[2023-06-08 19:16:40,383] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:16:40,386] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:16:40,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg08ac8685-3040-4afe-9ed3-a7e1e5c585e1/dqc_reference
[2023-06-08 19:16:41,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:16:41,587] [INFO] Task started: Prodigal
[2023-06-08 19:16:41,588] [INFO] Running command: gunzip -c /var/lib/cwl/stge07dde1f-098e-47fe-977a-c59ef257c159/GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:16:44,907] [INFO] Task succeeded: Prodigal
[2023-06-08 19:16:44,907] [INFO] Task started: HMMsearch
[2023-06-08 19:16:44,907] [INFO] Running command: hmmsearch --tblout GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08ac8685-3040-4afe-9ed3-a7e1e5c585e1/dqc_reference/reference_markers.hmm GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:16:45,135] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:16:45,137] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge07dde1f-098e-47fe-977a-c59ef257c159/GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 19:16:45,157] [INFO] Query marker FASTA was written to GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:16:45,157] [INFO] Task started: Blastn
[2023-06-08 19:16:45,157] [INFO] Running command: blastn -query GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg08ac8685-3040-4afe-9ed3-a7e1e5c585e1/dqc_reference/reference_markers.fasta -out GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:16:45,732] [INFO] Task succeeded: Blastn
[2023-06-08 19:16:45,736] [INFO] Selected 19 target genomes.
[2023-06-08 19:16:45,737] [INFO] Target genome list was writen to GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:16:45,739] [INFO] Task started: fastANI
[2023-06-08 19:16:45,739] [INFO] Running command: fastANI --query /var/lib/cwl/stge07dde1f-098e-47fe-977a-c59ef257c159/GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:16:55,098] [INFO] Task succeeded: fastANI
[2023-06-08 19:16:55,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08ac8685-3040-4afe-9ed3-a7e1e5c585e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:16:55,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08ac8685-3040-4afe-9ed3-a7e1e5c585e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:16:55,103] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:16:55,103] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 19:16:55,104] [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
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	77.3664	84	570	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 19:16:55,106] [INFO] DFAST Taxonomy check result was written to GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:16:55,106] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:16:55,107] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:16:55,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08ac8685-3040-4afe-9ed3-a7e1e5c585e1/dqc_reference/checkm_data
[2023-06-08 19:16:55,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:16:55,133] [INFO] Task started: CheckM
[2023-06-08 19:16:55,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:17:12,857] [INFO] Task succeeded: CheckM
[2023-06-08 19:17:12,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:17:12,879] [INFO] ===== Completeness check finished =====
[2023-06-08 19:17:12,879] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:17:12,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:17:12,880] [INFO] Task started: Blastn
[2023-06-08 19:17:12,880] [INFO] Running command: blastn -query GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg08ac8685-3040-4afe-9ed3-a7e1e5c585e1/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:17:13,726] [INFO] Task succeeded: Blastn
[2023-06-08 19:17:13,730] [INFO] Selected 8 target genomes.
[2023-06-08 19:17:13,731] [INFO] Target genome list was writen to GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:17:13,733] [INFO] Task started: fastANI
[2023-06-08 19:17:13,733] [INFO] Running command: fastANI --query /var/lib/cwl/stge07dde1f-098e-47fe-977a-c59ef257c159/GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:17:17,437] [INFO] Task succeeded: fastANI
[2023-06-08 19:17:17,444] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:17:17,444] [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_902760415.1	s__Eubacterium_Q sp002349225	98.3799	482	570	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.66	98.14	0.88	0.86	4	conclusive
GCA_000687975.1	s__Eubacterium_Q sp000687975	83.1416	411	570	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110635.1	s__Eubacterium_Q sp900110635	81.4253	326	570	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776395.1	s__Eubacterium_Q sp902776395	79.4361	165	570	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774915.1	s__Eubacterium_Q sp902777655	79.4236	208	570	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	96.59	95.67	0.86	0.82	3	-
GCA_017480495.1	s__Eubacterium_Q sp017480495	79.2213	136	570	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	97.26	97.26	0.72	0.72	2	-
GCA_902783605.1	s__Eubacterium_Q sp902783605	77.8131	165	570	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 19:17:17,446] [INFO] GTDB search result was written to GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:17:17,447] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:17:17,450] [INFO] DFAST_QC result json was written to GCA_947166325.1_SRR8387714_bin.17_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:17:17,450] [INFO] DFAST_QC completed!
[2023-06-08 19:17:17,450] [INFO] Total running time: 0h0m37s