[2024-01-24 15:10:40,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg11328db4-0872-40fe-88ba-36117b2e146e/dqc_reference
[2024-01-24 15:10:41,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:41,991] [INFO] Task started: Prodigal
[2024-01-24 15:10:41,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c4a3c5b-6e20-4e69-9bca-ea993f61166d/GCF_014836645.1_ASM1483664v1_genomic.fna.gz | prodigal -d GCF_014836645.1_ASM1483664v1_genomic.fna/cds.fna -a GCF_014836645.1_ASM1483664v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:50,740] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:50,740] [INFO] Task started: HMMsearch
[2024-01-24 15:10:50,741] [INFO] Running command: hmmsearch --tblout GCF_014836645.1_ASM1483664v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11328db4-0872-40fe-88ba-36117b2e146e/dqc_reference/reference_markers.hmm GCF_014836645.1_ASM1483664v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:51,054] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:51,056] [INFO] Found 6/6 markers.
[2024-01-24 15:10:51,091] [INFO] Query marker FASTA was written to GCF_014836645.1_ASM1483664v1_genomic.fna/markers.fasta
[2024-01-24 15:10:51,091] [INFO] Task started: Blastn
[2024-01-24 15:10:51,091] [INFO] Running command: blastn -query GCF_014836645.1_ASM1483664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11328db4-0872-40fe-88ba-36117b2e146e/dqc_reference/reference_markers.fasta -out GCF_014836645.1_ASM1483664v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:51,696] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:51,702] [INFO] Selected 13 target genomes.
[2024-01-24 15:10:51,703] [INFO] Target genome list was writen to GCF_014836645.1_ASM1483664v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:51,709] [INFO] Task started: fastANI
[2024-01-24 15:10:51,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c4a3c5b-6e20-4e69-9bca-ea993f61166d/GCF_014836645.1_ASM1483664v1_genomic.fna.gz --refList GCF_014836645.1_ASM1483664v1_genomic.fna/target_genomes.txt --output GCF_014836645.1_ASM1483664v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:00,828] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:00,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11328db4-0872-40fe-88ba-36117b2e146e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:00,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11328db4-0872-40fe-88ba-36117b2e146e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:00,836] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:00,836] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:00,836] [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
Fictibacillus norfolkensis	strain=Sa2CUA10	GCA_014836645.1	2762233	2762233	type	True	100.0	1332	1333	95	conclusive
Fictibacillus halophilus	strain=KCTC 33758	GCA_016401385.1	1610490	1610490	type	True	90.5582	1125	1333	95	below_threshold
Fictibacillus barbaricus	strain=CCM 4982	GCA_014635025.1	182136	182136	type	True	82.0013	752	1333	95	below_threshold
Fictibacillus barbaricus	strain=DSM 14730	GCA_017052555.1	182136	182136	type	True	81.9966	761	1333	95	below_threshold
Fictibacillus arsenicus	strain=Con a/3	GCA_001999465.1	255247	255247	type	True	81.0597	672	1333	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	76.6489	59	1333	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:00,842] [INFO] DFAST Taxonomy check result was written to GCF_014836645.1_ASM1483664v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:00,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:00,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:00,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11328db4-0872-40fe-88ba-36117b2e146e/dqc_reference/checkm_data
[2024-01-24 15:11:00,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:00,888] [INFO] Task started: CheckM
[2024-01-24 15:11:00,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836645.1_ASM1483664v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836645.1_ASM1483664v1_genomic.fna/checkm_input GCF_014836645.1_ASM1483664v1_genomic.fna/checkm_result
[2024-01-24 15:11:34,640] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:34,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:34,661] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:34,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:34,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836645.1_ASM1483664v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:34,662] [INFO] Task started: Blastn
[2024-01-24 15:11:34,662] [INFO] Running command: blastn -query GCF_014836645.1_ASM1483664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11328db4-0872-40fe-88ba-36117b2e146e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836645.1_ASM1483664v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:35,503] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:35,507] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:35,507] [INFO] Target genome list was writen to GCF_014836645.1_ASM1483664v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:35,516] [INFO] Task started: fastANI
[2024-01-24 15:11:35,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c4a3c5b-6e20-4e69-9bca-ea993f61166d/GCF_014836645.1_ASM1483664v1_genomic.fna.gz --refList GCF_014836645.1_ASM1483664v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836645.1_ASM1483664v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:44,358] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:44,366] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:44,366] [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_014836645.1	s__Fictibacillus sp014836645	100.0	1332	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007673525.1	s__Fictibacillus phosphorivorans_C	93.4721	1180	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	98.18	98.18	0.90	0.90	2	-
GCA_016401345.1	s__Fictibacillus nanhaiensis_A	91.7598	1145	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	97.66	97.26	0.91	0.88	5	-
GCF_005503015.1	s__Fictibacillus sp005503015	91.5637	1154	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001629705.1	s__Fictibacillus phosphorivorans_A	90.6852	1161	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	97.31	97.31	0.95	0.95	2	-
GCF_016401385.1	s__Fictibacillus halophilus	90.5582	1125	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017052515.1	s__Fictibacillus nanhaiensis_B	90.193	1107	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:44,368] [INFO] GTDB search result was written to GCF_014836645.1_ASM1483664v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:44,369] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:44,371] [INFO] DFAST_QC result json was written to GCF_014836645.1_ASM1483664v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:44,372] [INFO] DFAST_QC completed!
[2024-01-24 15:11:44,372] [INFO] Total running time: 0h1m4s