[2023-06-28 00:33:36,987] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:33:36,996] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:33:36,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg58f72940-3394-4724-b9d6-6a30668e0e79/dqc_reference
[2023-06-28 00:33:38,414] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:33:38,415] [INFO] Task started: Prodigal
[2023-06-28 00:33:38,415] [INFO] Running command: gunzip -c /var/lib/cwl/stg658630d2-b399-4480-8003-b87bfe287827/GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:33:57,408] [INFO] Task succeeded: Prodigal
[2023-06-28 00:33:57,409] [INFO] Task started: HMMsearch
[2023-06-28 00:33:57,409] [INFO] Running command: hmmsearch --tblout GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58f72940-3394-4724-b9d6-6a30668e0e79/dqc_reference/reference_markers.hmm GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:33:57,668] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:33:57,670] [INFO] Found 6/6 markers.
[2023-06-28 00:33:57,705] [INFO] Query marker FASTA was written to GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 00:33:57,706] [INFO] Task started: Blastn
[2023-06-28 00:33:57,706] [INFO] Running command: blastn -query GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg58f72940-3394-4724-b9d6-6a30668e0e79/dqc_reference/reference_markers.fasta -out GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:33:58,335] [INFO] Task succeeded: Blastn
[2023-06-28 00:33:58,339] [INFO] Selected 16 target genomes.
[2023-06-28 00:33:58,340] [INFO] Target genome list was writen to GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 00:33:58,342] [INFO] Task started: fastANI
[2023-06-28 00:33:58,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg658630d2-b399-4480-8003-b87bfe287827/GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:34:08,437] [INFO] Task succeeded: fastANI
[2023-06-28 00:34:08,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58f72940-3394-4724-b9d6-6a30668e0e79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:34:08,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58f72940-3394-4724-b9d6-6a30668e0e79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:34:08,440] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:34:08,440] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:34:08,440] [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 00:34:08,442] [INFO] DFAST Taxonomy check result was written to GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 00:34:08,443] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:34:08,443] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:34:08,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58f72940-3394-4724-b9d6-6a30668e0e79/dqc_reference/checkm_data
[2023-06-28 00:34:08,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:34:08,488] [INFO] Task started: CheckM
[2023-06-28 00:34:08,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 00:35:03,567] [INFO] Task succeeded: CheckM
[2023-06-28 00:35:03,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:35:03,591] [INFO] ===== Completeness check finished =====
[2023-06-28 00:35:03,592] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:35:03,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 00:35:03,592] [INFO] Task started: Blastn
[2023-06-28 00:35:03,593] [INFO] Running command: blastn -query GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg58f72940-3394-4724-b9d6-6a30668e0e79/dqc_reference/reference_markers_gtdb.fasta -out GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:35:04,561] [INFO] Task succeeded: Blastn
[2023-06-28 00:35:04,566] [INFO] Selected 16 target genomes.
[2023-06-28 00:35:04,566] [INFO] Target genome list was writen to GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:35:04,596] [INFO] Task started: fastANI
[2023-06-28 00:35:04,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg658630d2-b399-4480-8003-b87bfe287827/GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:35:15,183] [INFO] Task succeeded: fastANI
[2023-06-28 00:35:15,193] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:35:15,193] [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_014529625.1	s__UBA5691 sp002420265	95.3216	1113	1266	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	96.17	95.09	0.91	0.87	4	conclusive
GCA_002420185.1	s__UBA5691 sp002420185	92.5346	952	1266	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002474325.1	s__UBA5691 sp002474325	79.0983	82	1266	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	98.86	98.86	0.81	0.81	2	-
GCA_018700525.1	s__UBA5691 sp018700525	78.6795	149	1266	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.68	99.65	0.95	0.94	5	-
GCA_002694885.1	s__UBA5691 sp002694885	77.4672	108	1266	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.79	99.79	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-28 00:35:15,195] [INFO] GTDB search result was written to GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 00:35:15,196] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:35:15,200] [INFO] DFAST_QC result json was written to GCA_913045255.1_ERR599050_bin.137_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 00:35:15,200] [INFO] DFAST_QC completed!
[2023-06-28 00:35:15,200] [INFO] Total running time: 0h1m38s