[2023-06-29 21:45:49,644] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:45:49,646] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:45:49,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d890026-a9ff-4bbd-83fe-984f55983555/dqc_reference
[2023-06-29 21:45:50,882] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:45:50,883] [INFO] Task started: Prodigal
[2023-06-29 21:45:50,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg365852ea-f97b-4d1e-ab03-7a1dd46e1749/GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna.gz | prodigal -d GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/cds.fna -a GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:45:53,645] [INFO] Task succeeded: Prodigal
[2023-06-29 21:45:53,646] [INFO] Task started: HMMsearch
[2023-06-29 21:45:53,646] [INFO] Running command: hmmsearch --tblout GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d890026-a9ff-4bbd-83fe-984f55983555/dqc_reference/reference_markers.hmm GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:45:53,860] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:45:53,862] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg365852ea-f97b-4d1e-ab03-7a1dd46e1749/GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna.gz]
[2023-06-29 21:45:53,886] [INFO] Query marker FASTA was written to GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/markers.fasta
[2023-06-29 21:45:53,886] [INFO] Task started: Blastn
[2023-06-29 21:45:53,886] [INFO] Running command: blastn -query GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d890026-a9ff-4bbd-83fe-984f55983555/dqc_reference/reference_markers.fasta -out GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:45:54,388] [INFO] Task succeeded: Blastn
[2023-06-29 21:45:54,393] [INFO] Selected 18 target genomes.
[2023-06-29 21:45:54,393] [INFO] Target genome list was writen to GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/target_genomes.txt
[2023-06-29 21:45:54,400] [INFO] Task started: fastANI
[2023-06-29 21:45:54,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg365852ea-f97b-4d1e-ab03-7a1dd46e1749/GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna.gz --refList GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/target_genomes.txt --output GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:46:04,169] [INFO] Task succeeded: fastANI
[2023-06-29 21:46:04,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d890026-a9ff-4bbd-83fe-984f55983555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:46:04,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d890026-a9ff-4bbd-83fe-984f55983555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:46:04,175] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:46:04,176] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:46:04,176] [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
Methylotenera versatilis	strain=301	GCA_000093025.1	1055487	1055487	type	True	76.7456	51	322	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:46:04,178] [INFO] DFAST Taxonomy check result was written to GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/tc_result.tsv
[2023-06-29 21:46:04,179] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:46:04,179] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:46:04,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d890026-a9ff-4bbd-83fe-984f55983555/dqc_reference/checkm_data
[2023-06-29 21:46:04,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:46:04,201] [INFO] Task started: CheckM
[2023-06-29 21:46:04,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/checkm_input GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/checkm_result
[2023-06-29 21:46:20,414] [INFO] Task succeeded: CheckM
[2023-06-29 21:46:20,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:46:20,435] [INFO] ===== Completeness check finished =====
[2023-06-29 21:46:20,436] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:46:20,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/markers.fasta)
[2023-06-29 21:46:20,437] [INFO] Task started: Blastn
[2023-06-29 21:46:20,437] [INFO] Running command: blastn -query GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d890026-a9ff-4bbd-83fe-984f55983555/dqc_reference/reference_markers_gtdb.fasta -out GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:46:20,950] [INFO] Task succeeded: Blastn
[2023-06-29 21:46:20,954] [INFO] Selected 10 target genomes.
[2023-06-29 21:46:20,954] [INFO] Target genome list was writen to GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:46:20,960] [INFO] Task started: fastANI
[2023-06-29 21:46:20,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg365852ea-f97b-4d1e-ab03-7a1dd46e1749/GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna.gz --refList GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/target_genomes_gtdb.txt --output GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:46:24,158] [INFO] Task succeeded: fastANI
[2023-06-29 21:46:24,165] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:46:24,165] [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_903953055.1	s__Methylopumilus_A sp903953055	98.6985	287	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	99.11	98.29	0.90	0.83	22	conclusive
GCA_903909015.1	s__Methylopumilus_A sp903909015	82.8773	226	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	98.79	98.38	0.84	0.83	5	-
GCA_903870165.1	s__Methylopumilus_A sp903870165	80.128	167	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	99.91	99.91	0.89	0.89	2	-
GCA_903899965.1	s__Methylopumilus_A sp903899965	79.943	194	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	98.90	98.39	0.92	0.86	12	-
GCA_903870995.1	s__Methylopumilus_A sp903870995	79.8523	183	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	99.94	99.94	0.97	0.96	3	-
GCA_009926525.1	s__Methylopumilus_A sp009926525	79.8298	68	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953015.1	s__Methylopumilus_A turicensis	79.7839	171	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:46:24,168] [INFO] GTDB search result was written to GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/result_gtdb.tsv
[2023-06-29 21:46:24,168] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:46:24,173] [INFO] DFAST_QC result json was written to GCA_903896825.1_freshwater_MAG_---_KT_bin-2360_genomic.fna/dqc_result.json
[2023-06-29 21:46:24,173] [INFO] DFAST_QC completed!
[2023-06-29 21:46:24,173] [INFO] Total running time: 0h0m35s