[2023-06-05 07:16:25,041] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:16:25,046] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:16:25,047] [INFO] DQC Reference Directory: /var/lib/cwl/stgce4fdb42-be61-4288-bf5e-3aa882aeeed5/dqc_reference
[2023-06-05 07:16:27,033] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:16:27,034] [INFO] Task started: Prodigal
[2023-06-05 07:16:27,035] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f71addf-9ab7-448f-b524-647dc5ea7b8f/GCA_934841175.1_MTG224_bin.13.fa_genomic.fna.gz | prodigal -d GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/cds.fna -a GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:16:33,330] [INFO] Task succeeded: Prodigal
[2023-06-05 07:16:33,331] [INFO] Task started: HMMsearch
[2023-06-05 07:16:33,331] [INFO] Running command: hmmsearch --tblout GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce4fdb42-be61-4288-bf5e-3aa882aeeed5/dqc_reference/reference_markers.hmm GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:16:33,613] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:16:33,615] [INFO] Found 6/6 markers.
[2023-06-05 07:16:33,652] [INFO] Query marker FASTA was written to GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/markers.fasta
[2023-06-05 07:16:33,653] [INFO] Task started: Blastn
[2023-06-05 07:16:33,653] [INFO] Running command: blastn -query GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgce4fdb42-be61-4288-bf5e-3aa882aeeed5/dqc_reference/reference_markers.fasta -out GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:34,273] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:34,305] [INFO] Selected 11 target genomes.
[2023-06-05 07:16:34,306] [INFO] Target genome list was writen to GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/target_genomes.txt
[2023-06-05 07:16:34,308] [INFO] Task started: fastANI
[2023-06-05 07:16:34,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f71addf-9ab7-448f-b524-647dc5ea7b8f/GCA_934841175.1_MTG224_bin.13.fa_genomic.fna.gz --refList GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/target_genomes.txt --output GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:16:40,637] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:40,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce4fdb42-be61-4288-bf5e-3aa882aeeed5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:16:40,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce4fdb42-be61-4288-bf5e-3aa882aeeed5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:16:40,643] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 07:16:40,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 07:16:40,643] [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	97.1826	771	854	95	conclusive
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.6381	144	854	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.587	147	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:16:40,645] [INFO] DFAST Taxonomy check result was written to GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/tc_result.tsv
[2023-06-05 07:16:40,646] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:16:40,646] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:16:40,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce4fdb42-be61-4288-bf5e-3aa882aeeed5/dqc_reference/checkm_data
[2023-06-05 07:16:40,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:16:40,680] [INFO] Task started: CheckM
[2023-06-05 07:16:40,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/checkm_input GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/checkm_result
[2023-06-05 07:17:06,254] [INFO] Task succeeded: CheckM
[2023-06-05 07:17:06,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:17:06,276] [INFO] ===== Completeness check finished =====
[2023-06-05 07:17:06,277] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:17:06,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/markers.fasta)
[2023-06-05 07:17:06,278] [INFO] Task started: Blastn
[2023-06-05 07:17:06,278] [INFO] Running command: blastn -query GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgce4fdb42-be61-4288-bf5e-3aa882aeeed5/dqc_reference/reference_markers_gtdb.fasta -out GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:17:07,308] [INFO] Task succeeded: Blastn
[2023-06-05 07:17:07,312] [INFO] Selected 18 target genomes.
[2023-06-05 07:17:07,312] [INFO] Target genome list was writen to GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:17:07,319] [INFO] Task started: fastANI
[2023-06-05 07:17:07,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f71addf-9ab7-448f-b524-647dc5ea7b8f/GCA_934841175.1_MTG224_bin.13.fa_genomic.fna.gz --refList GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:17:15,956] [INFO] Task succeeded: fastANI
[2023-06-05 07:17:15,978] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:17:15,979] [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	97.2029	771	854	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	89.5076	586	854	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_902800795.1	s__Ruminococcus_D sp902800795	78.0757	162	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.42	97.23	0.92	0.92	3	-
GCA_902786965.1	s__Ruminococcus_D sp902786965	78.0677	138	854	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_900314975.1	s__Ruminococcus_D sp900314975	77.9854	140	854	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_900318545.1	s__Ruminococcus_D sp900318545	77.9825	142	854	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	-
GCF_000621805.1	s__Ruminococcus_D sp000621805	77.8886	145	854	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	77.8284	126	854	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_017484095.1	s__Ruminococcus_D sp017484095	77.7328	146	854	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_002391065.1	s__Ruminococcus_D sp002391065	77.7133	149	854	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_902767035.1	s__Ruminococcus_D sp902767035	77.6939	116	854	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	77.5677	148	854	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	-
GCA_002371625.1	s__Ruminococcus_D sp002371625	77.5123	105	854	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	-
GCF_000526775.1	s__Ruminococcus_D albus_A	77.4296	152	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.64	97.22	0.89	0.80	5	-
GCF_900109655.1	s__Ruminococcus_D albus_B	77.4193	143	854	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	-
GCA_902762735.1	s__Ruminococcus_D sp902762735	77.3626	138	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.61	97.61	0.90	0.90	2	-
GCA_900315755.1	s__Ruminococcus sp900315755	77.2415	57	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.83	98.23	0.88	0.82	4	-
GCA_902797535.1	s__Ruminococcus_D sp902797535	76.7154	65	854	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.84	97.84	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-06-05 07:17:15,981] [INFO] GTDB search result was written to GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 07:17:15,982] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:17:15,988] [INFO] DFAST_QC result json was written to GCA_934841175.1_MTG224_bin.13.fa_genomic.fna/dqc_result.json
[2023-06-05 07:17:15,989] [INFO] DFAST_QC completed!
[2023-06-05 07:17:15,989] [INFO] Total running time: 0h0m51s