[2024-01-25 20:17:50,861] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg13a656aa-ffbb-4bc1-9254-cc402ef373bd/dqc_reference
[2024-01-25 20:17:51,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:51,991] [INFO] Task started: Prodigal
[2024-01-25 20:17:51,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg290d9c09-a8dc-4704-9f05-8e77732d1c16/GCF_020443705.1_ASM2044370v1_genomic.fna.gz | prodigal -d GCF_020443705.1_ASM2044370v1_genomic.fna/cds.fna -a GCF_020443705.1_ASM2044370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:58,325] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:58,325] [INFO] Task started: HMMsearch
[2024-01-25 20:17:58,325] [INFO] Running command: hmmsearch --tblout GCF_020443705.1_ASM2044370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13a656aa-ffbb-4bc1-9254-cc402ef373bd/dqc_reference/reference_markers.hmm GCF_020443705.1_ASM2044370v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:58,572] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:58,574] [INFO] Found 6/6 markers.
[2024-01-25 20:17:58,608] [INFO] Query marker FASTA was written to GCF_020443705.1_ASM2044370v1_genomic.fna/markers.fasta
[2024-01-25 20:17:58,609] [INFO] Task started: Blastn
[2024-01-25 20:17:58,609] [INFO] Running command: blastn -query GCF_020443705.1_ASM2044370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13a656aa-ffbb-4bc1-9254-cc402ef373bd/dqc_reference/reference_markers.fasta -out GCF_020443705.1_ASM2044370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:59,152] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:59,155] [INFO] Selected 12 target genomes.
[2024-01-25 20:17:59,155] [INFO] Target genome list was writen to GCF_020443705.1_ASM2044370v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:59,156] [INFO] Task started: fastANI
[2024-01-25 20:17:59,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg290d9c09-a8dc-4704-9f05-8e77732d1c16/GCF_020443705.1_ASM2044370v1_genomic.fna.gz --refList GCF_020443705.1_ASM2044370v1_genomic.fna/target_genomes.txt --output GCF_020443705.1_ASM2044370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:09,491] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:09,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13a656aa-ffbb-4bc1-9254-cc402ef373bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:09,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13a656aa-ffbb-4bc1-9254-cc402ef373bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:09,499] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:09,499] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:09,499] [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 algoriphilum	strain=DSM 16153	GCA_020443705.1	198347	198347	type	True	100.0	1437	1444	95	conclusive
Clostridium psychrophilum	strain=DSM 14207	GCA_018861705.1	132926	132926	type	True	84.3097	833	1444	95	below_threshold
Clostridium estertheticum subsp. estertheticum	strain=DSM 8809	GCA_001877035.1	1552	238834	type	True	82.7219	815	1444	95	below_threshold
Clostridium estertheticum subsp. laramiense	strain=DSM 14864	GCA_008933175.2	205326	238834	type	True	82.6942	816	1444	95	below_threshold
Clostridium frigoris	strain=DSM 14204	GCA_018861865.1	205327	205327	type	True	82.6757	773	1444	95	below_threshold
Clostridium lacusfryxellense	strain=DSM 14205	GCA_018861735.1	205328	205328	type	True	82.0414	823	1444	95	below_threshold
Clostridium tagluense	strain=A121	GCA_003865095.1	360422	360422	type	True	81.8118	703	1444	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.2684	112	1444	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	76.1363	127	1444	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	76.0511	129	1444	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	75.7426	103	1444	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:09,501] [INFO] DFAST Taxonomy check result was written to GCF_020443705.1_ASM2044370v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:09,501] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:09,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:09,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13a656aa-ffbb-4bc1-9254-cc402ef373bd/dqc_reference/checkm_data
[2024-01-25 20:18:09,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:09,548] [INFO] Task started: CheckM
[2024-01-25 20:18:09,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020443705.1_ASM2044370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020443705.1_ASM2044370v1_genomic.fna/checkm_input GCF_020443705.1_ASM2044370v1_genomic.fna/checkm_result
[2024-01-25 20:18:33,343] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:33,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:33,365] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:33,365] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:33,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020443705.1_ASM2044370v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:33,369] [INFO] Task started: Blastn
[2024-01-25 20:18:33,369] [INFO] Running command: blastn -query GCF_020443705.1_ASM2044370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13a656aa-ffbb-4bc1-9254-cc402ef373bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_020443705.1_ASM2044370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:34,140] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:34,143] [INFO] Selected 10 target genomes.
[2024-01-25 20:18:34,143] [INFO] Target genome list was writen to GCF_020443705.1_ASM2044370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:34,146] [INFO] Task started: fastANI
[2024-01-25 20:18:34,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg290d9c09-a8dc-4704-9f05-8e77732d1c16/GCF_020443705.1_ASM2044370v1_genomic.fna.gz --refList GCF_020443705.1_ASM2044370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020443705.1_ASM2044370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:44,989] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:44,996] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:18:44,996] [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
GCA_002403785.1	s__Clostridium_AD sp002403785	88.4643	918	1444	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_018861705.1	s__Clostridium_AD psychrophilum	84.2921	834	1444	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	83.4191	710	1444	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_018861905.1	s__Clostridium_AD sp018861905	82.8679	822	1444	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	82.7809	830	1444	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	82.7353	812	1444	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_018861865.1	s__Clostridium_AD frigoris	82.7001	770	1444	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	82.5359	545	1444	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	82.0067	825	1444	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_003865095.1	s__Clostridium_AD tagluense	81.8139	704	1444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	96.49	95.92	0.80	0.78	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:44,998] [INFO] GTDB search result was written to GCF_020443705.1_ASM2044370v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:44,998] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:45,001] [INFO] DFAST_QC result json was written to GCF_020443705.1_ASM2044370v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:45,001] [INFO] DFAST_QC completed!
[2024-01-25 20:18:45,001] [INFO] Total running time: 0h0m54s