[2024-01-24 12:44:42,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:42,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:42,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fc729e0-a71a-46bb-b1d9-e1bae13436b5/dqc_reference
[2024-01-24 12:44:43,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:43,612] [INFO] Task started: Prodigal
[2024-01-24 12:44:43,612] [INFO] Running command: gunzip -c /var/lib/cwl/stgd354940e-4084-4a50-8039-a9283f659d00/GCF_018861705.1_ASM1886170v1_genomic.fna.gz | prodigal -d GCF_018861705.1_ASM1886170v1_genomic.fna/cds.fna -a GCF_018861705.1_ASM1886170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:49,801] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:49,802] [INFO] Task started: HMMsearch
[2024-01-24 12:44:49,802] [INFO] Running command: hmmsearch --tblout GCF_018861705.1_ASM1886170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fc729e0-a71a-46bb-b1d9-e1bae13436b5/dqc_reference/reference_markers.hmm GCF_018861705.1_ASM1886170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:50,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:50,166] [INFO] Found 6/6 markers.
[2024-01-24 12:44:50,203] [INFO] Query marker FASTA was written to GCF_018861705.1_ASM1886170v1_genomic.fna/markers.fasta
[2024-01-24 12:44:50,204] [INFO] Task started: Blastn
[2024-01-24 12:44:50,204] [INFO] Running command: blastn -query GCF_018861705.1_ASM1886170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fc729e0-a71a-46bb-b1d9-e1bae13436b5/dqc_reference/reference_markers.fasta -out GCF_018861705.1_ASM1886170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:50,812] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:50,816] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:50,816] [INFO] Target genome list was writen to GCF_018861705.1_ASM1886170v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:50,852] [INFO] Task started: fastANI
[2024-01-24 12:44:50,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgd354940e-4084-4a50-8039-a9283f659d00/GCF_018861705.1_ASM1886170v1_genomic.fna.gz --refList GCF_018861705.1_ASM1886170v1_genomic.fna/target_genomes.txt --output GCF_018861705.1_ASM1886170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:01,529] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:01,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fc729e0-a71a-46bb-b1d9-e1bae13436b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:01,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fc729e0-a71a-46bb-b1d9-e1bae13436b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:01,540] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:01,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:01,540] [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 psychrophilum	strain=DSM 14207	GCA_018861705.1	132926	132926	type	True	100.0	1221	1230	95	conclusive
Clostridium algoriphilum	strain=DSM 16153	GCA_020443705.1	198347	198347	type	True	84.5462	836	1230	95	below_threshold
Clostridium frigoris	strain=DSM 14204	GCA_018861865.1	205327	205327	type	True	83.3018	764	1230	95	below_threshold
Clostridium estertheticum subsp. estertheticum	strain=DSM 8809	GCA_001877035.1	1552	238834	type	True	82.6518	758	1230	95	below_threshold
Clostridium estertheticum subsp. laramiense	strain=DSM 14864	GCA_008933175.2	205326	238834	type	True	82.5835	786	1230	95	below_threshold
Clostridium lacusfryxellense	strain=DSM 14205	GCA_018861735.1	205328	205328	type	True	81.6316	697	1230	95	below_threshold
Clostridium bowmanii	strain=DSM 14206	GCA_018861315.1	132925	132925	type	True	80.7455	629	1230	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.17	70	1230	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	75.9532	97	1230	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	75.8412	106	1230	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	75.6278	93	1230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:01,542] [INFO] DFAST Taxonomy check result was written to GCF_018861705.1_ASM1886170v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:01,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:01,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:01,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fc729e0-a71a-46bb-b1d9-e1bae13436b5/dqc_reference/checkm_data
[2024-01-24 12:45:01,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:01,587] [INFO] Task started: CheckM
[2024-01-24 12:45:01,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018861705.1_ASM1886170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018861705.1_ASM1886170v1_genomic.fna/checkm_input GCF_018861705.1_ASM1886170v1_genomic.fna/checkm_result
[2024-01-24 12:45:27,395] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:27,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:27,423] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:27,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:27,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018861705.1_ASM1886170v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:27,424] [INFO] Task started: Blastn
[2024-01-24 12:45:27,425] [INFO] Running command: blastn -query GCF_018861705.1_ASM1886170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fc729e0-a71a-46bb-b1d9-e1bae13436b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_018861705.1_ASM1886170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:28,251] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:28,255] [INFO] Selected 8 target genomes.
[2024-01-24 12:45:28,255] [INFO] Target genome list was writen to GCF_018861705.1_ASM1886170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:28,277] [INFO] Task started: fastANI
[2024-01-24 12:45:28,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgd354940e-4084-4a50-8039-a9283f659d00/GCF_018861705.1_ASM1886170v1_genomic.fna.gz --refList GCF_018861705.1_ASM1886170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018861705.1_ASM1886170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:36,385] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:36,399] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:36,399] [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_018861705.1	s__Clostridium_AD psychrophilum	100.0	1221	1230	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
GCA_002403785.1	s__Clostridium_AD sp002403785	84.865	737	1230	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	83.2856	765	1230	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_018861905.1	s__Clostridium_AD sp018861905	82.8475	788	1230	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_001877035.1	s__Clostridium_AD estertheticum	82.6588	758	1230	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_018861325.1	s__Clostridium_AD estertheticum_C	82.529	764	1230	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_011065905.1	s__Clostridium_AD estertheticum_B	81.9127	611	1230	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_016650095.1	s__Clostridium_AD sp016650095	80.9884	474	1230	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 12:45:36,401] [INFO] GTDB search result was written to GCF_018861705.1_ASM1886170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:36,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:36,404] [INFO] DFAST_QC result json was written to GCF_018861705.1_ASM1886170v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:36,405] [INFO] DFAST_QC completed!
[2024-01-24 12:45:36,405] [INFO] Total running time: 0h0m54s