[2023-06-13 18:13:32,173] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:13:32,175] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:13:32,176] [INFO] DQC Reference Directory: /var/lib/cwl/stg96c3c088-6fc8-4eca-843b-7b34a2979f2e/dqc_reference
[2023-06-13 18:13:33,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:13:33,410] [INFO] Task started: Prodigal
[2023-06-13 18:13:33,411] [INFO] Running command: gunzip -c /var/lib/cwl/stg24cb3b79-c371-4f50-aebd-79d314642cd7/GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:13:44,292] [INFO] Task succeeded: Prodigal
[2023-06-13 18:13:44,293] [INFO] Task started: HMMsearch
[2023-06-13 18:13:44,293] [INFO] Running command: hmmsearch --tblout GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96c3c088-6fc8-4eca-843b-7b34a2979f2e/dqc_reference/reference_markers.hmm GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:13:44,485] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:13:44,487] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg24cb3b79-c371-4f50-aebd-79d314642cd7/GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 18:13:44,512] [INFO] Query marker FASTA was written to GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 18:13:44,512] [INFO] Task started: Blastn
[2023-06-13 18:13:44,513] [INFO] Running command: blastn -query GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg96c3c088-6fc8-4eca-843b-7b34a2979f2e/dqc_reference/reference_markers.fasta -out GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:13:45,094] [INFO] Task succeeded: Blastn
[2023-06-13 18:13:45,098] [INFO] Selected 10 target genomes.
[2023-06-13 18:13:45,098] [INFO] Target genome list was writen to GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 18:13:45,100] [INFO] Task started: fastANI
[2023-06-13 18:13:45,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg24cb3b79-c371-4f50-aebd-79d314642cd7/GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:13:50,779] [INFO] Task succeeded: fastANI
[2023-06-13 18:13:50,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96c3c088-6fc8-4eca-843b-7b34a2979f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:13:50,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96c3c088-6fc8-4eca-843b-7b34a2979f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:13:50,799] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:13:50,799] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 18:13:50,799] [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=JC50	GCA_025145645.1	1288121	1288121	type	True	82.7195	413	643	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	82.7013	414	643	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	82.6511	423	643	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	82.3334	360	643	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	82.1631	420	643	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	82.1596	398	643	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	82.137	400	643	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	81.987	399	643	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	81.2967	357	643	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	81.1976	363	643	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:13:50,802] [INFO] DFAST Taxonomy check result was written to GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 18:13:50,803] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:13:50,803] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:13:50,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96c3c088-6fc8-4eca-843b-7b34a2979f2e/dqc_reference/checkm_data
[2023-06-13 18:13:50,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:13:50,834] [INFO] Task started: CheckM
[2023-06-13 18:13:50,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 18:14:24,431] [INFO] Task succeeded: CheckM
[2023-06-13 18:14:24,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:14:24,459] [INFO] ===== Completeness check finished =====
[2023-06-13 18:14:24,459] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:14:24,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 18:14:24,460] [INFO] Task started: Blastn
[2023-06-13 18:14:24,461] [INFO] Running command: blastn -query GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg96c3c088-6fc8-4eca-843b-7b34a2979f2e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:14:25,243] [INFO] Task succeeded: Blastn
[2023-06-13 18:14:25,248] [INFO] Selected 13 target genomes.
[2023-06-13 18:14:25,248] [INFO] Target genome list was writen to GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:14:25,249] [INFO] Task started: fastANI
[2023-06-13 18:14:25,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg24cb3b79-c371-4f50-aebd-79d314642cd7/GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:14:32,347] [INFO] Task succeeded: fastANI
[2023-06-13 18:14:32,366] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 18:14:32,367] [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_900544265.1	s__Alistipes merdavium	83.314	367	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCA_902362705.1	s__Alistipes sp002358415	83.0904	353	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.62	98.83	0.97	0.92	7	-
GCF_000312145.1	s__Alistipes senegalensis	82.6511	423	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCA_910576555.1	s__Alistipes sp910576555	82.6356	370	643	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	82.2944	378	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCA_019115605.1	s__Alistipes faecigallinarum	82.2013	328	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210575.1	s__Alistipes shahii	82.1741	397	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCF_900083545.1	s__Alistipes provencensis	82.1631	420	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001941065.1	s__Alistipes sp001941065	82.0623	372	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107675.1	s__Alistipes timonensis	81.9745	400	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.44	0.92	0.87	7	-
GCA_014796635.1	s__Alistipes sp014796635	81.4323	200	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374505.1	s__Alistipes onderdonkii	81.1981	363	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.63	96.86	0.89	0.82	44	-
GCA_902388705.1	s__Alistipes sp902388705	81.0696	333	643	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.98	97.96	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-13 18:14:32,369] [INFO] GTDB search result was written to GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 18:14:32,370] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:14:32,374] [INFO] DFAST_QC result json was written to GCA_947178025.1_SRR14411258_bin.3_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 18:14:32,374] [INFO] DFAST_QC completed!
[2023-06-13 18:14:32,374] [INFO] Total running time: 0h1m0s