[2024-01-24 14:39:59,377] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:59,379] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:59,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e01f2fa-5e4f-4e5d-bd05-223942e68e6c/dqc_reference
[2024-01-24 14:40:00,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:00,737] [INFO] Task started: Prodigal
[2024-01-24 14:40:00,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg406c62b7-fb26-4ec0-ae76-26dfa04b7956/GCF_008152325.1_ASM815232v1_genomic.fna.gz | prodigal -d GCF_008152325.1_ASM815232v1_genomic.fna/cds.fna -a GCF_008152325.1_ASM815232v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:06,561] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:06,562] [INFO] Task started: HMMsearch
[2024-01-24 14:40:06,562] [INFO] Running command: hmmsearch --tblout GCF_008152325.1_ASM815232v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e01f2fa-5e4f-4e5d-bd05-223942e68e6c/dqc_reference/reference_markers.hmm GCF_008152325.1_ASM815232v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:06,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:06,851] [INFO] Found 6/6 markers.
[2024-01-24 14:40:06,882] [INFO] Query marker FASTA was written to GCF_008152325.1_ASM815232v1_genomic.fna/markers.fasta
[2024-01-24 14:40:06,883] [INFO] Task started: Blastn
[2024-01-24 14:40:06,883] [INFO] Running command: blastn -query GCF_008152325.1_ASM815232v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e01f2fa-5e4f-4e5d-bd05-223942e68e6c/dqc_reference/reference_markers.fasta -out GCF_008152325.1_ASM815232v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:07,564] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:07,568] [INFO] Selected 16 target genomes.
[2024-01-24 14:40:07,568] [INFO] Target genome list was writen to GCF_008152325.1_ASM815232v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:07,580] [INFO] Task started: fastANI
[2024-01-24 14:40:07,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg406c62b7-fb26-4ec0-ae76-26dfa04b7956/GCF_008152325.1_ASM815232v1_genomic.fna.gz --refList GCF_008152325.1_ASM815232v1_genomic.fna/target_genomes.txt --output GCF_008152325.1_ASM815232v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:17,982] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:17,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e01f2fa-5e4f-4e5d-bd05-223942e68e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:17,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e01f2fa-5e4f-4e5d-bd05-223942e68e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:17,997] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:17,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:17,997] [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
Crassaminicella thermophila	strain=SY095	GCA_008152325.1	2599308	2599308	type	True	100.0	1027	1027	95	conclusive
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	80.4184	560	1027	95	below_threshold
Anaeromicrobium sediminis	strain=DY2726D	GCA_002270055.1	1478221	1478221	type	True	77.0087	182	1027	95	below_threshold
Caminicella sporogenes	strain=AM 1114	GCA_003609595.1	166485	166485	type	True	76.832	160	1027	95	below_threshold
Caminicella sporogenes	strain=DSM 14501	GCA_900142285.1	166485	166485	type	True	76.6953	162	1027	95	below_threshold
Paramaledivibacter caminithermalis	strain=DSM 15212	GCA_900142245.1	191027	191027	type	True	76.661	115	1027	95	below_threshold
Alkaliphilus flagellatus	strain=MSJ-5	GCA_018919215.1	2841507	2841507	type	True	76.5559	91	1027	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	76.5249	92	1027	95	below_threshold
Maledivibacter halophilus	strain=M1	GCA_900167445.1	36842	36842	type	True	76.149	137	1027	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	75.8357	68	1027	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	75.7332	64	1027	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	75.6394	68	1027	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.553	68	1027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:17,999] [INFO] DFAST Taxonomy check result was written to GCF_008152325.1_ASM815232v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:18,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:18,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:18,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e01f2fa-5e4f-4e5d-bd05-223942e68e6c/dqc_reference/checkm_data
[2024-01-24 14:40:18,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:18,033] [INFO] Task started: CheckM
[2024-01-24 14:40:18,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008152325.1_ASM815232v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008152325.1_ASM815232v1_genomic.fna/checkm_input GCF_008152325.1_ASM815232v1_genomic.fna/checkm_result
[2024-01-24 14:40:41,981] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:41,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:42,005] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:42,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:42,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008152325.1_ASM815232v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:42,006] [INFO] Task started: Blastn
[2024-01-24 14:40:42,006] [INFO] Running command: blastn -query GCF_008152325.1_ASM815232v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e01f2fa-5e4f-4e5d-bd05-223942e68e6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_008152325.1_ASM815232v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:42,884] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:42,887] [INFO] Selected 13 target genomes.
[2024-01-24 14:40:42,888] [INFO] Target genome list was writen to GCF_008152325.1_ASM815232v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:42,908] [INFO] Task started: fastANI
[2024-01-24 14:40:42,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg406c62b7-fb26-4ec0-ae76-26dfa04b7956/GCF_008152325.1_ASM815232v1_genomic.fna.gz --refList GCF_008152325.1_ASM815232v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008152325.1_ASM815232v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:51,386] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:51,396] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:51,396] [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_008152325.1	s__SY095 sp008152325	100.0	1027	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__SY095	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019203185.1	s__143-21 sp019203185	81.1462	508	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__143-21	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345705.1	s__Marinisporobacter balticus	79.2081	494	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Marinisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282725.1	s__Inediibacterium massiliense	78.5346	323	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Inediibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138215.1	s__Inediibacterium nitritogenes	77.8276	313	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Inediibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686845.1	s__JADPRS01 sp015686845	77.7268	251	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__JADPRS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002270055.1	s__Anaeromicrobium sediminis	77.0587	183	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Anaeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142285.1	s__Caminicella sporogenes	76.6977	162	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Caminicella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900142245.1	s__Paramaledivibacter caminithermalis	76.6653	118	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001316435.1	s__Caloranaerobacter sp001316435	76.343	79	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900243075.1	s__Clostridioides difficile_D	75.6381	62	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides	95.0	99.09	99.09	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:51,398] [INFO] GTDB search result was written to GCF_008152325.1_ASM815232v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:51,398] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:51,403] [INFO] DFAST_QC result json was written to GCF_008152325.1_ASM815232v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:51,403] [INFO] DFAST_QC completed!
[2024-01-24 14:40:51,403] [INFO] Total running time: 0h0m52s