[2023-06-30 11:59:40,308] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:59:40,310] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:59:40,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg68b8b0aa-839f-4de2-b056-f61a46f05b28/dqc_reference
[2023-06-30 11:59:42,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:59:42,080] [INFO] Task started: Prodigal
[2023-06-30 11:59:42,080] [INFO] Running command: gunzip -c /var/lib/cwl/stg38772f89-d300-447d-aae3-f2fb849fc661/GCA_019136775.1_ASM1913677v1_genomic.fna.gz | prodigal -d GCA_019136775.1_ASM1913677v1_genomic.fna/cds.fna -a GCA_019136775.1_ASM1913677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:59:48,301] [INFO] Task succeeded: Prodigal
[2023-06-30 11:59:48,301] [INFO] Task started: HMMsearch
[2023-06-30 11:59:48,301] [INFO] Running command: hmmsearch --tblout GCA_019136775.1_ASM1913677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68b8b0aa-839f-4de2-b056-f61a46f05b28/dqc_reference/reference_markers.hmm GCA_019136775.1_ASM1913677v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:59:48,533] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:59:48,535] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg38772f89-d300-447d-aae3-f2fb849fc661/GCA_019136775.1_ASM1913677v1_genomic.fna.gz]
[2023-06-30 11:59:48,560] [INFO] Query marker FASTA was written to GCA_019136775.1_ASM1913677v1_genomic.fna/markers.fasta
[2023-06-30 11:59:48,560] [INFO] Task started: Blastn
[2023-06-30 11:59:48,560] [INFO] Running command: blastn -query GCA_019136775.1_ASM1913677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68b8b0aa-839f-4de2-b056-f61a46f05b28/dqc_reference/reference_markers.fasta -out GCA_019136775.1_ASM1913677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:59:49,231] [INFO] Task succeeded: Blastn
[2023-06-30 11:59:49,236] [INFO] Selected 23 target genomes.
[2023-06-30 11:59:49,237] [INFO] Target genome list was writen to GCA_019136775.1_ASM1913677v1_genomic.fna/target_genomes.txt
[2023-06-30 11:59:49,242] [INFO] Task started: fastANI
[2023-06-30 11:59:49,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg38772f89-d300-447d-aae3-f2fb849fc661/GCA_019136775.1_ASM1913677v1_genomic.fna.gz --refList GCA_019136775.1_ASM1913677v1_genomic.fna/target_genomes.txt --output GCA_019136775.1_ASM1913677v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:00:10,472] [INFO] Task succeeded: fastANI
[2023-06-30 12:00:10,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68b8b0aa-839f-4de2-b056-f61a46f05b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:00:10,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68b8b0aa-839f-4de2-b056-f61a46f05b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:00:10,480] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:00:10,480] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:00:10,480] [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	76.9608	149	628	95	below_threshold
Sphaerochaeta globosa	strain=Buddy	GCA_000190435.1	1131703	1131703	type	True	76.7482	97	628	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:00:10,483] [INFO] DFAST Taxonomy check result was written to GCA_019136775.1_ASM1913677v1_genomic.fna/tc_result.tsv
[2023-06-30 12:00:10,483] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:00:10,483] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:00:10,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68b8b0aa-839f-4de2-b056-f61a46f05b28/dqc_reference/checkm_data
[2023-06-30 12:00:10,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:00:10,514] [INFO] Task started: CheckM
[2023-06-30 12:00:10,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019136775.1_ASM1913677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019136775.1_ASM1913677v1_genomic.fna/checkm_input GCA_019136775.1_ASM1913677v1_genomic.fna/checkm_result
[2023-06-30 12:00:35,640] [INFO] Task succeeded: CheckM
[2023-06-30 12:00:35,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.61%
Contamintation: 19.44%
Strain heterogeneity: 64.29%
--------------------------------------------------------------------------------
[2023-06-30 12:00:35,669] [INFO] ===== Completeness check finished =====
[2023-06-30 12:00:35,669] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:00:35,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019136775.1_ASM1913677v1_genomic.fna/markers.fasta)
[2023-06-30 12:00:35,670] [INFO] Task started: Blastn
[2023-06-30 12:00:35,670] [INFO] Running command: blastn -query GCA_019136775.1_ASM1913677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68b8b0aa-839f-4de2-b056-f61a46f05b28/dqc_reference/reference_markers_gtdb.fasta -out GCA_019136775.1_ASM1913677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:00:36,754] [INFO] Task succeeded: Blastn
[2023-06-30 12:00:36,760] [INFO] Selected 15 target genomes.
[2023-06-30 12:00:36,760] [INFO] Target genome list was writen to GCA_019136775.1_ASM1913677v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:00:36,770] [INFO] Task started: fastANI
[2023-06-30 12:00:36,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg38772f89-d300-447d-aae3-f2fb849fc661/GCA_019136775.1_ASM1913677v1_genomic.fna.gz --refList GCA_019136775.1_ASM1913677v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019136775.1_ASM1913677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:00:43,928] [INFO] Task succeeded: fastANI
[2023-06-30 12:00:43,947] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:00:43,947] [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_001604325.1	s__Sphaerochaeta sp001604325	98.6075	382	628	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.87	98.79	0.85	0.79	4	conclusive
GCA_001603105.1	s__Sphaerochaeta sp001603105	81.439	352	628	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	77.3138	91	628	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012800465.1	s__Sphaerochaeta sp012800465	77.2758	91	628	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	77.0282	154	628	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.32	97.53	0.87	0.80	11	-
GCA_012514185.1	s__Sphaerochaeta sp012514185	76.9485	134	628	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	76.8467	112	628	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	76.7418	130	628	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	76.4867	55	628	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004294855.1	s__Sphaerochaeta sp004294855	76.4829	103	628	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	97.83	97.73	0.85	0.79	4	-
--------------------------------------------------------------------------------
[2023-06-30 12:00:43,950] [INFO] GTDB search result was written to GCA_019136775.1_ASM1913677v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:00:43,951] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:00:43,955] [INFO] DFAST_QC result json was written to GCA_019136775.1_ASM1913677v1_genomic.fna/dqc_result.json
[2023-06-30 12:00:43,955] [INFO] DFAST_QC completed!
[2023-06-30 12:00:43,955] [INFO] Total running time: 0h1m4s