[2024-01-24 14:05:36,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg24f6983e-867f-4353-a7cb-74ae55d45815/dqc_reference
[2024-01-24 14:05:37,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:37,942] [INFO] Task started: Prodigal
[2024-01-24 14:05:37,943] [INFO] Running command: gunzip -c /var/lib/cwl/stgc353bfa4-1542-47b4-8b11-c03492201658/GCF_003429665.1_ASM342966v1_genomic.fna.gz | prodigal -d GCF_003429665.1_ASM342966v1_genomic.fna/cds.fna -a GCF_003429665.1_ASM342966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:47,118] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:47,119] [INFO] Task started: HMMsearch
[2024-01-24 14:05:47,119] [INFO] Running command: hmmsearch --tblout GCF_003429665.1_ASM342966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24f6983e-867f-4353-a7cb-74ae55d45815/dqc_reference/reference_markers.hmm GCF_003429665.1_ASM342966v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:47,445] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:47,446] [INFO] Found 6/6 markers.
[2024-01-24 14:05:47,476] [INFO] Query marker FASTA was written to GCF_003429665.1_ASM342966v1_genomic.fna/markers.fasta
[2024-01-24 14:05:47,477] [INFO] Task started: Blastn
[2024-01-24 14:05:47,477] [INFO] Running command: blastn -query GCF_003429665.1_ASM342966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24f6983e-867f-4353-a7cb-74ae55d45815/dqc_reference/reference_markers.fasta -out GCF_003429665.1_ASM342966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:48,055] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:48,058] [INFO] Selected 11 target genomes.
[2024-01-24 14:05:48,059] [INFO] Target genome list was writen to GCF_003429665.1_ASM342966v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:48,066] [INFO] Task started: fastANI
[2024-01-24 14:05:48,066] [INFO] Running command: fastANI --query /var/lib/cwl/stgc353bfa4-1542-47b4-8b11-c03492201658/GCF_003429665.1_ASM342966v1_genomic.fna.gz --refList GCF_003429665.1_ASM342966v1_genomic.fna/target_genomes.txt --output GCF_003429665.1_ASM342966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:55,168] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:55,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24f6983e-867f-4353-a7cb-74ae55d45815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:55,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24f6983e-867f-4353-a7cb-74ae55d45815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:55,176] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:55,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:55,176] [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
Sphaerochaeta halotolerans	strain=4-11	GCA_003429665.1	2293840	2293840	type	True	100.0	952	953	95	conclusive
Sphaerochaeta globosa	strain=Buddy	GCA_000190435.1	1131703	1131703	type	True	78.3392	186	953	95	below_threshold
Sphaerochaeta associata	strain=GLS2T	GCA_022869165.1	1129264	1129264	type	True	78.0685	215	953	95	below_threshold
Sphaerochaeta pleomorpha	strain=Grapes	GCA_000236685.1	1131707	1131707	type	True	77.339	89	953	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:55,177] [INFO] DFAST Taxonomy check result was written to GCF_003429665.1_ASM342966v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:55,178] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:55,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:55,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24f6983e-867f-4353-a7cb-74ae55d45815/dqc_reference/checkm_data
[2024-01-24 14:05:55,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:55,211] [INFO] Task started: CheckM
[2024-01-24 14:05:55,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003429665.1_ASM342966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003429665.1_ASM342966v1_genomic.fna/checkm_input GCF_003429665.1_ASM342966v1_genomic.fna/checkm_result
[2024-01-24 14:06:27,116] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:27,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:27,134] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:27,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:27,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003429665.1_ASM342966v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:27,135] [INFO] Task started: Blastn
[2024-01-24 14:06:27,135] [INFO] Running command: blastn -query GCF_003429665.1_ASM342966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24f6983e-867f-4353-a7cb-74ae55d45815/dqc_reference/reference_markers_gtdb.fasta -out GCF_003429665.1_ASM342966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:27,955] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:27,958] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:27,958] [INFO] Target genome list was writen to GCF_003429665.1_ASM342966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:28,013] [INFO] Task started: fastANI
[2024-01-24 14:06:28,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgc353bfa4-1542-47b4-8b11-c03492201658/GCF_003429665.1_ASM342966v1_genomic.fna.gz --refList GCF_003429665.1_ASM342966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003429665.1_ASM342966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:35,505] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:35,516] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:35,516] [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_003429665.1	s__Sphaerochaeta halotolerans	100.0	952	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.82	98.46	0.91	0.89	4	conclusive
GCA_018399495.1	s__Sphaerochaeta sp018399495	84.7385	634	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406725.1	s__Sphaerochaeta sp016406725	84.39	559	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190435.1	s__Sphaerochaeta globosa	78.3473	185	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003247345.1	s__Sphaerochaeta sp003247345	78.2923	175	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519125.1	s__Sphaerochaeta sp012519125	78.098	152	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432715.1	s__Sphaerochaeta sp002432715	78.0513	205	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.32	97.53	0.87	0.80	11	-
GCA_001603115.1	s__Sphaerochaeta sp001603115	77.9746	159	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012511235.1	s__Sphaerochaeta sp012511235	77.4615	137	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.08	98.08	0.92	0.92	2	-
GCF_000236685.1	s__Sphaerochaeta pleomorpha	77.3726	87	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514185.1	s__Sphaerochaeta sp012514185	77.3608	151	953	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:35,518] [INFO] GTDB search result was written to GCF_003429665.1_ASM342966v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:35,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:35,526] [INFO] DFAST_QC result json was written to GCF_003429665.1_ASM342966v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:35,526] [INFO] DFAST_QC completed!
[2024-01-24 14:06:35,526] [INFO] Total running time: 0h0m59s