[2023-06-28 02:22:15,178] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:22:15,191] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:22:15,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a26330f-a1f0-46e6-b3fc-960f62af7160/dqc_reference
[2023-06-28 02:22:16,392] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:22:16,393] [INFO] Task started: Prodigal
[2023-06-28 02:22:16,394] [INFO] Running command: gunzip -c /var/lib/cwl/stg8720b611-4bf0-47e5-85b2-cf8bd3d8d052/GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:22:30,058] [INFO] Task succeeded: Prodigal
[2023-06-28 02:22:30,058] [INFO] Task started: HMMsearch
[2023-06-28 02:22:30,059] [INFO] Running command: hmmsearch --tblout GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a26330f-a1f0-46e6-b3fc-960f62af7160/dqc_reference/reference_markers.hmm GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:22:30,292] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:22:30,293] [INFO] Found 6/6 markers.
[2023-06-28 02:22:30,344] [INFO] Query marker FASTA was written to GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 02:22:30,345] [INFO] Task started: Blastn
[2023-06-28 02:22:30,345] [INFO] Running command: blastn -query GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a26330f-a1f0-46e6-b3fc-960f62af7160/dqc_reference/reference_markers.fasta -out GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:22:30,922] [INFO] Task succeeded: Blastn
[2023-06-28 02:22:30,925] [INFO] Selected 25 target genomes.
[2023-06-28 02:22:30,926] [INFO] Target genome list was writen to GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 02:22:30,927] [INFO] Task started: fastANI
[2023-06-28 02:22:30,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg8720b611-4bf0-47e5-85b2-cf8bd3d8d052/GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:22:45,143] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:45,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a26330f-a1f0-46e6-b3fc-960f62af7160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:22:45,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a26330f-a1f0-46e6-b3fc-960f62af7160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:22:45,145] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:22:45,145] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 02:22:45,145] [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 02:22:45,147] [INFO] DFAST Taxonomy check result was written to GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 02:22:45,147] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:22:45,147] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:22:45,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a26330f-a1f0-46e6-b3fc-960f62af7160/dqc_reference/checkm_data
[2023-06-28 02:22:45,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:22:45,192] [INFO] Task started: CheckM
[2023-06-28 02:22:45,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 02:23:29,001] [INFO] Task succeeded: CheckM
[2023-06-28 02:23:29,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:23:29,019] [INFO] ===== Completeness check finished =====
[2023-06-28 02:23:29,019] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:23:29,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 02:23:29,019] [INFO] Task started: Blastn
[2023-06-28 02:23:29,019] [INFO] Running command: blastn -query GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a26330f-a1f0-46e6-b3fc-960f62af7160/dqc_reference/reference_markers_gtdb.fasta -out GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:23:29,788] [INFO] Task succeeded: Blastn
[2023-06-28 02:23:29,791] [INFO] Selected 12 target genomes.
[2023-06-28 02:23:29,791] [INFO] Target genome list was writen to GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:23:29,794] [INFO] Task started: fastANI
[2023-06-28 02:23:29,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg8720b611-4bf0-47e5-85b2-cf8bd3d8d052/GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:23:36,762] [INFO] Task succeeded: fastANI
[2023-06-28 02:23:36,768] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:23:36,769] [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_016928515.1	s__BM516 sp016928515	78.7325	511	1513	d__Bacteria;p__Bacteroidota;c__SZUA-365;o__SZUA-365;f__SZUA-365;g__BM516	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869275.1	s__BM516 sp002869275	77.7575	344	1513	d__Bacteria;p__Bacteroidota;c__SZUA-365;o__SZUA-365;f__SZUA-365;g__BM516	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018224415.1	s__SZUA-365 sp018224415	77.6867	289	1513	d__Bacteria;p__Bacteroidota;c__SZUA-365;o__SZUA-365;f__SZUA-365;g__SZUA-365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003246455.1	s__SZUA-365 sp003246455	77.6837	359	1513	d__Bacteria;p__Bacteroidota;c__SZUA-365;o__SZUA-365;f__SZUA-365;g__SZUA-365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860565.1	s__SZUA-365 sp014860565	77.6608	385	1513	d__Bacteria;p__Bacteroidota;c__SZUA-365;o__SZUA-365;f__SZUA-365;g__SZUA-365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218045.1	s__JACRFB01 sp016218045	76.5871	145	1513	d__Bacteria;p__Bacteroidota;c__SZUA-365;o__SZUA-365;f__SZUA-365;g__JACRFB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 02:23:36,770] [INFO] GTDB search result was written to GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 02:23:36,771] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:23:36,773] [INFO] DFAST_QC result json was written to GCA_913061095.1_SRR6201696_bin.5_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 02:23:36,773] [INFO] DFAST_QC completed!
[2023-06-28 02:23:36,773] [INFO] Total running time: 0h1m22s