[2023-06-13 12:28:01,179] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:28:01,183] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:28:01,183] [INFO] DQC Reference Directory: /var/lib/cwl/stg95a39223-ca2b-49f9-a478-9595ed57c749/dqc_reference
[2023-06-13 12:28:02,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:28:02,832] [INFO] Task started: Prodigal
[2023-06-13 12:28:02,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3990c30-c8ec-4743-a3a1-2a7f0bb0247e/GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:28:20,278] [INFO] Task succeeded: Prodigal
[2023-06-13 12:28:20,279] [INFO] Task started: HMMsearch
[2023-06-13 12:28:20,279] [INFO] Running command: hmmsearch --tblout GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95a39223-ca2b-49f9-a478-9595ed57c749/dqc_reference/reference_markers.hmm GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:28:20,546] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:28:20,548] [INFO] Found 6/6 markers.
[2023-06-13 12:28:20,591] [INFO] Query marker FASTA was written to GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 12:28:20,592] [INFO] Task started: Blastn
[2023-06-13 12:28:20,592] [INFO] Running command: blastn -query GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg95a39223-ca2b-49f9-a478-9595ed57c749/dqc_reference/reference_markers.fasta -out GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:28:21,255] [INFO] Task succeeded: Blastn
[2023-06-13 12:28:21,259] [INFO] Selected 9 target genomes.
[2023-06-13 12:28:21,259] [INFO] Target genome list was writen to GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 12:28:21,260] [INFO] Task started: fastANI
[2023-06-13 12:28:21,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3990c30-c8ec-4743-a3a1-2a7f0bb0247e/GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:28:28,317] [INFO] Task succeeded: fastANI
[2023-06-13 12:28:28,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95a39223-ca2b-49f9-a478-9595ed57c749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:28:28,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95a39223-ca2b-49f9-a478-9595ed57c749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:28:28,326] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 12:28:28,327] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 12:28:28,327] [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 finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	98.3036	916	1065	95	conclusive
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	85.4022	723	1065	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	85.3238	722	1065	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	85.1461	680	1065	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	84.8002	634	1065	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	84.7292	651	1065	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	83.9024	600	1065	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	82.1354	560	1065	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	77.1662	129	1065	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 12:28:28,329] [INFO] DFAST Taxonomy check result was written to GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 12:28:28,329] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:28:28,330] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:28:28,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95a39223-ca2b-49f9-a478-9595ed57c749/dqc_reference/checkm_data
[2023-06-13 12:28:28,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:28:28,374] [INFO] Task started: CheckM
[2023-06-13 12:28:28,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 12:29:17,213] [INFO] Task succeeded: CheckM
[2023-06-13 12:29:17,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 12:29:17,238] [INFO] ===== Completeness check finished =====
[2023-06-13 12:29:17,238] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:29:17,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 12:29:17,239] [INFO] Task started: Blastn
[2023-06-13 12:29:17,239] [INFO] Running command: blastn -query GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg95a39223-ca2b-49f9-a478-9595ed57c749/dqc_reference/reference_markers_gtdb.fasta -out GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:29:18,187] [INFO] Task succeeded: Blastn
[2023-06-13 12:29:18,192] [INFO] Selected 11 target genomes.
[2023-06-13 12:29:18,192] [INFO] Target genome list was writen to GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:29:18,195] [INFO] Task started: fastANI
[2023-06-13 12:29:18,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3990c30-c8ec-4743-a3a1-2a7f0bb0247e/GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:29:26,412] [INFO] Task succeeded: fastANI
[2023-06-13 12:29:26,429] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 12:29:26,429] [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_000265365.1	s__Alistipes finegoldii	98.3226	915	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	conclusive
GCF_000374505.1	s__Alistipes onderdonkii	85.3263	722	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.63	96.86	0.89	0.82	44	-
GCF_000210575.1	s__Alistipes shahii	84.7446	650	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCA_902388705.1	s__Alistipes sp902388705	84.4719	596	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.98	97.96	0.93	0.92	3	-
GCF_000312145.1	s__Alistipes senegalensis	83.9997	589	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCA_900541585.1	s__Alistipes sp900541585	83.7541	560	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCF_900083545.1	s__Alistipes provencensis	83.0541	562	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107675.1	s__Alistipes timonensis	82.6241	556	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.44	0.92	0.87	7	-
GCA_001941065.1	s__Alistipes sp001941065	82.3119	532	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576555.1	s__Alistipes sp910576555	81.29	441	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434235.1	s__Alistipes avistercoris	81.0167	483	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.12	0.90	0.84	7	-
--------------------------------------------------------------------------------
[2023-06-13 12:29:26,434] [INFO] GTDB search result was written to GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 12:29:26,434] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:29:26,439] [INFO] DFAST_QC result json was written to GCA_947644035.1_SRR17794286_bin.21_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 12:29:26,439] [INFO] DFAST_QC completed!
[2023-06-13 12:29:26,440] [INFO] Total running time: 0h1m25s