[2024-01-24 12:22:48,504] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b0ea900-4259-4fe8-88d3-83db367b0923/dqc_reference
[2024-01-24 12:22:49,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,720] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ea93e83-c761-4070-b25d-7b24c04e67b3/GCF_018861735.1_ASM1886173v1_genomic.fna.gz | prodigal -d GCF_018861735.1_ASM1886173v1_genomic.fna/cds.fna -a GCF_018861735.1_ASM1886173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:58,340] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:58,341] [INFO] Task started: HMMsearch
[2024-01-24 12:22:58,341] [INFO] Running command: hmmsearch --tblout GCF_018861735.1_ASM1886173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b0ea900-4259-4fe8-88d3-83db367b0923/dqc_reference/reference_markers.hmm GCF_018861735.1_ASM1886173v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:58,669] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:58,671] [INFO] Found 6/6 markers.
[2024-01-24 12:22:58,722] [INFO] Query marker FASTA was written to GCF_018861735.1_ASM1886173v1_genomic.fna/markers.fasta
[2024-01-24 12:22:58,723] [INFO] Task started: Blastn
[2024-01-24 12:22:58,723] [INFO] Running command: blastn -query GCF_018861735.1_ASM1886173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b0ea900-4259-4fe8-88d3-83db367b0923/dqc_reference/reference_markers.fasta -out GCF_018861735.1_ASM1886173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:59,289] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:59,293] [INFO] Selected 14 target genomes.
[2024-01-24 12:22:59,294] [INFO] Target genome list was writen to GCF_018861735.1_ASM1886173v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:59,300] [INFO] Task started: fastANI
[2024-01-24 12:22:59,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea93e83-c761-4070-b25d-7b24c04e67b3/GCF_018861735.1_ASM1886173v1_genomic.fna.gz --refList GCF_018861735.1_ASM1886173v1_genomic.fna/target_genomes.txt --output GCF_018861735.1_ASM1886173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:11,455] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:11,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b0ea900-4259-4fe8-88d3-83db367b0923/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:11,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b0ea900-4259-4fe8-88d3-83db367b0923/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:11,467] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:11,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:11,468] [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
Clostridium lacusfryxellense	strain=DSM 14205	GCA_018861735.1	205328	205328	type	True	100.0	1709	1716	95	conclusive
Clostridium algoriphilum	strain=DSM 16153	GCA_020443705.1	198347	198347	type	True	82.0254	828	1716	95	below_threshold
Clostridium frigoris	strain=DSM 14204	GCA_018861865.1	205327	205327	type	True	81.8927	768	1716	95	below_threshold
Clostridium estertheticum subsp. laramiense	strain=DSM 14864	GCA_008933175.2	205326	238834	type	True	81.8295	817	1716	95	below_threshold
Clostridium estertheticum subsp. estertheticum	strain=DSM 8809	GCA_001877035.1	1552	238834	type	True	81.8037	815	1716	95	below_threshold
Clostridium psychrophilum	strain=DSM 14207	GCA_018861705.1	132926	132926	type	True	81.5044	702	1716	95	below_threshold
Clostridium tagluense	strain=A121	GCA_003865095.1	360422	360422	type	True	81.2245	709	1716	95	below_threshold
Clostridium bowmanii	strain=DSM 14206	GCA_020176155.1	132925	132925	type	True	81.1902	774	1716	95	below_threshold
Clostridium bowmanii	strain=DSM 14206	GCA_018861315.1	132925	132925	type	True	81.1691	774	1716	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.0778	120	1716	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.0194	126	1716	95	below_threshold
Clostridium grantii	strain=DSM 8605	GCA_900129965.1	40575	40575	type	True	75.974	146	1716	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	75.8118	131	1716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:11,469] [INFO] DFAST Taxonomy check result was written to GCF_018861735.1_ASM1886173v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:11,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:11,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:11,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b0ea900-4259-4fe8-88d3-83db367b0923/dqc_reference/checkm_data
[2024-01-24 12:23:11,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:11,522] [INFO] Task started: CheckM
[2024-01-24 12:23:11,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018861735.1_ASM1886173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018861735.1_ASM1886173v1_genomic.fna/checkm_input GCF_018861735.1_ASM1886173v1_genomic.fna/checkm_result
[2024-01-24 12:23:42,597] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:42,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:42,625] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:42,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:42,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018861735.1_ASM1886173v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:42,626] [INFO] Task started: Blastn
[2024-01-24 12:23:42,626] [INFO] Running command: blastn -query GCF_018861735.1_ASM1886173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b0ea900-4259-4fe8-88d3-83db367b0923/dqc_reference/reference_markers_gtdb.fasta -out GCF_018861735.1_ASM1886173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:43,425] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:43,430] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:43,430] [INFO] Target genome list was writen to GCF_018861735.1_ASM1886173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:43,466] [INFO] Task started: fastANI
[2024-01-24 12:23:43,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea93e83-c761-4070-b25d-7b24c04e67b3/GCF_018861735.1_ASM1886173v1_genomic.fna.gz --refList GCF_018861735.1_ASM1886173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018861735.1_ASM1886173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:53,006] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:53,015] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:53,015] [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_018861735.1	s__Clostridium_AD lacusfryxellense	100.0	1709	1716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011065905.1	s__Clostridium_AD estertheticum_B	82.4396	714	1716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	97.19	97.19	0.83	0.83	2	-
GCA_002403785.1	s__Clostridium_AD sp002403785	82.3412	723	1716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861865.1	s__Clostridium_AD frigoris	81.9206	764	1716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861325.1	s__Clostridium_AD estertheticum_C	81.8173	820	1716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	97.28	95.54	0.84	0.79	3	-
GCF_001877035.1	s__Clostridium_AD estertheticum	81.8107	817	1716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	98.08	95.13	0.86	0.81	10	-
GCF_018861905.1	s__Clostridium_AD sp018861905	81.7563	821	1716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650095.1	s__Clostridium_AD sp016650095	81.6046	556	1716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861315.1	s__Clostridium_AD bowmanii	81.2234	767	1716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:53,016] [INFO] GTDB search result was written to GCF_018861735.1_ASM1886173v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:53,017] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:53,021] [INFO] DFAST_QC result json was written to GCF_018861735.1_ASM1886173v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:53,021] [INFO] DFAST_QC completed!
[2024-01-24 12:23:53,022] [INFO] Total running time: 0h1m5s