[2024-01-25 19:56:20,477] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:20,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:20,479] [INFO] DQC Reference Directory: /var/lib/cwl/stga8611b25-0784-41bb-83b1-611528cbe607/dqc_reference
[2024-01-25 19:56:21,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:21,762] [INFO] Task started: Prodigal
[2024-01-25 19:56:21,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg66da5892-cc28-4b1f-9c2f-4ab475a837d0/GCF_014193895.1_ASM1419389v1_genomic.fna.gz | prodigal -d GCF_014193895.1_ASM1419389v1_genomic.fna/cds.fna -a GCF_014193895.1_ASM1419389v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:29,503] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:29,503] [INFO] Task started: HMMsearch
[2024-01-25 19:56:29,503] [INFO] Running command: hmmsearch --tblout GCF_014193895.1_ASM1419389v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8611b25-0784-41bb-83b1-611528cbe607/dqc_reference/reference_markers.hmm GCF_014193895.1_ASM1419389v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:29,790] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:29,792] [INFO] Found 6/6 markers.
[2024-01-25 19:56:29,830] [INFO] Query marker FASTA was written to GCF_014193895.1_ASM1419389v1_genomic.fna/markers.fasta
[2024-01-25 19:56:29,830] [INFO] Task started: Blastn
[2024-01-25 19:56:29,830] [INFO] Running command: blastn -query GCF_014193895.1_ASM1419389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8611b25-0784-41bb-83b1-611528cbe607/dqc_reference/reference_markers.fasta -out GCF_014193895.1_ASM1419389v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:30,373] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:30,376] [INFO] Selected 23 target genomes.
[2024-01-25 19:56:30,376] [INFO] Target genome list was writen to GCF_014193895.1_ASM1419389v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:30,391] [INFO] Task started: fastANI
[2024-01-25 19:56:30,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg66da5892-cc28-4b1f-9c2f-4ab475a837d0/GCF_014193895.1_ASM1419389v1_genomic.fna.gz --refList GCF_014193895.1_ASM1419389v1_genomic.fna/target_genomes.txt --output GCF_014193895.1_ASM1419389v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:50,588] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:50,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8611b25-0784-41bb-83b1-611528cbe607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:50,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8611b25-0784-41bb-83b1-611528cbe607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:50,598] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:56:50,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:50,598] [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 fungisolvens	strain=TW1	GCA_014193895.1	1604897	1604897	type	True	100.0	1755	1757	95	conclusive
Clostridium zeae	strain=CSC2	GCA_017312485.1	2759022	2759022	type	True	90.7474	1433	1757	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	81.3746	849	1757	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	78.2642	229	1757	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	77.8095	149	1757	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	77.7556	183	1757	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	77.7305	222	1757	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	77.602	257	1757	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	77.2834	173	1757	95	below_threshold
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	76.8864	129	1757	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	76.8061	207	1757	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	76.7933	195	1757	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.1272	138	1757	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	76.0528	51	1757	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:50,600] [INFO] DFAST Taxonomy check result was written to GCF_014193895.1_ASM1419389v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:50,600] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:50,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:50,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8611b25-0784-41bb-83b1-611528cbe607/dqc_reference/checkm_data
[2024-01-25 19:56:50,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:50,655] [INFO] Task started: CheckM
[2024-01-25 19:56:50,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014193895.1_ASM1419389v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014193895.1_ASM1419389v1_genomic.fna/checkm_input GCF_014193895.1_ASM1419389v1_genomic.fna/checkm_result
[2024-01-25 19:57:17,499] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:17,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:17,519] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:17,519] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:17,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014193895.1_ASM1419389v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:17,521] [INFO] Task started: Blastn
[2024-01-25 19:57:17,521] [INFO] Running command: blastn -query GCF_014193895.1_ASM1419389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8611b25-0784-41bb-83b1-611528cbe607/dqc_reference/reference_markers_gtdb.fasta -out GCF_014193895.1_ASM1419389v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:18,355] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:18,358] [INFO] Selected 10 target genomes.
[2024-01-25 19:57:18,358] [INFO] Target genome list was writen to GCF_014193895.1_ASM1419389v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:18,380] [INFO] Task started: fastANI
[2024-01-25 19:57:18,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg66da5892-cc28-4b1f-9c2f-4ab475a837d0/GCF_014193895.1_ASM1419389v1_genomic.fna.gz --refList GCF_014193895.1_ASM1419389v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014193895.1_ASM1419389v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:29,763] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:29,769] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:29,769] [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_014193895.1	s__Clostridium_AR fungisolvens	100.0	1754	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017312485.1	s__Clostridium_AR sp017312485	90.7352	1435	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595795.1	s__Clostridium_AR sp016595795	89.0753	1325	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004015185.1	s__Clostridium_AR sp004015185	81.3984	848	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928445.1	s__Clostridium_AR sp009928445	81.0051	849	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900456775.1	s__Clostridium_P ventriculi	77.6601	150	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.93	98.34	0.95	0.94	8	-
GCF_015550425.1	s__Clostridium sp015550425	77.0701	183	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.01	99.01	0.93	0.93	2	-
GCA_900759995.1	s__Clostridium sp900759995	76.7307	162	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.46	98.18	0.80	0.79	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:29,771] [INFO] GTDB search result was written to GCF_014193895.1_ASM1419389v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:29,771] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:29,774] [INFO] DFAST_QC result json was written to GCF_014193895.1_ASM1419389v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:29,774] [INFO] DFAST_QC completed!
[2024-01-25 19:57:29,774] [INFO] Total running time: 0h1m9s