastn -query GCF_002216775.1_ASM221677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4818bb3c-549e-4254-bfd8-f9fd172347b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002216775.1_ASM221677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:35,252] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:35,255] [INFO] Selected 25 target genomes.
[2024-01-24 11:13:35,255] [INFO] Target genome list was writen to GCF_002216775.1_ASM221677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:35,271] [INFO] Task started: fastANI
[2024-01-24 11:13:35,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f43a50-73fa-4073-8315-6081253b4efd/GCF_002216775.1_ASM221677v1_genomic.fna.gz --refList GCF_002216775.1_ASM221677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002216775.1_ASM221677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:51,580] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:51,594] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:51,594] [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_002216775.1	s__Virgibacillus_F phasianinus	100.0	1357	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002224365.1	s__Virgibacillus_F necropolis	79.8662	593	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268595.1	s__Paraliobacillus_A zengyii	79.2683	76	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_000011245.1	s__Oceanobacillus iheyensis	78.5283	78	1357	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_900187325.1	s__Virgibacillus_E ndiopensis	78.3343	224	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000724085.1	s__Virgibacillus manasiensis	78.3043	109	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638995.1	s__Virgibacillus_E oceani	78.184	200	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870085.1	s__BH258 sp005870085	77.611	71	1357	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_900110695.1	s__Lentibacillus subterraneus	77.4069	165	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_002266285.1	s__Virgibacillus_G indicus	77.3486	172	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730295.1	s__LJ137 sp003730295	77.2788	99	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__LJ137	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112045.1	s__Lentibacillus halodurans	77.2567	107	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649735.1	s__Salinibacillus xinjiangensis	77.0923	52	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628505.1	s__Oceanobacillus halophilus	76.8829	119	1357	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_001659985.1	s__Oceanobacillus sp001659985	76.677	109	1357	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_900129485.1	s__Ornithinibacillus halophilus	76.6295	120	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004145795.1	s__Lentibacillus lipolyticus	76.6292	79	1357	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:51,595] [INFO] GTDB search result was written to GCF_002216775.1_ASM221677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:51,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:51,599] [INFO] DFAST_QC result json was written to GCF_002216775.1_ASM221677v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:51,599] [INFO] DFAST_QC completed!
[2024-01-24 11:13:51,600] [INFO] Total running time: 0h1m15s