[2023-06-28 20:56:05,654] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:56:05,656] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:56:05,656] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4871876-8d01-44ad-bd78-8ddb12940c69/dqc_reference
[2023-06-28 20:56:06,835] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:56:06,835] [INFO] Task started: Prodigal
[2023-06-28 20:56:06,836] [INFO] Running command: gunzip -c /var/lib/cwl/stgc374c2e1-2642-457c-9260-5b2293f1d0bd/GCA_017543335.1_ASM1754333v1_genomic.fna.gz | prodigal -d GCA_017543335.1_ASM1754333v1_genomic.fna/cds.fna -a GCA_017543335.1_ASM1754333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:56:11,660] [INFO] Task succeeded: Prodigal
[2023-06-28 20:56:11,660] [INFO] Task started: HMMsearch
[2023-06-28 20:56:11,661] [INFO] Running command: hmmsearch --tblout GCA_017543335.1_ASM1754333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4871876-8d01-44ad-bd78-8ddb12940c69/dqc_reference/reference_markers.hmm GCA_017543335.1_ASM1754333v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:56:11,929] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:56:11,931] [INFO] Found 6/6 markers.
[2023-06-28 20:56:11,960] [INFO] Query marker FASTA was written to GCA_017543335.1_ASM1754333v1_genomic.fna/markers.fasta
[2023-06-28 20:56:11,960] [INFO] Task started: Blastn
[2023-06-28 20:56:11,960] [INFO] Running command: blastn -query GCA_017543335.1_ASM1754333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4871876-8d01-44ad-bd78-8ddb12940c69/dqc_reference/reference_markers.fasta -out GCA_017543335.1_ASM1754333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:56:12,584] [INFO] Task succeeded: Blastn
[2023-06-28 20:56:12,588] [INFO] Selected 19 target genomes.
[2023-06-28 20:56:12,588] [INFO] Target genome list was writen to GCA_017543335.1_ASM1754333v1_genomic.fna/target_genomes.txt
[2023-06-28 20:56:12,594] [INFO] Task started: fastANI
[2023-06-28 20:56:12,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgc374c2e1-2642-457c-9260-5b2293f1d0bd/GCA_017543335.1_ASM1754333v1_genomic.fna.gz --refList GCA_017543335.1_ASM1754333v1_genomic.fna/target_genomes.txt --output GCA_017543335.1_ASM1754333v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:56:23,180] [INFO] Task succeeded: fastANI
[2023-06-28 20:56:23,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4871876-8d01-44ad-bd78-8ddb12940c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:56:23,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4871876-8d01-44ad-bd78-8ddb12940c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:56:23,191] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:56:23,191] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:56:23,192] [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 flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	78.9561	268	769	95	below_threshold
Ruminococcus bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	77.1011	54	769	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	76.1245	54	769	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	76.1002	55	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:56:23,195] [INFO] DFAST Taxonomy check result was written to GCA_017543335.1_ASM1754333v1_genomic.fna/tc_result.tsv
[2023-06-28 20:56:23,196] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:56:23,196] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:56:23,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4871876-8d01-44ad-bd78-8ddb12940c69/dqc_reference/checkm_data
[2023-06-28 20:56:23,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:56:23,226] [INFO] Task started: CheckM
[2023-06-28 20:56:23,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017543335.1_ASM1754333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017543335.1_ASM1754333v1_genomic.fna/checkm_input GCA_017543335.1_ASM1754333v1_genomic.fna/checkm_result
[2023-06-28 20:56:45,328] [INFO] Task succeeded: CheckM
[2023-06-28 20:56:45,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:56:45,355] [INFO] ===== Completeness check finished =====
[2023-06-28 20:56:45,355] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:56:45,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017543335.1_ASM1754333v1_genomic.fna/markers.fasta)
[2023-06-28 20:56:45,356] [INFO] Task started: Blastn
[2023-06-28 20:56:45,356] [INFO] Running command: blastn -query GCA_017543335.1_ASM1754333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4871876-8d01-44ad-bd78-8ddb12940c69/dqc_reference/reference_markers_gtdb.fasta -out GCA_017543335.1_ASM1754333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:56:46,395] [INFO] Task succeeded: Blastn
[2023-06-28 20:56:46,400] [INFO] Selected 14 target genomes.
[2023-06-28 20:56:46,400] [INFO] Target genome list was writen to GCA_017543335.1_ASM1754333v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:56:46,409] [INFO] Task started: fastANI
[2023-06-28 20:56:46,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgc374c2e1-2642-457c-9260-5b2293f1d0bd/GCA_017543335.1_ASM1754333v1_genomic.fna.gz --refList GCA_017543335.1_ASM1754333v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017543335.1_ASM1754333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:56:54,518] [INFO] Task succeeded: fastANI
[2023-06-28 20:56:54,535] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:56:54,535] [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_017543335.1	s__Ruminococcus sp017543335	100.0	763	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.36	98.36	0.90	0.90	2	conclusive
GCA_017441505.1	s__Ruminococcus sp017441505	94.5171	573	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371825.1	s__Ruminococcus flavefaciens_L	79.9615	358	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.29	98.12	0.89	0.86	3	-
GCA_001604035.1	s__Ruminococcus sp001604035	79.8392	295	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.76	98.76	0.77	0.77	2	-
GCA_012718885.1	s__Ruminococcus sp012718885	79.7803	292	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780115.1	s__Ruminococcus flavefaciens_Y	79.1162	184	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762855.1	s__Ruminococcus flavefaciens_V	79.0754	302	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.58	98.43	0.85	0.84	3	-
GCF_000518765.1	s__Ruminococcus flavefaciens	78.93	269	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108555.1	s__Ruminococcus flavefaciens_P	78.8971	283	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119075.1	s__Ruminococcus flavefaciens_Q	78.8008	235	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.02	98.02	0.91	0.91	2	-
GCF_000621845.1	s__Ruminococcus flavefaciens_E	78.6202	256	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.76	97.66	0.87	0.87	4	-
GCA_017461395.1	s__Ruminococcus sp017461395	78.443	181	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905199285.1	s__Ruminococcus sp905199285	78.1996	186	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462565.1	s__Ruminococcus sp017462565	78.1157	222	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:56:54,537] [INFO] GTDB search result was written to GCA_017543335.1_ASM1754333v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:56:54,537] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:56:54,541] [INFO] DFAST_QC result json was written to GCA_017543335.1_ASM1754333v1_genomic.fna/dqc_result.json
[2023-06-28 20:56:54,541] [INFO] DFAST_QC completed!
[2023-06-28 20:56:54,541] [INFO] Total running time: 0h0m49s