[2023-06-17 00:12:05,545] [INFO] DFAST_QC pipeline started.
[2023-06-17 00:12:05,547] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 00:12:05,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg423cea51-9d53-4f9e-bf09-5d929fd15895/dqc_reference
[2023-06-17 00:12:06,779] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 00:12:06,781] [INFO] Task started: Prodigal
[2023-06-17 00:12:06,781] [INFO] Running command: gunzip -c /var/lib/cwl/stgff1c3700-8691-4535-97bc-387c5cecd86f/GCA_009914975.1_ASM991497v1_genomic.fna.gz | prodigal -d GCA_009914975.1_ASM991497v1_genomic.fna/cds.fna -a GCA_009914975.1_ASM991497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 00:12:21,123] [INFO] Task succeeded: Prodigal
[2023-06-17 00:12:21,123] [INFO] Task started: HMMsearch
[2023-06-17 00:12:21,123] [INFO] Running command: hmmsearch --tblout GCA_009914975.1_ASM991497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg423cea51-9d53-4f9e-bf09-5d929fd15895/dqc_reference/reference_markers.hmm GCA_009914975.1_ASM991497v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 00:12:21,423] [INFO] Task succeeded: HMMsearch
[2023-06-17 00:12:21,425] [INFO] Found 6/6 markers.
[2023-06-17 00:12:21,494] [INFO] Query marker FASTA was written to GCA_009914975.1_ASM991497v1_genomic.fna/markers.fasta
[2023-06-17 00:12:21,495] [INFO] Task started: Blastn
[2023-06-17 00:12:21,495] [INFO] Running command: blastn -query GCA_009914975.1_ASM991497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg423cea51-9d53-4f9e-bf09-5d929fd15895/dqc_reference/reference_markers.fasta -out GCA_009914975.1_ASM991497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:12:22,099] [INFO] Task succeeded: Blastn
[2023-06-17 00:12:22,105] [INFO] Selected 22 target genomes.
[2023-06-17 00:12:22,106] [INFO] Target genome list was writen to GCA_009914975.1_ASM991497v1_genomic.fna/target_genomes.txt
[2023-06-17 00:12:22,113] [INFO] Task started: fastANI
[2023-06-17 00:12:22,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgff1c3700-8691-4535-97bc-387c5cecd86f/GCA_009914975.1_ASM991497v1_genomic.fna.gz --refList GCA_009914975.1_ASM991497v1_genomic.fna/target_genomes.txt --output GCA_009914975.1_ASM991497v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 00:12:39,088] [INFO] Task succeeded: fastANI
[2023-06-17 00:12:39,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg423cea51-9d53-4f9e-bf09-5d929fd15895/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 00:12:39,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg423cea51-9d53-4f9e-bf09-5d929fd15895/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 00:12:39,101] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 00:12:39,101] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 00:12:39,101] [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 associata	strain=GLS2T	GCA_022869165.1	1129264	1129264	type	True	79.2441	201	918	95	below_threshold
Sphaerochaeta globosa	strain=Buddy	GCA_000190435.1	1131703	1131703	type	True	78.0913	175	918	95	below_threshold
Sphaerochaeta halotolerans	strain=4-11	GCA_003429665.1	2293840	2293840	type	True	76.9109	102	918	95	below_threshold
Sphaerochaeta pleomorpha	strain=Grapes	GCA_000236685.1	1131707	1131707	type	True	76.8349	97	918	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 00:12:39,107] [INFO] DFAST Taxonomy check result was written to GCA_009914975.1_ASM991497v1_genomic.fna/tc_result.tsv
[2023-06-17 00:12:39,107] [INFO] ===== Taxonomy check completed =====
[2023-06-17 00:12:39,107] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 00:12:39,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg423cea51-9d53-4f9e-bf09-5d929fd15895/dqc_reference/checkm_data
[2023-06-17 00:12:39,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 00:12:39,172] [INFO] Task started: CheckM
[2023-06-17 00:12:39,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009914975.1_ASM991497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009914975.1_ASM991497v1_genomic.fna/checkm_input GCA_009914975.1_ASM991497v1_genomic.fna/checkm_result
[2023-06-17 00:13:25,258] [INFO] Task succeeded: CheckM
[2023-06-17 00:13:25,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.21%
Contamintation: 36.57%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-17 00:13:25,286] [INFO] ===== Completeness check finished =====
[2023-06-17 00:13:25,286] [INFO] ===== Start GTDB Search =====
[2023-06-17 00:13:25,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009914975.1_ASM991497v1_genomic.fna/markers.fasta)
[2023-06-17 00:13:25,287] [INFO] Task started: Blastn
[2023-06-17 00:13:25,287] [INFO] Running command: blastn -query GCA_009914975.1_ASM991497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg423cea51-9d53-4f9e-bf09-5d929fd15895/dqc_reference/reference_markers_gtdb.fasta -out GCA_009914975.1_ASM991497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:13:26,151] [INFO] Task succeeded: Blastn
[2023-06-17 00:13:26,154] [INFO] Selected 21 target genomes.
[2023-06-17 00:13:26,154] [INFO] Target genome list was writen to GCA_009914975.1_ASM991497v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 00:13:26,189] [INFO] Task started: fastANI
[2023-06-17 00:13:26,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgff1c3700-8691-4535-97bc-387c5cecd86f/GCA_009914975.1_ASM991497v1_genomic.fna.gz --refList GCA_009914975.1_ASM991497v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009914975.1_ASM991497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 00:13:34,711] [INFO] Task succeeded: fastANI
[2023-06-17 00:13:34,722] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 00:13:34,723] [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_012519125.1	s__Sphaerochaeta sp012519125	89.1061	197	918	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603115.1	s__Sphaerochaeta sp001603115	85.7475	222	918	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342655.1	s__Sphaerochaeta sp016342655	82.9996	475	918	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446545.1	s__Sphaerochaeta sp003446545	82.5303	350	918	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	99.24	99.24	0.91	0.91	2	-
GCA_009930195.1	s__Sphaerochaeta sp009930195	81.3781	206	918	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	99.24	99.24	0.76	0.76	2	-
GCA_012838275.1	s__Sphaerochaeta sp012838275	81.2761	343	918	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	79.4605	171	918	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	78.7889	197	918	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.32	97.53	0.87	0.80	11	-
GCA_012511235.1	s__Sphaerochaeta sp012511235	78.6491	141	918	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.08	98.08	0.92	0.92	2	-
GCF_000190435.1	s__Sphaerochaeta globosa	78.0913	175	918	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	77.5717	111	918	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603105.1	s__Sphaerochaeta sp001603105	76.5906	78	918	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	76.2115	65	918	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 00:13:34,725] [INFO] GTDB search result was written to GCA_009914975.1_ASM991497v1_genomic.fna/result_gtdb.tsv
[2023-06-17 00:13:34,725] [INFO] ===== GTDB Search completed =====
[2023-06-17 00:13:34,728] [INFO] DFAST_QC result json was written to GCA_009914975.1_ASM991497v1_genomic.fna/dqc_result.json
[2023-06-17 00:13:34,728] [INFO] DFAST_QC completed!
[2023-06-17 00:13:34,729] [INFO] Total running time: 0h1m29s