[2023-06-28 13:51:39,671] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:51:39,674] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:51:39,674] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6341384-6766-4029-b42d-64c8c6495e58/dqc_reference
[2023-06-28 13:51:40,773] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:51:40,774] [INFO] Task started: Prodigal
[2023-06-28 13:51:40,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg86fa6939-88a3-490e-85e8-759aafa30348/GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:51:47,360] [INFO] Task succeeded: Prodigal
[2023-06-28 13:51:47,360] [INFO] Task started: HMMsearch
[2023-06-28 13:51:47,360] [INFO] Running command: hmmsearch --tblout GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6341384-6766-4029-b42d-64c8c6495e58/dqc_reference/reference_markers.hmm GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:51:47,561] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:51:47,562] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg86fa6939-88a3-490e-85e8-759aafa30348/GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 13:51:47,587] [INFO] Query marker FASTA was written to GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 13:51:47,587] [INFO] Task started: Blastn
[2023-06-28 13:51:47,588] [INFO] Running command: blastn -query GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6341384-6766-4029-b42d-64c8c6495e58/dqc_reference/reference_markers.fasta -out GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:51:48,160] [INFO] Task succeeded: Blastn
[2023-06-28 13:51:48,165] [INFO] Selected 23 target genomes.
[2023-06-28 13:51:48,166] [INFO] Target genome list was writen to GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 13:51:48,170] [INFO] Task started: fastANI
[2023-06-28 13:51:48,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg86fa6939-88a3-490e-85e8-759aafa30348/GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:52:02,743] [INFO] Task succeeded: fastANI
[2023-06-28 13:52:02,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6341384-6766-4029-b42d-64c8c6495e58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:52:02,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6341384-6766-4029-b42d-64c8c6495e58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:52:02,745] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:52:02,745] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 13:52:02,745] [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
--------------------------------------------------------------------------------
[2023-06-28 13:52:02,747] [INFO] DFAST Taxonomy check result was written to GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 13:52:02,747] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:52:02,747] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:52:02,747] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6341384-6766-4029-b42d-64c8c6495e58/dqc_reference/checkm_data
[2023-06-28 13:52:02,750] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:52:02,785] [INFO] Task started: CheckM
[2023-06-28 13:52:02,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 13:52:26,289] [INFO] Task succeeded: CheckM
[2023-06-28 13:52:26,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:52:26,304] [INFO] ===== Completeness check finished =====
[2023-06-28 13:52:26,304] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:52:26,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 13:52:26,305] [INFO] Task started: Blastn
[2023-06-28 13:52:26,305] [INFO] Running command: blastn -query GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6341384-6766-4029-b42d-64c8c6495e58/dqc_reference/reference_markers_gtdb.fasta -out GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:52:27,175] [INFO] Task succeeded: Blastn
[2023-06-28 13:52:27,178] [INFO] Selected 14 target genomes.
[2023-06-28 13:52:27,178] [INFO] Target genome list was writen to GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:52:27,183] [INFO] Task started: fastANI
[2023-06-28 13:52:27,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg86fa6939-88a3-490e-85e8-759aafa30348/GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:52:33,777] [INFO] Task succeeded: fastANI
[2023-06-28 13:52:33,783] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:52:33,783] [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_002171735.1	s__UBA868 sp002171735	98.8194	679	888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	98.83	98.60	0.84	0.82	3	conclusive
GCA_018661145.1	s__UBA868 sp018661145	90.432	551	888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.09	98.72	0.78	0.74	4	-
GCA_003529705.1	s__UBA868 sp003529705	82.5052	270	888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327725.1	s__UBA868 sp002327725	79.825	425	888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.85	99.69	0.88	0.82	5	-
GCA_002713825.1	s__UBA868 sp002713825	78.6019	158	888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845525.1	s__UBA868 sp016845525	78.5567	269	888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346525.1	s__UBA868 sp002346525	78.463	247	888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523045.1	s__UBA868 sp011523045	78.0349	291	888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:52:33,784] [INFO] GTDB search result was written to GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 13:52:33,785] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:52:33,787] [INFO] DFAST_QC result json was written to GCA_913051665.1_ERR599094_bin.94_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 13:52:33,787] [INFO] DFAST_QC completed!
[2023-06-28 13:52:33,787] [INFO] Total running time: 0h0m54s