[2023-06-28 10:01:04,728] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:01:04,732] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:01:04,733] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb2240d5-8d79-43f8-9e0f-9f46f5efb61e/dqc_reference
[2023-06-28 10:01:06,092] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:01:06,093] [INFO] Task started: Prodigal
[2023-06-28 10:01:06,093] [INFO] Running command: gunzip -c /var/lib/cwl/stge7b4d738-714d-4a8a-a1d5-1ac7125fff21/GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:01:13,407] [INFO] Task succeeded: Prodigal
[2023-06-28 10:01:13,408] [INFO] Task started: HMMsearch
[2023-06-28 10:01:13,408] [INFO] Running command: hmmsearch --tblout GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb2240d5-8d79-43f8-9e0f-9f46f5efb61e/dqc_reference/reference_markers.hmm GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:01:13,627] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:01:13,629] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge7b4d738-714d-4a8a-a1d5-1ac7125fff21/GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 10:01:13,653] [INFO] Query marker FASTA was written to GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 10:01:13,653] [INFO] Task started: Blastn
[2023-06-28 10:01:13,653] [INFO] Running command: blastn -query GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb2240d5-8d79-43f8-9e0f-9f46f5efb61e/dqc_reference/reference_markers.fasta -out GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:01:14,230] [INFO] Task succeeded: Blastn
[2023-06-28 10:01:14,234] [INFO] Selected 13 target genomes.
[2023-06-28 10:01:14,235] [INFO] Target genome list was writen to GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 10:01:14,238] [INFO] Task started: fastANI
[2023-06-28 10:01:14,238] [INFO] Running command: fastANI --query /var/lib/cwl/stge7b4d738-714d-4a8a-a1d5-1ac7125fff21/GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:01:22,776] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:22,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb2240d5-8d79-43f8-9e0f-9f46f5efb61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:01:22,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb2240d5-8d79-43f8-9e0f-9f46f5efb61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:01:22,779] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:01:22,779] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:01:22,779] [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 10:01:22,781] [INFO] DFAST Taxonomy check result was written to GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 10:01:22,782] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:01:22,782] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:01:22,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb2240d5-8d79-43f8-9e0f-9f46f5efb61e/dqc_reference/checkm_data
[2023-06-28 10:01:22,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:01:22,816] [INFO] Task started: CheckM
[2023-06-28 10:01:22,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 10:01:50,451] [INFO] Task succeeded: CheckM
[2023-06-28 10:01:50,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:01:50,473] [INFO] ===== Completeness check finished =====
[2023-06-28 10:01:50,473] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:01:50,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 10:01:50,474] [INFO] Task started: Blastn
[2023-06-28 10:01:50,474] [INFO] Running command: blastn -query GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb2240d5-8d79-43f8-9e0f-9f46f5efb61e/dqc_reference/reference_markers_gtdb.fasta -out GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:01:51,255] [INFO] Task succeeded: Blastn
[2023-06-28 10:01:51,261] [INFO] Selected 7 target genomes.
[2023-06-28 10:01:51,261] [INFO] Target genome list was writen to GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:01:51,263] [INFO] Task started: fastANI
[2023-06-28 10:01:51,263] [INFO] Running command: fastANI --query /var/lib/cwl/stge7b4d738-714d-4a8a-a1d5-1ac7125fff21/GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:01:54,288] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:54,294] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:01:54,294] [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_902605755.1	s__UBA4465 sp902605755	88.779	347	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691385.1	s__UBA4465 sp002691385	83.7067	431	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182375.1	s__UBA4465 sp905182375	81.7426	439	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479015.1	s__UBA4465 sp002470835	81.6629	476	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.62	98.40	0.95	0.92	11	-
GCA_002292365.1	s__UBA4465 sp002292365	81.3542	449	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.58	99.58	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-28 10:01:54,296] [INFO] GTDB search result was written to GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 10:01:54,296] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:01:54,299] [INFO] DFAST_QC result json was written to GCA_913045135.1_ERR599092_bin.90_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 10:01:54,299] [INFO] DFAST_QC completed!
[2023-06-28 10:01:54,299] [INFO] Total running time: 0h0m50s