[2023-06-29 21:41:52,494] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:41:52,496] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:41:52,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg3af59446-be3d-4990-805b-8a13f90b13a5/dqc_reference
[2023-06-29 21:41:53,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:41:53,895] [INFO] Task started: Prodigal
[2023-06-29 21:41:53,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg0853c3cd-5455-476a-84c8-9671cde794a8/GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna.gz | prodigal -d GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/cds.fna -a GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:42:01,136] [INFO] Task succeeded: Prodigal
[2023-06-29 21:42:01,137] [INFO] Task started: HMMsearch
[2023-06-29 21:42:01,137] [INFO] Running command: hmmsearch --tblout GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3af59446-be3d-4990-805b-8a13f90b13a5/dqc_reference/reference_markers.hmm GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:42:01,344] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:42:01,345] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg0853c3cd-5455-476a-84c8-9671cde794a8/GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna.gz]
[2023-06-29 21:42:01,381] [INFO] Query marker FASTA was written to GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/markers.fasta
[2023-06-29 21:42:01,381] [INFO] Task started: Blastn
[2023-06-29 21:42:01,381] [INFO] Running command: blastn -query GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/markers.fasta -db /var/lib/cwl/stg3af59446-be3d-4990-805b-8a13f90b13a5/dqc_reference/reference_markers.fasta -out GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:42:01,918] [INFO] Task succeeded: Blastn
[2023-06-29 21:42:01,922] [INFO] Selected 5 target genomes.
[2023-06-29 21:42:01,923] [INFO] Target genome list was writen to GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/target_genomes.txt
[2023-06-29 21:42:01,926] [INFO] Task started: fastANI
[2023-06-29 21:42:01,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg0853c3cd-5455-476a-84c8-9671cde794a8/GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna.gz --refList GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/target_genomes.txt --output GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:42:05,928] [INFO] Task succeeded: fastANI
[2023-06-29 21:42:05,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3af59446-be3d-4990-805b-8a13f90b13a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:42:05,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3af59446-be3d-4990-805b-8a13f90b13a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:42:05,931] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:42:05,931] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 21:42:05,932] [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
--------------------------------------------------------------------------------
[2023-06-29 21:42:05,934] [INFO] DFAST Taxonomy check result was written to GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/tc_result.tsv
[2023-06-29 21:42:05,935] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:42:05,935] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:42:05,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3af59446-be3d-4990-805b-8a13f90b13a5/dqc_reference/checkm_data
[2023-06-29 21:42:05,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:42:05,971] [INFO] Task started: CheckM
[2023-06-29 21:42:05,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/checkm_input GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/checkm_result
[2023-06-29 21:42:31,952] [INFO] Task succeeded: CheckM
[2023-06-29 21:42:31,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:42:31,974] [INFO] ===== Completeness check finished =====
[2023-06-29 21:42:31,975] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:42:31,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/markers.fasta)
[2023-06-29 21:42:31,976] [INFO] Task started: Blastn
[2023-06-29 21:42:31,976] [INFO] Running command: blastn -query GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/markers.fasta -db /var/lib/cwl/stg3af59446-be3d-4990-805b-8a13f90b13a5/dqc_reference/reference_markers_gtdb.fasta -out GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:42:32,434] [INFO] Task succeeded: Blastn
[2023-06-29 21:42:32,438] [INFO] Selected 5 target genomes.
[2023-06-29 21:42:32,438] [INFO] Target genome list was writen to GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:42:32,442] [INFO] Task started: fastANI
[2023-06-29 21:42:32,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg0853c3cd-5455-476a-84c8-9671cde794a8/GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna.gz --refList GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/target_genomes_gtdb.txt --output GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:42:35,888] [INFO] Task succeeded: fastANI
[2023-06-29 21:42:35,899] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 21:42:35,899] [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_903911925.1	s__Terracidiphilus sp903911925	78.5661	134	302	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134855.1	s__Terracidiphilus sp003134855	78.0693	77	302	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142015.1	s__Terracidiphilus sp003142015	77.6325	72	302	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.69	99.69	0.91	0.91	2	-
GCA_003133425.1	s__Terracidiphilus sp003133425	77.2685	81	302	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.36	99.32	0.83	0.80	3	-
--------------------------------------------------------------------------------
[2023-06-29 21:42:35,901] [INFO] GTDB search result was written to GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/result_gtdb.tsv
[2023-06-29 21:42:35,902] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:42:35,905] [INFO] DFAST_QC result json was written to GCA_903839175.1_freshwater_MAG_---_AM-lipid-02-D5_bin-0362_genomic.fna/dqc_result.json
[2023-06-29 21:42:35,905] [INFO] DFAST_QC completed!
[2023-06-29 21:42:35,906] [INFO] Total running time: 0h0m43s