[2024-01-25 18:05:50,439] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:50,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:50,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg897ee11b-725c-4893-a4d4-5f0d62c5db25/dqc_reference
[2024-01-25 18:05:51,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:51,590] [INFO] Task started: Prodigal
[2024-01-25 18:05:51,591] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb3791eb-88db-45c5-94b3-d0d1b2ccfeb9/GCF_000331995.1_ASM33199v1_genomic.fna.gz | prodigal -d GCF_000331995.1_ASM33199v1_genomic.fna/cds.fna -a GCF_000331995.1_ASM33199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:05:57,788] [INFO] Task succeeded: Prodigal
[2024-01-25 18:05:57,789] [INFO] Task started: HMMsearch
[2024-01-25 18:05:57,789] [INFO] Running command: hmmsearch --tblout GCF_000331995.1_ASM33199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg897ee11b-725c-4893-a4d4-5f0d62c5db25/dqc_reference/reference_markers.hmm GCF_000331995.1_ASM33199v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:05:58,009] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:05:58,010] [INFO] Found 6/6 markers.
[2024-01-25 18:05:58,033] [INFO] Query marker FASTA was written to GCF_000331995.1_ASM33199v1_genomic.fna/markers.fasta
[2024-01-25 18:05:58,034] [INFO] Task started: Blastn
[2024-01-25 18:05:58,034] [INFO] Running command: blastn -query GCF_000331995.1_ASM33199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg897ee11b-725c-4893-a4d4-5f0d62c5db25/dqc_reference/reference_markers.fasta -out GCF_000331995.1_ASM33199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:58,622] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:58,624] [INFO] Selected 9 target genomes.
[2024-01-25 18:05:58,625] [INFO] Target genome list was writen to GCF_000331995.1_ASM33199v1_genomic.fna/target_genomes.txt
[2024-01-25 18:05:58,629] [INFO] Task started: fastANI
[2024-01-25 18:05:58,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb3791eb-88db-45c5-94b3-d0d1b2ccfeb9/GCF_000331995.1_ASM33199v1_genomic.fna.gz --refList GCF_000331995.1_ASM33199v1_genomic.fna/target_genomes.txt --output GCF_000331995.1_ASM33199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:04,480] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:04,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg897ee11b-725c-4893-a4d4-5f0d62c5db25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:04,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg897ee11b-725c-4893-a4d4-5f0d62c5db25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:04,485] [INFO] Found 4 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:06:04,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:04,485] [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
Thermoclostridium stercorarium subsp. stercorarium	strain=DSM 8532	GCA_000331995.1	160845	1510	type	True	100.0	991	991	95	conclusive
Thermoclostridium stercorarium subsp. stercorarium	strain=DSM 8532	GCA_000349885.2	160845	1510	type	True	99.9966	988	991	95	conclusive
Thermoclostridium stercorarium subsp. thermolacticum	strain=DSM 2910	GCA_001697245.1	29351	1510	type	True	99.8102	955	991	95	conclusive
Thermoclostridium stercorarium subsp. leptospartum	strain=DSM 9219	GCA_001697285.1	160385	1510	type	True	99.5704	942	991	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 18:06:04,486] [INFO] DFAST Taxonomy check result was written to GCF_000331995.1_ASM33199v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:04,487] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:04,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:04,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg897ee11b-725c-4893-a4d4-5f0d62c5db25/dqc_reference/checkm_data
[2024-01-25 18:06:04,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:04,522] [INFO] Task started: CheckM
[2024-01-25 18:06:04,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000331995.1_ASM33199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000331995.1_ASM33199v1_genomic.fna/checkm_input GCF_000331995.1_ASM33199v1_genomic.fna/checkm_result
[2024-01-25 18:06:27,152] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:27,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:27,176] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:27,176] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:27,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000331995.1_ASM33199v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:27,177] [INFO] Task started: Blastn
[2024-01-25 18:06:27,177] [INFO] Running command: blastn -query GCF_000331995.1_ASM33199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg897ee11b-725c-4893-a4d4-5f0d62c5db25/dqc_reference/reference_markers_gtdb.fasta -out GCF_000331995.1_ASM33199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:28,188] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:28,191] [INFO] Selected 20 target genomes.
[2024-01-25 18:06:28,191] [INFO] Target genome list was writen to GCF_000331995.1_ASM33199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:28,206] [INFO] Task started: fastANI
[2024-01-25 18:06:28,206] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb3791eb-88db-45c5-94b3-d0d1b2ccfeb9/GCF_000331995.1_ASM33199v1_genomic.fna.gz --refList GCF_000331995.1_ASM33199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000331995.1_ASM33199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:37,680] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:37,684] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:37,684] [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_000331995.1	s__Thermoclostridium stercorarium	100.0	991	991	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium	95.0	99.79	99.59	0.97	0.95	5	conclusive
GCA_012521105.1	s__Thermoclostridium sp012521105	77.2201	338	991	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001513105.1	s__Thermoclostridium sp001513105	77.185	327	991	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium	95.0	99.92	99.92	0.94	0.94	2	-
GCA_012516065.1	s__DTU069 sp012516065	76.2244	70	991	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU069	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:37,686] [INFO] GTDB search result was written to GCF_000331995.1_ASM33199v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:37,686] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:37,688] [INFO] DFAST_QC result json was written to GCF_000331995.1_ASM33199v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:37,688] [INFO] DFAST_QC completed!
[2024-01-25 18:06:37,688] [INFO] Total running time: 0h0m47s