[2023-06-08 00:35:34,424] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:35:34,446] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:35:34,447] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb47febc-5bf9-42a3-92e7-331957a2a8f7/dqc_reference
[2023-06-08 00:35:36,917] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:35:36,918] [INFO] Task started: Prodigal
[2023-06-08 00:35:36,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cbc6308-06d0-427f-a7af-68caffc2dbb2/GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:35:41,764] [INFO] Task succeeded: Prodigal
[2023-06-08 00:35:41,765] [INFO] Task started: HMMsearch
[2023-06-08 00:35:41,765] [INFO] Running command: hmmsearch --tblout GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb47febc-5bf9-42a3-92e7-331957a2a8f7/dqc_reference/reference_markers.hmm GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:35:41,975] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:35:41,977] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1cbc6308-06d0-427f-a7af-68caffc2dbb2/GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 00:35:41,999] [INFO] Query marker FASTA was written to GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:35:41,999] [INFO] Task started: Blastn
[2023-06-08 00:35:41,999] [INFO] Running command: blastn -query GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb47febc-5bf9-42a3-92e7-331957a2a8f7/dqc_reference/reference_markers.fasta -out GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:42,586] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:42,590] [INFO] Selected 18 target genomes.
[2023-06-08 00:35:42,591] [INFO] Target genome list was writen to GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:35:42,594] [INFO] Task started: fastANI
[2023-06-08 00:35:42,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cbc6308-06d0-427f-a7af-68caffc2dbb2/GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:35:54,424] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:54,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb47febc-5bf9-42a3-92e7-331957a2a8f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:35:54,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb47febc-5bf9-42a3-92e7-331957a2a8f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:35:54,427] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:35:54,427] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:35:54,427] [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
--------------------------------------------------------------------------------
[2023-06-08 00:35:54,428] [INFO] DFAST Taxonomy check result was written to GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:35:54,429] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:35:54,429] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:35:54,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb47febc-5bf9-42a3-92e7-331957a2a8f7/dqc_reference/checkm_data
[2023-06-08 00:35:54,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:35:54,457] [INFO] Task started: CheckM
[2023-06-08 00:35:54,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:36:14,735] [INFO] Task succeeded: CheckM
[2023-06-08 00:36:14,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 00:36:14,767] [INFO] ===== Completeness check finished =====
[2023-06-08 00:36:14,767] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:36:14,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:36:14,768] [INFO] Task started: Blastn
[2023-06-08 00:36:14,768] [INFO] Running command: blastn -query GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb47febc-5bf9-42a3-92e7-331957a2a8f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:36:15,595] [INFO] Task succeeded: Blastn
[2023-06-08 00:36:15,599] [INFO] Selected 14 target genomes.
[2023-06-08 00:36:15,599] [INFO] Target genome list was writen to GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:36:15,605] [INFO] Task started: fastANI
[2023-06-08 00:36:15,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cbc6308-06d0-427f-a7af-68caffc2dbb2/GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:36:24,802] [INFO] Task succeeded: fastANI
[2023-06-08 00:36:24,817] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:36:24,817] [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_900771305.1	s__RUG572 sp900771305	98.0999	416	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900547945.1	s__RUG572 sp900547945	81.8051	317	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	99.14	98.30	0.90	0.80	3	-
GCA_016302985.1	s__RUG572 sp016302985	80.7229	276	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803135.1	s__RUG572 sp902803135	78.5732	199	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427485.1	s__RUG572 sp017427485	78.3757	224	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769585.1	s__RUG572 sp902769585	78.3268	181	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320225.1	s__RUG572 sp900320225	78.2746	235	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	99.22	98.67	0.91	0.88	3	-
GCA_017459225.1	s__RUG572 sp017459225	78.1932	130	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017563185.1	s__RUG572 sp017563185	78.0857	156	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430155.1	s__RUG572 sp017430155	77.9917	168	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779075.1	s__RUG572 sp902779075	77.8379	171	512	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 00:36:24,819] [INFO] GTDB search result was written to GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:36:24,819] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:36:24,822] [INFO] DFAST_QC result json was written to GCA_945483205.1_SRR7188237_bin.15_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:36:24,822] [INFO] DFAST_QC completed!
[2023-06-08 00:36:24,822] [INFO] Total running time: 0h0m50s