[2024-01-25 20:16:20,628] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:20,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:20,630] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3ced311-c96f-4563-b1e1-11746b50deb5/dqc_reference
[2024-01-25 20:16:21,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:21,830] [INFO] Task started: Prodigal
[2024-01-25 20:16:21,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg07866d72-6a9c-488f-bbae-e78270ce49f9/GCF_008933175.2_ASM893317v2_genomic.fna.gz | prodigal -d GCF_008933175.2_ASM893317v2_genomic.fna/cds.fna -a GCF_008933175.2_ASM893317v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:29,568] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:29,569] [INFO] Task started: HMMsearch
[2024-01-25 20:16:29,569] [INFO] Running command: hmmsearch --tblout GCF_008933175.2_ASM893317v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3ced311-c96f-4563-b1e1-11746b50deb5/dqc_reference/reference_markers.hmm GCF_008933175.2_ASM893317v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:29,852] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:29,853] [INFO] Found 6/6 markers.
[2024-01-25 20:16:29,893] [INFO] Query marker FASTA was written to GCF_008933175.2_ASM893317v2_genomic.fna/markers.fasta
[2024-01-25 20:16:29,893] [INFO] Task started: Blastn
[2024-01-25 20:16:29,893] [INFO] Running command: blastn -query GCF_008933175.2_ASM893317v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3ced311-c96f-4563-b1e1-11746b50deb5/dqc_reference/reference_markers.fasta -out GCF_008933175.2_ASM893317v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:30,438] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:30,442] [INFO] Selected 12 target genomes.
[2024-01-25 20:16:30,442] [INFO] Target genome list was writen to GCF_008933175.2_ASM893317v2_genomic.fna/target_genomes.txt
[2024-01-25 20:16:30,446] [INFO] Task started: fastANI
[2024-01-25 20:16:30,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg07866d72-6a9c-488f-bbae-e78270ce49f9/GCF_008933175.2_ASM893317v2_genomic.fna.gz --refList GCF_008933175.2_ASM893317v2_genomic.fna/target_genomes.txt --output GCF_008933175.2_ASM893317v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:42,997] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:42,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3ced311-c96f-4563-b1e1-11746b50deb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:42,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3ced311-c96f-4563-b1e1-11746b50deb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:43,006] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:16:43,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:43,006] [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 estertheticum subsp. laramiense	strain=DSM 14864	GCA_008933175.2	205326	238834	type	True	100.0	1687	1690	95	conclusive
Clostridium estertheticum subsp. estertheticum	strain=DSM 8809	GCA_001877035.1	1552	238834	type	True	99.7882	1544	1690	95	conclusive
Clostridium frigoris	strain=DSM 14204	GCA_018861865.1	205327	205327	type	True	89.3485	999	1690	95	below_threshold
Clostridium algoriphilum	strain=DSM 16153	GCA_020443705.1	198347	198347	type	True	82.7975	814	1690	95	below_threshold
Clostridium psychrophilum	strain=DSM 14207	GCA_018861705.1	132926	132926	type	True	82.4624	781	1690	95	below_threshold
Clostridium lacusfryxellense	strain=DSM 14205	GCA_018861735.1	205328	205328	type	True	81.7952	833	1690	95	below_threshold
Clostridium tagluense	strain=A121	GCA_003865095.1	360422	360422	type	True	81.3376	718	1690	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	77.6977	163	1690	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	77.6384	166	1690	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	77.5195	160	1690	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	77.0322	192	1690	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.1773	168	1690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:43,013] [INFO] DFAST Taxonomy check result was written to GCF_008933175.2_ASM893317v2_genomic.fna/tc_result.tsv
[2024-01-25 20:16:43,014] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:43,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:43,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3ced311-c96f-4563-b1e1-11746b50deb5/dqc_reference/checkm_data
[2024-01-25 20:16:43,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:43,065] [INFO] Task started: CheckM
[2024-01-25 20:16:43,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008933175.2_ASM893317v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008933175.2_ASM893317v2_genomic.fna/checkm_input GCF_008933175.2_ASM893317v2_genomic.fna/checkm_result
[2024-01-25 20:17:09,384] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:09,385] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:09,404] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:09,404] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:09,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008933175.2_ASM893317v2_genomic.fna/markers.fasta)
[2024-01-25 20:17:09,404] [INFO] Task started: Blastn
[2024-01-25 20:17:09,404] [INFO] Running command: blastn -query GCF_008933175.2_ASM893317v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3ced311-c96f-4563-b1e1-11746b50deb5/dqc_reference/reference_markers_gtdb.fasta -out GCF_008933175.2_ASM893317v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:10,125] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:10,128] [INFO] Selected 8 target genomes.
[2024-01-25 20:17:10,128] [INFO] Target genome list was writen to GCF_008933175.2_ASM893317v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:10,149] [INFO] Task started: fastANI
[2024-01-25 20:17:10,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg07866d72-6a9c-488f-bbae-e78270ce49f9/GCF_008933175.2_ASM893317v2_genomic.fna.gz --refList GCF_008933175.2_ASM893317v2_genomic.fna/target_genomes_gtdb.txt --output GCF_008933175.2_ASM893317v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:20,026] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:20,032] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:20,032] [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_001877035.1	s__Clostridium_AD estertheticum	99.7882	1544	1690	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	conclusive
GCF_018861325.1	s__Clostridium_AD estertheticum_C	94.1163	1261	1690	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_018861905.1	s__Clostridium_AD sp018861905	94.045	1247	1690	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	89.3524	999	1690	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_002403785.1	s__Clostridium_AD sp002403785	82.809	745	1690	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_011065905.1	s__Clostridium_AD estertheticum_B	82.6017	736	1690	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	-
GCF_018861705.1	s__Clostridium_AD psychrophilum	82.4007	787	1690	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_018861735.1	s__Clostridium_AD lacusfryxellense	81.7677	836	1690	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	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:20,035] [INFO] GTDB search result was written to GCF_008933175.2_ASM893317v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:20,036] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:20,039] [INFO] DFAST_QC result json was written to GCF_008933175.2_ASM893317v2_genomic.fna/dqc_result.json
[2024-01-25 20:17:20,039] [INFO] DFAST_QC completed!
[2024-01-25 20:17:20,039] [INFO] Total running time: 0h0m59s