[2023-06-08 20:04:32,484] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:04:32,494] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:04:32,494] [INFO] DQC Reference Directory: /var/lib/cwl/stga605aa95-0fc0-4124-a417-f1e175ca1008/dqc_reference
[2023-06-08 20:04:34,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:04:34,075] [INFO] Task started: Prodigal
[2023-06-08 20:04:34,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg36ec0d51-daa7-4161-a116-f5923ab91b80/GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:04:50,574] [INFO] Task succeeded: Prodigal
[2023-06-08 20:04:50,574] [INFO] Task started: HMMsearch
[2023-06-08 20:04:50,574] [INFO] Running command: hmmsearch --tblout GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga605aa95-0fc0-4124-a417-f1e175ca1008/dqc_reference/reference_markers.hmm GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:04:50,822] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:04:50,824] [INFO] Found 6/6 markers.
[2023-06-08 20:04:50,858] [INFO] Query marker FASTA was written to GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:04:50,859] [INFO] Task started: Blastn
[2023-06-08 20:04:50,859] [INFO] Running command: blastn -query GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga605aa95-0fc0-4124-a417-f1e175ca1008/dqc_reference/reference_markers.fasta -out GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:04:51,502] [INFO] Task succeeded: Blastn
[2023-06-08 20:04:51,506] [INFO] Selected 25 target genomes.
[2023-06-08 20:04:51,507] [INFO] Target genome list was writen to GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:04:51,510] [INFO] Task started: fastANI
[2023-06-08 20:04:51,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg36ec0d51-daa7-4161-a116-f5923ab91b80/GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:05:05,259] [INFO] Task succeeded: fastANI
[2023-06-08 20:05:05,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga605aa95-0fc0-4124-a417-f1e175ca1008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:05:05,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga605aa95-0fc0-4124-a417-f1e175ca1008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:05:05,265] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:05:05,265] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:05:05,266] [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
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.6191	71	902	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.4632	52	902	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.3608	55	902	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.1708	52	902	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:05:05,267] [INFO] DFAST Taxonomy check result was written to GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:05:05,268] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:05:05,268] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:05:05,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga605aa95-0fc0-4124-a417-f1e175ca1008/dqc_reference/checkm_data
[2023-06-08 20:05:05,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:05:05,305] [INFO] Task started: CheckM
[2023-06-08 20:05:05,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:05:55,386] [INFO] Task succeeded: CheckM
[2023-06-08 20:05:55,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.85%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-08 20:05:55,414] [INFO] ===== Completeness check finished =====
[2023-06-08 20:05:55,414] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:05:55,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:05:55,415] [INFO] Task started: Blastn
[2023-06-08 20:05:55,415] [INFO] Running command: blastn -query GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga605aa95-0fc0-4124-a417-f1e175ca1008/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:05:56,366] [INFO] Task succeeded: Blastn
[2023-06-08 20:05:56,371] [INFO] Selected 22 target genomes.
[2023-06-08 20:05:56,371] [INFO] Target genome list was writen to GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:05:56,381] [INFO] Task started: fastANI
[2023-06-08 20:05:56,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg36ec0d51-daa7-4161-a116-f5923ab91b80/GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:06:08,676] [INFO] Task succeeded: fastANI
[2023-06-08 20:06:08,697] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 20:06:08,697] [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_017470425.1	s__UBA4372 sp017470425	79.6177	237	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.15	97.15	0.50	0.50	2	-
GCA_017429945.1	s__UBA4372 sp017429945	79.5215	244	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965425.1	s__UBA4372 sp017965425	79.235	256	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318115.1	s__UBA4372 sp900318115	79.2061	301	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.30	96.55	0.83	0.74	7	-
GCA_902771725.1	s__UBA4372 sp902771725	79.0935	306	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779845.1	s__UBA4372 sp902779845	79.06	266	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.82	95.27	0.82	0.79	4	-
GCA_017429525.1	s__UBA4372 sp017429525	79.0375	285	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.71	96.71	0.77	0.77	2	-
GCA_900316355.1	s__UBA4372 sp900316355	78.976	297	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.71	97.42	0.94	0.87	3	-
GCA_905233765.1	s__UBA4372 sp905233765	78.779	238	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280855.1	s__UBA4372 sp016280855	78.1758	228	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803195.1	s__UBA4372 sp902803195	78.1479	194	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286165.1	s__UBA4372 sp016286165	78.1138	217	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017535725.1	s__UBA4372 sp017535725	78.1034	206	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619335.1	s__UBA4372 sp017619335	78.0553	228	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781315.1	s__Prevotella sp902781315	77.4741	116	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.55	96.55	0.79	0.79	2	-
GCA_017524545.1	s__UBA4372 sp017524545	76.7334	112	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017503065.1	s__UBA4372 sp017503065	76.5135	69	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066245.1	s__Alloprevotella sp018066245	76.5014	60	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465905.1	s__UBA1189 sp017465905	76.1551	59	902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1189	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:06:08,699] [INFO] GTDB search result was written to GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:06:08,700] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:06:08,703] [INFO] DFAST_QC result json was written to GCA_947166655.1_SRR8387715_bin.78_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:06:08,703] [INFO] DFAST_QC completed!
[2023-06-08 20:06:08,704] [INFO] Total running time: 0h1m36s