[2023-06-08 07:02:48,797] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:02:48,800] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:02:48,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgb80fcce2-646f-4420-a743-2d70ea6d831e/dqc_reference
[2023-06-08 07:02:52,819] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:02:52,820] [INFO] Task started: Prodigal
[2023-06-08 07:02:52,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a35687a-a583-438a-9c09-66e97fa7dac9/GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:02:56,126] [INFO] Task succeeded: Prodigal
[2023-06-08 07:02:56,127] [INFO] Task started: HMMsearch
[2023-06-08 07:02:56,127] [INFO] Running command: hmmsearch --tblout GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb80fcce2-646f-4420-a743-2d70ea6d831e/dqc_reference/reference_markers.hmm GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:02:56,409] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:02:56,410] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5a35687a-a583-438a-9c09-66e97fa7dac9/GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 07:02:56,434] [INFO] Query marker FASTA was written to GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 07:02:56,435] [INFO] Task started: Blastn
[2023-06-08 07:02:56,435] [INFO] Running command: blastn -query GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb80fcce2-646f-4420-a743-2d70ea6d831e/dqc_reference/reference_markers.fasta -out GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:02:58,762] [INFO] Task succeeded: Blastn
[2023-06-08 07:02:58,774] [INFO] Selected 25 target genomes.
[2023-06-08 07:02:58,774] [INFO] Target genome list was writen to GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 07:02:58,779] [INFO] Task started: fastANI
[2023-06-08 07:02:58,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a35687a-a583-438a-9c09-66e97fa7dac9/GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:03:13,358] [INFO] Task succeeded: fastANI
[2023-06-08 07:03:13,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb80fcce2-646f-4420-a743-2d70ea6d831e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:03:13,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb80fcce2-646f-4420-a743-2d70ea6d831e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:03:13,365] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:03:13,366] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:03:13,366] [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
Succinivibrio dextrinosolvens	strain=DSM 3072	GCA_900167015.1	83771	83771	type	True	79.0349	149	549	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:03:13,368] [INFO] DFAST Taxonomy check result was written to GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 07:03:13,368] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:03:13,369] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:03:13,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb80fcce2-646f-4420-a743-2d70ea6d831e/dqc_reference/checkm_data
[2023-06-08 07:03:13,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:03:13,438] [INFO] Task started: CheckM
[2023-06-08 07:03:13,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 07:03:32,808] [INFO] Task succeeded: CheckM
[2023-06-08 07:03:32,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 6.25%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-08 07:03:32,842] [INFO] ===== Completeness check finished =====
[2023-06-08 07:03:32,843] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:03:32,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 07:03:32,846] [INFO] Task started: Blastn
[2023-06-08 07:03:32,846] [INFO] Running command: blastn -query GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb80fcce2-646f-4420-a743-2d70ea6d831e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:03:33,841] [INFO] Task succeeded: Blastn
[2023-06-08 07:03:33,845] [INFO] Selected 9 target genomes.
[2023-06-08 07:03:33,846] [INFO] Target genome list was writen to GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:03:33,850] [INFO] Task started: fastANI
[2023-06-08 07:03:33,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a35687a-a583-438a-9c09-66e97fa7dac9/GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:03:37,776] [INFO] Task succeeded: fastANI
[2023-06-08 07:03:37,789] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:03:37,790] [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_000431835.1	s__Succinivibrio sp000431835	95.8827	468	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.12	95.78	0.87	0.82	11	conclusive
GCA_900315395.1	s__Succinivibrio sp900315395	90.6031	455	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.82	99.64	0.93	0.87	3	-
GCA_002449335.1	s__Succinivibrio sp002449335	89.9861	472	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.89	95.86	0.90	0.86	3	-
GCA_004556245.1	s__Succinivibrio hippei_B	80.1174	152	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316375.1	s__Succinivibrio sp900316375	79.674	218	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.95	99.95	0.97	0.97	2	-
GCA_012519775.1	s__Succinivibrio sp012519775	79.5739	192	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785325.1	s__Succinivibrio sp003456415	79.4838	203	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.60	98.18	0.90	0.86	5	-
GCA_900316175.1	s__Succinivibrio sp900316175	78.9564	156	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.29	98.66	0.86	0.80	9	-
GCF_011065405.1	s__Succinivibrio dextrinosolvens_A	78.7636	136	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.30	97.32	0.93	0.84	6	-
--------------------------------------------------------------------------------
[2023-06-08 07:03:37,792] [INFO] GTDB search result was written to GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 07:03:37,792] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:03:37,796] [INFO] DFAST_QC result json was written to GCA_945829335.1_SRR5240750_bin.41_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 07:03:37,796] [INFO] DFAST_QC completed!
[2023-06-08 07:03:37,796] [INFO] Total running time: 0h0m49s