[2023-06-04 17:57:54,318] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:57:55,386] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:57:55,386] [INFO] DQC Reference Directory: /var/lib/cwl/stgb325a54e-3719-430f-94d9-08faf7ed9e6c/dqc_reference
[2023-06-04 17:57:56,585] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:57:56,586] [INFO] Task started: Prodigal
[2023-06-04 17:57:56,586] [INFO] Running command: gunzip -c /var/lib/cwl/stg92568a76-fe11-420c-bbaf-8aa0dab4df38/GCA_934487005.1_ERR7738552_bin.369_genomic.fna.gz | prodigal -d GCA_934487005.1_ERR7738552_bin.369_genomic.fna/cds.fna -a GCA_934487005.1_ERR7738552_bin.369_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:58:04,015] [INFO] Task succeeded: Prodigal
[2023-06-04 17:58:04,016] [INFO] Task started: HMMsearch
[2023-06-04 17:58:04,016] [INFO] Running command: hmmsearch --tblout GCA_934487005.1_ERR7738552_bin.369_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb325a54e-3719-430f-94d9-08faf7ed9e6c/dqc_reference/reference_markers.hmm GCA_934487005.1_ERR7738552_bin.369_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:58:04,271] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:58:04,272] [INFO] Found 6/6 markers.
[2023-06-04 17:58:04,339] [INFO] Query marker FASTA was written to GCA_934487005.1_ERR7738552_bin.369_genomic.fna/markers.fasta
[2023-06-04 17:58:04,340] [INFO] Task started: Blastn
[2023-06-04 17:58:04,340] [INFO] Running command: blastn -query GCA_934487005.1_ERR7738552_bin.369_genomic.fna/markers.fasta -db /var/lib/cwl/stgb325a54e-3719-430f-94d9-08faf7ed9e6c/dqc_reference/reference_markers.fasta -out GCA_934487005.1_ERR7738552_bin.369_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:58:04,917] [INFO] Task succeeded: Blastn
[2023-06-04 17:58:04,939] [INFO] Selected 15 target genomes.
[2023-06-04 17:58:04,939] [INFO] Target genome list was writen to GCA_934487005.1_ERR7738552_bin.369_genomic.fna/target_genomes.txt
[2023-06-04 17:58:05,025] [INFO] Task started: fastANI
[2023-06-04 17:58:05,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg92568a76-fe11-420c-bbaf-8aa0dab4df38/GCA_934487005.1_ERR7738552_bin.369_genomic.fna.gz --refList GCA_934487005.1_ERR7738552_bin.369_genomic.fna/target_genomes.txt --output GCA_934487005.1_ERR7738552_bin.369_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:58:15,908] [INFO] Task succeeded: fastANI
[2023-06-04 17:58:15,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb325a54e-3719-430f-94d9-08faf7ed9e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:58:15,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb325a54e-3719-430f-94d9-08faf7ed9e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:58:15,917] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:58:15,918] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:58:15,918] [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	82.1513	596	1114	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.5142	101	1114	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.4853	102	1114	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:58:15,920] [INFO] DFAST Taxonomy check result was written to GCA_934487005.1_ERR7738552_bin.369_genomic.fna/tc_result.tsv
[2023-06-04 17:58:15,921] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:58:15,921] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:58:15,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb325a54e-3719-430f-94d9-08faf7ed9e6c/dqc_reference/checkm_data
[2023-06-04 17:58:15,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:58:15,959] [INFO] Task started: CheckM
[2023-06-04 17:58:15,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934487005.1_ERR7738552_bin.369_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934487005.1_ERR7738552_bin.369_genomic.fna/checkm_input GCA_934487005.1_ERR7738552_bin.369_genomic.fna/checkm_result
[2023-06-04 17:58:44,353] [INFO] Task succeeded: CheckM
[2023-06-04 17:58:44,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:58:44,378] [INFO] ===== Completeness check finished =====
[2023-06-04 17:58:44,378] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:58:44,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934487005.1_ERR7738552_bin.369_genomic.fna/markers.fasta)
[2023-06-04 17:58:44,379] [INFO] Task started: Blastn
[2023-06-04 17:58:44,379] [INFO] Running command: blastn -query GCA_934487005.1_ERR7738552_bin.369_genomic.fna/markers.fasta -db /var/lib/cwl/stgb325a54e-3719-430f-94d9-08faf7ed9e6c/dqc_reference/reference_markers_gtdb.fasta -out GCA_934487005.1_ERR7738552_bin.369_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:58:45,247] [INFO] Task succeeded: Blastn
[2023-06-04 17:58:45,252] [INFO] Selected 10 target genomes.
[2023-06-04 17:58:45,253] [INFO] Target genome list was writen to GCA_934487005.1_ERR7738552_bin.369_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:58:45,551] [INFO] Task started: fastANI
[2023-06-04 17:58:45,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg92568a76-fe11-420c-bbaf-8aa0dab4df38/GCA_934487005.1_ERR7738552_bin.369_genomic.fna.gz --refList GCA_934487005.1_ERR7738552_bin.369_genomic.fna/target_genomes_gtdb.txt --output GCA_934487005.1_ERR7738552_bin.369_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:58:53,992] [INFO] Task succeeded: fastANI
[2023-06-04 17:58:54,003] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:58:54,004] [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_900119075.1	s__Ruminococcus flavefaciens_Q	96.3179	901	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.02	98.02	0.91	0.91	2	conclusive
GCF_000621845.1	s__Ruminococcus flavefaciens_E	94.1591	872	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.76	97.66	0.87	0.87	4	-
GCF_000526795.1	s__Ruminococcus flavefaciens_D	86.6324	815	1114	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_004554385.1	s__Ruminococcus flavefaciens_T	85.209	616	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.08	98.08	0.79	0.79	2	-
GCF_900143025.1	s__Ruminococcus flavefaciens_I	82.6085	616	1114	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_017519415.1	s__Ruminococcus sp017519415	82.4724	402	1114	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	82.033	614	1114	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	82.032	363	1114	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_016283395.1	s__Ruminococcus sp016283395	82.011	564	1114	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_900116855.1	s__Ruminococcus flavefaciens_R	81.6929	584	1114	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.90	97.16	0.91	0.76	13	-
--------------------------------------------------------------------------------
[2023-06-04 17:58:54,006] [INFO] GTDB search result was written to GCA_934487005.1_ERR7738552_bin.369_genomic.fna/result_gtdb.tsv
[2023-06-04 17:58:54,007] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:58:54,009] [INFO] DFAST_QC result json was written to GCA_934487005.1_ERR7738552_bin.369_genomic.fna/dqc_result.json
[2023-06-04 17:58:54,010] [INFO] DFAST_QC completed!
[2023-06-04 17:58:54,010] [INFO] Total running time: 0h0m60s