[2023-06-08 15:21:47,917] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:21:47,920] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:21:47,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bc97b1b-63d0-4692-a24b-7f654d4b3509/dqc_reference
[2023-06-08 15:21:49,538] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:21:49,539] [INFO] Task started: Prodigal
[2023-06-08 15:21:49,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cc7fc8c-853c-450e-a746-f876a81d213f/GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:21:52,673] [INFO] Task succeeded: Prodigal
[2023-06-08 15:21:52,673] [INFO] Task started: HMMsearch
[2023-06-08 15:21:52,673] [INFO] Running command: hmmsearch --tblout GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bc97b1b-63d0-4692-a24b-7f654d4b3509/dqc_reference/reference_markers.hmm GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:21:52,883] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:21:52,885] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2cc7fc8c-853c-450e-a746-f876a81d213f/GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 15:21:52,915] [INFO] Query marker FASTA was written to GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 15:21:52,915] [INFO] Task started: Blastn
[2023-06-08 15:21:52,916] [INFO] Running command: blastn -query GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bc97b1b-63d0-4692-a24b-7f654d4b3509/dqc_reference/reference_markers.fasta -out GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:21:53,518] [INFO] Task succeeded: Blastn
[2023-06-08 15:21:53,522] [INFO] Selected 11 target genomes.
[2023-06-08 15:21:53,523] [INFO] Target genome list was writen to GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 15:21:53,523] [INFO] Task started: fastANI
[2023-06-08 15:21:53,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cc7fc8c-853c-450e-a746-f876a81d213f/GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:21:59,000] [INFO] Task succeeded: fastANI
[2023-06-08 15:21:59,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bc97b1b-63d0-4692-a24b-7f654d4b3509/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:21:59,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bc97b1b-63d0-4692-a24b-7f654d4b3509/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:21:59,002] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:21:59,003] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 15:21:59,003] [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 15:21:59,005] [INFO] DFAST Taxonomy check result was written to GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 15:21:59,005] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:21:59,005] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:21:59,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bc97b1b-63d0-4692-a24b-7f654d4b3509/dqc_reference/checkm_data
[2023-06-08 15:21:59,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:21:59,030] [INFO] Task started: CheckM
[2023-06-08 15:21:59,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 15:22:17,149] [INFO] Task succeeded: CheckM
[2023-06-08 15:22:17,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 15:22:17,169] [INFO] ===== Completeness check finished =====
[2023-06-08 15:22:17,170] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:22:17,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 15:22:17,171] [INFO] Task started: Blastn
[2023-06-08 15:22:17,171] [INFO] Running command: blastn -query GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bc97b1b-63d0-4692-a24b-7f654d4b3509/dqc_reference/reference_markers_gtdb.fasta -out GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:22:18,130] [INFO] Task succeeded: Blastn
[2023-06-08 15:22:18,136] [INFO] Selected 15 target genomes.
[2023-06-08 15:22:18,136] [INFO] Target genome list was writen to GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:22:18,139] [INFO] Task started: fastANI
[2023-06-08 15:22:18,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cc7fc8c-853c-450e-a746-f876a81d213f/GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:22:23,223] [INFO] Task succeeded: fastANI
[2023-06-08 15:22:23,236] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 15:22:23,236] [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_016287985.1	s__CAG-196 sp016287985	77.989	179	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236055.1	s__CAG-196 sp905236055	77.8445	194	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779645.1	s__CAG-196 sp902779645	77.5089	145	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788575.1	s__CAG-196 sp902788575	77.5039	123	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902763805.1	s__CAG-196 sp902763805	77.4416	126	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775025.1	s__CAG-196 sp902775025	77.4327	135	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797965.1	s__CAG-196 sp902797965	77.383	126	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803165.1	s__CAG-196 sp902803165	77.3767	172	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791985.1	s__UBA2813 sp902791985	77.2931	60	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777605.1	s__CAG-196 sp902777605	77.2678	135	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579975.1	s__CAG-196 sp910579975	77.2133	137	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236505.1	s__CAG-196 sp905236505	77.0765	99	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796585.1	s__CAG-196 sp902796585	76.8361	94	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782905.1	s__CAG-196 sp902782905	76.6354	100	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797575.1	s__CAG-196 sp902797575	76.4335	96	496	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 15:22:23,239] [INFO] GTDB search result was written to GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 15:22:23,240] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:22:23,251] [INFO] DFAST_QC result json was written to GCA_945487905.1_SRR7188236_bin.56_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 15:22:23,252] [INFO] DFAST_QC completed!
[2023-06-08 15:22:23,252] [INFO] Total running time: 0h0m35s