[2023-06-30 23:02:47,216] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:02:47,233] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:02:47,233] [INFO] DQC Reference Directory: /var/lib/cwl/stg805615e2-5f4f-44d4-921a-b673cccba955/dqc_reference
[2023-06-30 23:02:49,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:02:49,166] [INFO] Task started: Prodigal
[2023-06-30 23:02:49,166] [INFO] Running command: gunzip -c /var/lib/cwl/stgfecc5df3-2036-4133-9b63-c8efc12f517a/GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna.gz | prodigal -d GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/cds.fna -a GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:02:54,505] [INFO] Task succeeded: Prodigal
[2023-06-30 23:02:54,505] [INFO] Task started: HMMsearch
[2023-06-30 23:02:54,505] [INFO] Running command: hmmsearch --tblout GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg805615e2-5f4f-44d4-921a-b673cccba955/dqc_reference/reference_markers.hmm GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:02:54,896] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:02:54,898] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfecc5df3-2036-4133-9b63-c8efc12f517a/GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna.gz]
[2023-06-30 23:02:54,931] [INFO] Query marker FASTA was written to GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/markers.fasta
[2023-06-30 23:02:54,931] [INFO] Task started: Blastn
[2023-06-30 23:02:54,932] [INFO] Running command: blastn -query GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/markers.fasta -db /var/lib/cwl/stg805615e2-5f4f-44d4-921a-b673cccba955/dqc_reference/reference_markers.fasta -out GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:02:55,638] [INFO] Task succeeded: Blastn
[2023-06-30 23:02:55,646] [INFO] Selected 10 target genomes.
[2023-06-30 23:02:55,647] [INFO] Target genome list was writen to GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/target_genomes.txt
[2023-06-30 23:02:55,652] [INFO] Task started: fastANI
[2023-06-30 23:02:55,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgfecc5df3-2036-4133-9b63-c8efc12f517a/GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna.gz --refList GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/target_genomes.txt --output GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:03:03,773] [INFO] Task succeeded: fastANI
[2023-06-30 23:03:03,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg805615e2-5f4f-44d4-921a-b673cccba955/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:03:03,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg805615e2-5f4f-44d4-921a-b673cccba955/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:03:03,776] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 23:03:03,776] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 23:03:03,776] [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
--------------------------------------------------------------------------------
[2023-06-30 23:03:03,779] [INFO] DFAST Taxonomy check result was written to GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/tc_result.tsv
[2023-06-30 23:03:03,779] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:03:03,780] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:03:03,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg805615e2-5f4f-44d4-921a-b673cccba955/dqc_reference/checkm_data
[2023-06-30 23:03:03,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:03:03,819] [INFO] Task started: CheckM
[2023-06-30 23:03:03,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/checkm_input GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/checkm_result
[2023-06-30 23:03:26,053] [INFO] Task succeeded: CheckM
[2023-06-30 23:03:26,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:03:26,074] [INFO] ===== Completeness check finished =====
[2023-06-30 23:03:26,075] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:03:26,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/markers.fasta)
[2023-06-30 23:03:26,075] [INFO] Task started: Blastn
[2023-06-30 23:03:26,076] [INFO] Running command: blastn -query GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/markers.fasta -db /var/lib/cwl/stg805615e2-5f4f-44d4-921a-b673cccba955/dqc_reference/reference_markers_gtdb.fasta -out GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:03:26,788] [INFO] Task succeeded: Blastn
[2023-06-30 23:03:26,792] [INFO] Selected 8 target genomes.
[2023-06-30 23:03:26,793] [INFO] Target genome list was writen to GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:03:26,795] [INFO] Task started: fastANI
[2023-06-30 23:03:26,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgfecc5df3-2036-4133-9b63-c8efc12f517a/GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna.gz --refList GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/target_genomes_gtdb.txt --output GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:03:31,003] [INFO] Task succeeded: fastANI
[2023-06-30 23:03:31,013] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 23:03:31,013] [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_903879915.1	s__UBA9959 sp903879915	99.7284	491	500	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	99.89	99.83	0.96	0.95	7	conclusive
GCA_001799615.1	s__UBA9959 sp001799615	80.3874	243	500	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	99.99	99.99	0.97	0.97	2	-
GCA_001799995.1	s__UBA9959 sp001799995	80.3166	217	500	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	99.83	99.83	0.93	0.93	2	-
GCA_001799735.1	s__UBA9959 sp001799735	80.1248	243	500	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873295.1	s__UBA9959 sp903873295	79.8121	239	500	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001800275.1	s__UBA9959 sp001800275	79.6038	189	500	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	99.62	99.62	0.85	0.85	2	-
GCA_016234365.1	s__UBA9959 sp016234365	79.5676	218	500	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016207645.1	s__UBA9959 sp016207645	79.1418	205	500	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 23:03:31,015] [INFO] GTDB search result was written to GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/result_gtdb.tsv
[2023-06-30 23:03:31,016] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:03:31,019] [INFO] DFAST_QC result json was written to GCA_903907415.1_freshwater_MAG_---_MJ111018B_bin-0999_genomic.fna/dqc_result.json
[2023-06-30 23:03:31,019] [INFO] DFAST_QC completed!
[2023-06-30 23:03:31,019] [INFO] Total running time: 0h0m44s