[2023-06-13 21:21:32,371] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:21:32,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:21:32,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e53407f-11ad-4741-a3c5-ec4a5229f558/dqc_reference
[2023-06-13 21:21:33,634] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:21:33,635] [INFO] Task started: Prodigal
[2023-06-13 21:21:33,636] [INFO] Running command: gunzip -c /var/lib/cwl/stgb67099ec-bd44-4764-b265-406d3d8666e6/GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:21:43,629] [INFO] Task succeeded: Prodigal
[2023-06-13 21:21:43,630] [INFO] Task started: HMMsearch
[2023-06-13 21:21:43,630] [INFO] Running command: hmmsearch --tblout GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e53407f-11ad-4741-a3c5-ec4a5229f558/dqc_reference/reference_markers.hmm GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:21:43,875] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:21:43,876] [INFO] Found 6/6 markers.
[2023-06-13 21:21:43,896] [INFO] Query marker FASTA was written to GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 21:21:43,897] [INFO] Task started: Blastn
[2023-06-13 21:21:43,897] [INFO] Running command: blastn -query GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e53407f-11ad-4741-a3c5-ec4a5229f558/dqc_reference/reference_markers.fasta -out GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:44,502] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:44,510] [INFO] Selected 16 target genomes.
[2023-06-13 21:21:44,511] [INFO] Target genome list was writen to GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 21:21:44,512] [INFO] Task started: fastANI
[2023-06-13 21:21:44,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgb67099ec-bd44-4764-b265-406d3d8666e6/GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:21:53,330] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:53,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e53407f-11ad-4741-a3c5-ec4a5229f558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:21:53,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e53407f-11ad-4741-a3c5-ec4a5229f558/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:21:53,347] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:21:53,347] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:21:53,347] [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 dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	80.3847	328	635	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	80.3488	350	635	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	80.297	353	635	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	80.2624	369	635	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	80.2565	358	635	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	80.2359	358	635	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	80.1016	303	635	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	79.9914	366	635	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	79.5906	333	635	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	79.5056	292	635	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	79.4135	321	635	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	79.377	322	635	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	79.3402	321	635	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	79.3065	305	635	95	below_threshold
Alistipes putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	78.7489	220	635	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	77.0997	111	635	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:21:53,350] [INFO] DFAST Taxonomy check result was written to GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 21:21:53,350] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:21:53,350] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:21:53,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e53407f-11ad-4741-a3c5-ec4a5229f558/dqc_reference/checkm_data
[2023-06-13 21:21:53,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:21:53,378] [INFO] Task started: CheckM
[2023-06-13 21:21:53,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 21:22:24,912] [INFO] Task succeeded: CheckM
[2023-06-13 21:22:24,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:22:24,939] [INFO] ===== Completeness check finished =====
[2023-06-13 21:22:24,940] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:22:24,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 21:22:24,941] [INFO] Task started: Blastn
[2023-06-13 21:22:24,941] [INFO] Running command: blastn -query GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e53407f-11ad-4741-a3c5-ec4a5229f558/dqc_reference/reference_markers_gtdb.fasta -out GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:22:25,871] [INFO] Task succeeded: Blastn
[2023-06-13 21:22:25,876] [INFO] Selected 20 target genomes.
[2023-06-13 21:22:25,876] [INFO] Target genome list was writen to GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:22:25,880] [INFO] Task started: fastANI
[2023-06-13 21:22:25,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgb67099ec-bd44-4764-b265-406d3d8666e6/GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:22:35,081] [INFO] Task succeeded: fastANI
[2023-06-13 21:22:35,101] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 21:22:35,101] [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_910577475.1	s__Alistipes sp910577475	99.0142	603	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902362705.1	s__Alistipes sp002358415	81.359	335	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.62	98.83	0.97	0.92	7	-
GCA_900544265.1	s__Alistipes merdavium	80.9328	339	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCA_910576555.1	s__Alistipes sp910576555	80.7019	354	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542505.1	s__Alistipes stercorigallinarum	80.5907	311	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCF_900290115.1	s__Alistipes excrementigallinarum	80.5765	339	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
GCA_900553175.1	s__Alistipes sp900553175	80.4664	232	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542685.1	s__Alistipes dispar	80.3847	328	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.96	0.94	0.89	7	-
GCA_009774895.1	s__Alistipes sp009774895	80.3715	241	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.77	98.77	0.97	0.97	2	-
GCF_000312145.1	s__Alistipes senegalensis	80.2451	357	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCA_910575495.1	s__Alistipes sp910575495	80.1689	318	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.23	98.47	0.95	0.90	3	-
GCA_015059965.1	s__Alistipes sp015059965	79.9789	313	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541585.1	s__Alistipes sp900541585	79.7906	339	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCF_000265365.1	s__Alistipes finegoldii	79.575	334	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCF_006542665.1	s__Alistipes communis	79.5054	292	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.74	98.62	0.92	0.87	10	-
GCA_904502075.1	s__Alistipes sp904502075	79.4421	219	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000374505.1	s__Alistipes onderdonkii	79.3771	321	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.63	96.86	0.89	0.82	44	-
GCA_019113885.1	s__Alistipes intestinipullorum	79.1743	241	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587675.1	s__Alistipes sp910587675	78.7623	214	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154465.1	s__Alistipes putredinis	78.7306	221	635	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.94	97.62	0.91	0.76	28	-
--------------------------------------------------------------------------------
[2023-06-13 21:22:35,104] [INFO] GTDB search result was written to GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 21:22:35,104] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:22:35,109] [INFO] DFAST_QC result json was written to GCA_947039995.1_ERR8099097_bin.29_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 21:22:35,109] [INFO] DFAST_QC completed!
[2023-06-13 21:22:35,109] [INFO] Total running time: 0h1m3s