[2023-06-28 12:49:24,138] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:24,143] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:24,143] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd083036-8657-4d55-9c95-274f3b49f1bb/dqc_reference
[2023-06-28 12:49:25,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:25,419] [INFO] Task started: Prodigal
[2023-06-28 12:49:25,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e58b3b8-4c44-4b8a-8429-f9ca48486b4d/GCA_944325975.1_BRZ_EB_bin34_genomic.fna.gz | prodigal -d GCA_944325975.1_BRZ_EB_bin34_genomic.fna/cds.fna -a GCA_944325975.1_BRZ_EB_bin34_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:49:38,473] [INFO] Task succeeded: Prodigal
[2023-06-28 12:49:38,473] [INFO] Task started: HMMsearch
[2023-06-28 12:49:38,473] [INFO] Running command: hmmsearch --tblout GCA_944325975.1_BRZ_EB_bin34_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd083036-8657-4d55-9c95-274f3b49f1bb/dqc_reference/reference_markers.hmm GCA_944325975.1_BRZ_EB_bin34_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:49:38,730] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:49:38,732] [INFO] Found 6/6 markers.
[2023-06-28 12:49:38,755] [INFO] Query marker FASTA was written to GCA_944325975.1_BRZ_EB_bin34_genomic.fna/markers.fasta
[2023-06-28 12:49:38,756] [INFO] Task started: Blastn
[2023-06-28 12:49:38,756] [INFO] Running command: blastn -query GCA_944325975.1_BRZ_EB_bin34_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd083036-8657-4d55-9c95-274f3b49f1bb/dqc_reference/reference_markers.fasta -out GCA_944325975.1_BRZ_EB_bin34_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:39,378] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:39,382] [INFO] Selected 26 target genomes.
[2023-06-28 12:49:39,382] [INFO] Target genome list was writen to GCA_944325975.1_BRZ_EB_bin34_genomic.fna/target_genomes.txt
[2023-06-28 12:49:39,384] [INFO] Task started: fastANI
[2023-06-28 12:49:39,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e58b3b8-4c44-4b8a-8429-f9ca48486b4d/GCA_944325975.1_BRZ_EB_bin34_genomic.fna.gz --refList GCA_944325975.1_BRZ_EB_bin34_genomic.fna/target_genomes.txt --output GCA_944325975.1_BRZ_EB_bin34_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:49:56,916] [INFO] Task succeeded: fastANI
[2023-06-28 12:49:56,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd083036-8657-4d55-9c95-274f3b49f1bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:49:56,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd083036-8657-4d55-9c95-274f3b49f1bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:49:56,932] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:49:56,932] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:49:56,932] [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
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	77.3259	111	762	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	77.2639	102	762	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	77.2291	109	762	95	below_threshold
Alistipes putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	77.05	83	762	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.9664	102	762	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.9554	101	762	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.8299	116	762	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	76.6532	99	762	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_000321205.1	1470347	1470347	type	True	76.5579	64	762	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	76.5387	99	762	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	76.5218	70	762	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	76.4924	71	762	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	76.4608	66	762	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	76.2785	85	762	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:49:56,935] [INFO] DFAST Taxonomy check result was written to GCA_944325975.1_BRZ_EB_bin34_genomic.fna/tc_result.tsv
[2023-06-28 12:49:56,936] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:49:56,937] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:49:56,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd083036-8657-4d55-9c95-274f3b49f1bb/dqc_reference/checkm_data
[2023-06-28 12:49:56,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:49:56,974] [INFO] Task started: CheckM
[2023-06-28 12:49:56,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944325975.1_BRZ_EB_bin34_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944325975.1_BRZ_EB_bin34_genomic.fna/checkm_input GCA_944325975.1_BRZ_EB_bin34_genomic.fna/checkm_result
[2023-06-28 12:50:36,080] [INFO] Task succeeded: CheckM
[2023-06-28 12:50:36,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:50:36,103] [INFO] ===== Completeness check finished =====
[2023-06-28 12:50:36,103] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:50:36,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944325975.1_BRZ_EB_bin34_genomic.fna/markers.fasta)
[2023-06-28 12:50:36,104] [INFO] Task started: Blastn
[2023-06-28 12:50:36,104] [INFO] Running command: blastn -query GCA_944325975.1_BRZ_EB_bin34_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd083036-8657-4d55-9c95-274f3b49f1bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_944325975.1_BRZ_EB_bin34_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:50:36,949] [INFO] Task succeeded: Blastn
[2023-06-28 12:50:36,954] [INFO] Selected 14 target genomes.
[2023-06-28 12:50:36,954] [INFO] Target genome list was writen to GCA_944325975.1_BRZ_EB_bin34_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:50:36,957] [INFO] Task started: fastANI
[2023-06-28 12:50:36,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e58b3b8-4c44-4b8a-8429-f9ca48486b4d/GCA_944325975.1_BRZ_EB_bin34_genomic.fna.gz --refList GCA_944325975.1_BRZ_EB_bin34_genomic.fna/target_genomes_gtdb.txt --output GCA_944325975.1_BRZ_EB_bin34_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:50:42,719] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:42,736] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:50:42,736] [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_900104605.1	s__Tidjanibacter inops_A	99.0799	721	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	99.31	98.92	0.96	0.89	16	conclusive
GCA_019114205.1	s__Tidjanibacter gallistercoris	83.2002	502	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577285.1	s__Tidjanibacter sp910577285	82.5809	517	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116245.1	s__Tidjanibacter faecipullorum	79.1521	274	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542505.1	s__Alistipes stercorigallinarum	77.7673	91	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCA_014982715.1	s__DSM-108975 sp014982715	77.2689	101	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__DSM-108975	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154465.1	s__Alistipes putredinis	77.0831	81	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.94	97.62	0.91	0.76	28	-
GCA_017935625.1	s__RGIG9113 sp017935625	76.961	111	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG9113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576555.1	s__Alistipes sp910576555	76.8505	92	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546065.1	s__Alistipes merdipullorum	76.3993	53	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.89	97.88	0.91	0.90	3	-
GCA_900549685.1	s__Alistipes_A sp900549685	76.2256	57	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:50:42,738] [INFO] GTDB search result was written to GCA_944325975.1_BRZ_EB_bin34_genomic.fna/result_gtdb.tsv
[2023-06-28 12:50:42,739] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:50:42,743] [INFO] DFAST_QC result json was written to GCA_944325975.1_BRZ_EB_bin34_genomic.fna/dqc_result.json
[2023-06-28 12:50:42,743] [INFO] DFAST_QC completed!
[2023-06-28 12:50:42,743] [INFO] Total running time: 0h1m19s