[2023-06-19 05:51:43,214] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:51:43,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:51:43,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg0baef9ce-93c1-4609-a3d2-47212c050465/dqc_reference
[2023-06-19 05:51:44,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:51:44,609] [INFO] Task started: Prodigal
[2023-06-19 05:51:44,609] [INFO] Running command: gunzip -c /var/lib/cwl/stg736ca5b1-844d-4d24-97df-02a11837de5a/GCA_018382215.1_ASM1838221v1_genomic.fna.gz | prodigal -d GCA_018382215.1_ASM1838221v1_genomic.fna/cds.fna -a GCA_018382215.1_ASM1838221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:51:48,871] [INFO] Task succeeded: Prodigal
[2023-06-19 05:51:48,871] [INFO] Task started: HMMsearch
[2023-06-19 05:51:48,871] [INFO] Running command: hmmsearch --tblout GCA_018382215.1_ASM1838221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0baef9ce-93c1-4609-a3d2-47212c050465/dqc_reference/reference_markers.hmm GCA_018382215.1_ASM1838221v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:51:49,152] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:51:49,154] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg736ca5b1-844d-4d24-97df-02a11837de5a/GCA_018382215.1_ASM1838221v1_genomic.fna.gz]
[2023-06-19 05:51:49,190] [INFO] Query marker FASTA was written to GCA_018382215.1_ASM1838221v1_genomic.fna/markers.fasta
[2023-06-19 05:51:49,190] [INFO] Task started: Blastn
[2023-06-19 05:51:49,191] [INFO] Running command: blastn -query GCA_018382215.1_ASM1838221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0baef9ce-93c1-4609-a3d2-47212c050465/dqc_reference/reference_markers.fasta -out GCA_018382215.1_ASM1838221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:51:49,799] [INFO] Task succeeded: Blastn
[2023-06-19 05:51:49,804] [INFO] Selected 12 target genomes.
[2023-06-19 05:51:49,804] [INFO] Target genome list was writen to GCA_018382215.1_ASM1838221v1_genomic.fna/target_genomes.txt
[2023-06-19 05:51:49,805] [INFO] Task started: fastANI
[2023-06-19 05:51:49,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg736ca5b1-844d-4d24-97df-02a11837de5a/GCA_018382215.1_ASM1838221v1_genomic.fna.gz --refList GCA_018382215.1_ASM1838221v1_genomic.fna/target_genomes.txt --output GCA_018382215.1_ASM1838221v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:51:56,078] [INFO] Task succeeded: fastANI
[2023-06-19 05:51:56,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0baef9ce-93c1-4609-a3d2-47212c050465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:51:56,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0baef9ce-93c1-4609-a3d2-47212c050465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:51:56,085] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 05:51:56,085] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 05:51:56,085] [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 bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	97.4522	379	409	95	conclusive
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.5465	64	409	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.5436	64	409	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:51:56,090] [INFO] DFAST Taxonomy check result was written to GCA_018382215.1_ASM1838221v1_genomic.fna/tc_result.tsv
[2023-06-19 05:51:56,091] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:51:56,091] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:51:56,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0baef9ce-93c1-4609-a3d2-47212c050465/dqc_reference/checkm_data
[2023-06-19 05:51:56,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:51:56,119] [INFO] Task started: CheckM
[2023-06-19 05:51:56,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018382215.1_ASM1838221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018382215.1_ASM1838221v1_genomic.fna/checkm_input GCA_018382215.1_ASM1838221v1_genomic.fna/checkm_result
[2023-06-19 05:52:17,283] [INFO] Task succeeded: CheckM
[2023-06-19 05:52:17,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.37%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:52:17,326] [INFO] ===== Completeness check finished =====
[2023-06-19 05:52:17,326] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:52:17,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018382215.1_ASM1838221v1_genomic.fna/markers.fasta)
[2023-06-19 05:52:17,327] [INFO] Task started: Blastn
[2023-06-19 05:52:17,328] [INFO] Running command: blastn -query GCA_018382215.1_ASM1838221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0baef9ce-93c1-4609-a3d2-47212c050465/dqc_reference/reference_markers_gtdb.fasta -out GCA_018382215.1_ASM1838221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:52:18,253] [INFO] Task succeeded: Blastn
[2023-06-19 05:52:18,257] [INFO] Selected 16 target genomes.
[2023-06-19 05:52:18,257] [INFO] Target genome list was writen to GCA_018382215.1_ASM1838221v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:52:18,259] [INFO] Task started: fastANI
[2023-06-19 05:52:18,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg736ca5b1-844d-4d24-97df-02a11837de5a/GCA_018382215.1_ASM1838221v1_genomic.fna.gz --refList GCA_018382215.1_ASM1838221v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018382215.1_ASM1838221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:52:25,373] [INFO] Task succeeded: fastANI
[2023-06-19 05:52:25,389] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:52:25,390] [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_000723465.1	s__Ruminococcus_D bicirculans	97.4522	379	409	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.50	96.68	0.89	0.80	66	conclusive
GCA_900539095.1	s__Ruminococcus_D sp900539095	89.1938	315	409	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.71	97.55	0.88	0.82	3	-
GCA_902786965.1	s__Ruminococcus_D sp902786965	78.0398	54	409	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	-
GCA_900319075.1	s__Ruminococcus_D sp900319075	77.7853	53	409	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_002391065.1	s__Ruminococcus_D sp002391065	77.6594	65	409	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	-
GCF_900112155.1	s__Ruminococcus_D albus_D	77.5586	68	409	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	-
GCF_000179635.2	s__Ruminococcus_D albus	77.5465	64	409	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.29	97.69	0.91	0.87	8	-
GCF_000621805.1	s__Ruminococcus_D sp000621805	77.3196	65	409	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_017484095.1	s__Ruminococcus_D sp017484095	77.2563	72	409	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_900318545.1	s__Ruminococcus_D sp900318545	77.1302	66	409	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.38	97.31	0.84	0.77	8	-
GCA_902767035.1	s__Ruminococcus_D sp902767035	76.9623	59	409	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_017626015.1	s__Ruminococcus_D sp017626015	76.8918	75	409	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	-
GCF_900109655.1	s__Ruminococcus_D albus_B	76.8319	59	409	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	96.54	96.54	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-19 05:52:25,392] [INFO] GTDB search result was written to GCA_018382215.1_ASM1838221v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:52:25,393] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:52:25,399] [INFO] DFAST_QC result json was written to GCA_018382215.1_ASM1838221v1_genomic.fna/dqc_result.json
[2023-06-19 05:52:25,399] [INFO] DFAST_QC completed!
[2023-06-19 05:52:25,399] [INFO] Total running time: 0h0m42s