[2024-01-24 12:53:56,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b8a6fe3-9caa-4f01-afee-5359571b53d1/dqc_reference
[2024-01-24 12:53:57,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:57,936] [INFO] Task started: Prodigal
[2024-01-24 12:53:57,936] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd39a2cc-ce48-42ad-a0eb-f92141cfc806/GCF_000236685.1_ASM23668v1_genomic.fna.gz | prodigal -d GCF_000236685.1_ASM23668v1_genomic.fna/cds.fna -a GCF_000236685.1_ASM23668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:08,438] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:08,438] [INFO] Task started: HMMsearch
[2024-01-24 12:54:08,439] [INFO] Running command: hmmsearch --tblout GCF_000236685.1_ASM23668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b8a6fe3-9caa-4f01-afee-5359571b53d1/dqc_reference/reference_markers.hmm GCF_000236685.1_ASM23668v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:08,671] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:08,672] [INFO] Found 6/6 markers.
[2024-01-24 12:54:08,714] [INFO] Query marker FASTA was written to GCF_000236685.1_ASM23668v1_genomic.fna/markers.fasta
[2024-01-24 12:54:08,714] [INFO] Task started: Blastn
[2024-01-24 12:54:08,715] [INFO] Running command: blastn -query GCF_000236685.1_ASM23668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b8a6fe3-9caa-4f01-afee-5359571b53d1/dqc_reference/reference_markers.fasta -out GCF_000236685.1_ASM23668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:09,327] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:09,332] [INFO] Selected 10 target genomes.
[2024-01-24 12:54:09,332] [INFO] Target genome list was writen to GCF_000236685.1_ASM23668v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:09,351] [INFO] Task started: fastANI
[2024-01-24 12:54:09,351] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd39a2cc-ce48-42ad-a0eb-f92141cfc806/GCF_000236685.1_ASM23668v1_genomic.fna.gz --refList GCF_000236685.1_ASM23668v1_genomic.fna/target_genomes.txt --output GCF_000236685.1_ASM23668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:15,624] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:15,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b8a6fe3-9caa-4f01-afee-5359571b53d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:15,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b8a6fe3-9caa-4f01-afee-5359571b53d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:15,631] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:15,631] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:15,631] [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 pleomorpha	strain=Grapes	GCA_000236685.1	1131707	1131707	type	True	100.0	1196	1196	95	conclusive
Sphaerochaeta associata	strain=GLS2T	GCA_022869165.1	1129264	1129264	type	True	80.1432	133	1196	95	below_threshold
Sphaerochaeta globosa	strain=Buddy	GCA_000190435.1	1131703	1131703	type	True	78.4635	121	1196	95	below_threshold
Sphaerochaeta halotolerans	strain=4-11	GCA_003429665.1	2293840	2293840	type	True	77.6164	93	1196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:15,633] [INFO] DFAST Taxonomy check result was written to GCF_000236685.1_ASM23668v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:15,634] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:15,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:15,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b8a6fe3-9caa-4f01-afee-5359571b53d1/dqc_reference/checkm_data
[2024-01-24 12:54:15,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:15,671] [INFO] Task started: CheckM
[2024-01-24 12:54:15,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000236685.1_ASM23668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000236685.1_ASM23668v1_genomic.fna/checkm_input GCF_000236685.1_ASM23668v1_genomic.fna/checkm_result
[2024-01-24 12:54:48,523] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:48,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:48,553] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:48,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:48,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000236685.1_ASM23668v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:48,554] [INFO] Task started: Blastn
[2024-01-24 12:54:48,554] [INFO] Running command: blastn -query GCF_000236685.1_ASM23668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b8a6fe3-9caa-4f01-afee-5359571b53d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000236685.1_ASM23668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:49,327] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:49,331] [INFO] Selected 21 target genomes.
[2024-01-24 12:54:49,332] [INFO] Target genome list was writen to GCF_000236685.1_ASM23668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:49,356] [INFO] Task started: fastANI
[2024-01-24 12:54:49,356] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd39a2cc-ce48-42ad-a0eb-f92141cfc806/GCF_000236685.1_ASM23668v1_genomic.fna.gz --refList GCF_000236685.1_ASM23668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000236685.1_ASM23668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:00,284] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:00,295] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:00,296] [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_000236685.1	s__Sphaerochaeta pleomorpha	100.0	1195	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002839335.1	s__UBA8525 sp002839335	82.9331	58	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA8525	95.0	98.90	98.83	0.90	0.88	5	-
GCA_002839355.1	s__UBA8525 sp002839355	82.8389	53	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA8525	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190435.1	s__Sphaerochaeta globosa	78.4635	121	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838275.1	s__Sphaerochaeta sp012838275	78.1136	90	1196	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	78.0101	116	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.32	97.53	0.87	0.80	11	-
GCF_016406725.1	s__Sphaerochaeta sp016406725	77.9089	85	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429665.1	s__Sphaerochaeta halotolerans	77.6237	92	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.82	98.46	0.91	0.89	4	-
GCA_003446545.1	s__Sphaerochaeta sp003446545	77.5024	83	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	99.24	99.24	0.91	0.91	2	-
GCA_016342655.1	s__Sphaerochaeta sp016342655	77.404	148	1196	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	77.2523	74	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009930195.1	s__Sphaerochaeta sp009930195	76.9398	100	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	99.24	99.24	0.76	0.76	2	-
GCA_012511235.1	s__Sphaerochaeta sp012511235	76.8463	73	1196	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.08	98.08	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:00,297] [INFO] GTDB search result was written to GCF_000236685.1_ASM23668v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:00,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:00,301] [INFO] DFAST_QC result json was written to GCF_000236685.1_ASM23668v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:00,301] [INFO] DFAST_QC completed!
[2024-01-24 12:55:00,302] [INFO] Total running time: 0h1m4s