[2023-06-28 22:09:54,488] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:09:54,489] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:09:54,489] [INFO] DQC Reference Directory: /var/lib/cwl/stgf405da7f-e0ef-406f-b98c-d8a41f917b39/dqc_reference
[2023-06-28 22:09:55,735] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:09:55,736] [INFO] Task started: Prodigal
[2023-06-28 22:09:55,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg50d7bd0e-0f7d-46ab-86ac-7e2c59f4dddd/GCA_017441595.1_ASM1744159v1_genomic.fna.gz | prodigal -d GCA_017441595.1_ASM1744159v1_genomic.fna/cds.fna -a GCA_017441595.1_ASM1744159v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:10:01,645] [INFO] Task succeeded: Prodigal
[2023-06-28 22:10:01,645] [INFO] Task started: HMMsearch
[2023-06-28 22:10:01,645] [INFO] Running command: hmmsearch --tblout GCA_017441595.1_ASM1744159v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf405da7f-e0ef-406f-b98c-d8a41f917b39/dqc_reference/reference_markers.hmm GCA_017441595.1_ASM1744159v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:10:02,097] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:10:02,099] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg50d7bd0e-0f7d-46ab-86ac-7e2c59f4dddd/GCA_017441595.1_ASM1744159v1_genomic.fna.gz]
[2023-06-28 22:10:02,146] [INFO] Query marker FASTA was written to GCA_017441595.1_ASM1744159v1_genomic.fna/markers.fasta
[2023-06-28 22:10:02,147] [INFO] Task started: Blastn
[2023-06-28 22:10:02,147] [INFO] Running command: blastn -query GCA_017441595.1_ASM1744159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf405da7f-e0ef-406f-b98c-d8a41f917b39/dqc_reference/reference_markers.fasta -out GCA_017441595.1_ASM1744159v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:10:03,037] [INFO] Task succeeded: Blastn
[2023-06-28 22:10:03,041] [INFO] Selected 12 target genomes.
[2023-06-28 22:10:03,041] [INFO] Target genome list was writen to GCA_017441595.1_ASM1744159v1_genomic.fna/target_genomes.txt
[2023-06-28 22:10:03,045] [INFO] Task started: fastANI
[2023-06-28 22:10:03,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg50d7bd0e-0f7d-46ab-86ac-7e2c59f4dddd/GCA_017441595.1_ASM1744159v1_genomic.fna.gz --refList GCA_017441595.1_ASM1744159v1_genomic.fna/target_genomes.txt --output GCA_017441595.1_ASM1744159v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:10:10,105] [INFO] Task succeeded: fastANI
[2023-06-28 22:10:10,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf405da7f-e0ef-406f-b98c-d8a41f917b39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:10:10,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf405da7f-e0ef-406f-b98c-d8a41f917b39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:10:10,112] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:10:10,112] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:10:10,112] [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
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.7674	118	766	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.7568	121	766	95	below_threshold
Ruminococcus bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	77.6933	134	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:10:10,114] [INFO] DFAST Taxonomy check result was written to GCA_017441595.1_ASM1744159v1_genomic.fna/tc_result.tsv
[2023-06-28 22:10:10,115] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:10:10,115] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:10:10,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf405da7f-e0ef-406f-b98c-d8a41f917b39/dqc_reference/checkm_data
[2023-06-28 22:10:10,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:10:10,144] [INFO] Task started: CheckM
[2023-06-28 22:10:10,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017441595.1_ASM1744159v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017441595.1_ASM1744159v1_genomic.fna/checkm_input GCA_017441595.1_ASM1744159v1_genomic.fna/checkm_result
[2023-06-28 22:10:33,420] [INFO] Task succeeded: CheckM
[2023-06-28 22:10:33,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 22:10:33,442] [INFO] ===== Completeness check finished =====
[2023-06-28 22:10:33,443] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:10:33,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017441595.1_ASM1744159v1_genomic.fna/markers.fasta)
[2023-06-28 22:10:33,443] [INFO] Task started: Blastn
[2023-06-28 22:10:33,443] [INFO] Running command: blastn -query GCA_017441595.1_ASM1744159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf405da7f-e0ef-406f-b98c-d8a41f917b39/dqc_reference/reference_markers_gtdb.fasta -out GCA_017441595.1_ASM1744159v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:10:34,451] [INFO] Task succeeded: Blastn
[2023-06-28 22:10:34,455] [INFO] Selected 8 target genomes.
[2023-06-28 22:10:34,456] [INFO] Target genome list was writen to GCA_017441595.1_ASM1744159v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:10:34,482] [INFO] Task started: fastANI
[2023-06-28 22:10:34,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg50d7bd0e-0f7d-46ab-86ac-7e2c59f4dddd/GCA_017441595.1_ASM1744159v1_genomic.fna.gz --refList GCA_017441595.1_ASM1744159v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017441595.1_ASM1744159v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:10:39,034] [INFO] Task succeeded: fastANI
[2023-06-28 22:10:39,042] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:10:39,042] [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_902786965.1	s__Ruminococcus_D sp902786965	97.245	603	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.48	97.28	0.83	0.79	5	conclusive
GCA_900314975.1	s__Ruminococcus_D sp900314975	88.4609	560	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.52	97.44	0.93	0.89	4	-
GCA_902787825.1	s__Ruminococcus_D sp902787825	82.4626	422	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319075.1	s__Ruminococcus_D sp900319075	82.2507	317	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.31	96.98	0.90	0.83	16	-
GCA_902786975.1	s__Ruminococcus_D sp902786975	81.1656	396	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.61	98.61	0.94	0.94	2	-
GCF_000621805.1	s__Ruminococcus_D sp000621805	81.0374	326	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371625.1	s__Ruminococcus_D sp002371625	81.0057	332	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.14	97.32	0.90	0.85	5	-
GCA_017534595.1	s__Ruminococcus_D sp017534595	76.7726	111	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:10:39,044] [INFO] GTDB search result was written to GCA_017441595.1_ASM1744159v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:10:39,045] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:10:39,048] [INFO] DFAST_QC result json was written to GCA_017441595.1_ASM1744159v1_genomic.fna/dqc_result.json
[2023-06-28 22:10:39,048] [INFO] DFAST_QC completed!
[2023-06-28 22:10:39,048] [INFO] Total running time: 0h0m45s