[2023-06-30 19:53:17,328] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:53:17,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:53:17,333] [INFO] DQC Reference Directory: /var/lib/cwl/stga7c563fd-7bef-46c9-ac73-530b820c6224/dqc_reference
[2023-06-30 19:53:19,098] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:53:19,098] [INFO] Task started: Prodigal
[2023-06-30 19:53:19,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg169c8830-75e2-4b25-9efc-efdf3c319fa8/GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna.gz | prodigal -d GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/cds.fna -a GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:53:41,199] [INFO] Task succeeded: Prodigal
[2023-06-30 19:53:41,200] [INFO] Task started: HMMsearch
[2023-06-30 19:53:41,200] [INFO] Running command: hmmsearch --tblout GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7c563fd-7bef-46c9-ac73-530b820c6224/dqc_reference/reference_markers.hmm GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:53:41,479] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:53:41,481] [INFO] Found 6/6 markers.
[2023-06-30 19:53:41,526] [INFO] Query marker FASTA was written to GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/markers.fasta
[2023-06-30 19:53:41,526] [INFO] Task started: Blastn
[2023-06-30 19:53:41,527] [INFO] Running command: blastn -query GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/markers.fasta -db /var/lib/cwl/stga7c563fd-7bef-46c9-ac73-530b820c6224/dqc_reference/reference_markers.fasta -out GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:53:42,111] [INFO] Task succeeded: Blastn
[2023-06-30 19:53:42,116] [INFO] Selected 22 target genomes.
[2023-06-30 19:53:42,117] [INFO] Target genome list was writen to GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/target_genomes.txt
[2023-06-30 19:53:42,118] [INFO] Task started: fastANI
[2023-06-30 19:53:42,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg169c8830-75e2-4b25-9efc-efdf3c319fa8/GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna.gz --refList GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/target_genomes.txt --output GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:53:55,775] [INFO] Task succeeded: fastANI
[2023-06-30 19:53:55,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7c563fd-7bef-46c9-ac73-530b820c6224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:53:55,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7c563fd-7bef-46c9-ac73-530b820c6224/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:53:55,791] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:53:55,791] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 19:53:55,791] [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 19:53:55,793] [INFO] DFAST Taxonomy check result was written to GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/tc_result.tsv
[2023-06-30 19:53:55,794] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:53:55,795] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:53:55,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7c563fd-7bef-46c9-ac73-530b820c6224/dqc_reference/checkm_data
[2023-06-30 19:53:55,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:53:55,853] [INFO] Task started: CheckM
[2023-06-30 19:53:55,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/checkm_input GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/checkm_result
[2023-06-30 19:55:00,832] [INFO] Task succeeded: CheckM
[2023-06-30 19:55:00,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 15.28%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-30 19:55:00,859] [INFO] ===== Completeness check finished =====
[2023-06-30 19:55:00,859] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:55:00,860] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/markers.fasta)
[2023-06-30 19:55:00,860] [INFO] Task started: Blastn
[2023-06-30 19:55:00,860] [INFO] Running command: blastn -query GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/markers.fasta -db /var/lib/cwl/stga7c563fd-7bef-46c9-ac73-530b820c6224/dqc_reference/reference_markers_gtdb.fasta -out GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:55:01,612] [INFO] Task succeeded: Blastn
[2023-06-30 19:55:01,650] [INFO] Selected 12 target genomes.
[2023-06-30 19:55:01,650] [INFO] Target genome list was writen to GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:55:01,655] [INFO] Task started: fastANI
[2023-06-30 19:55:01,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg169c8830-75e2-4b25-9efc-efdf3c319fa8/GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna.gz --refList GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/target_genomes_gtdb.txt --output GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:55:10,894] [INFO] Task succeeded: fastANI
[2023-06-30 19:55:10,905] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:55:10,906] [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_903851365.1	s__UBA12481 sp903851365	99.7723	1473	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12481;g__UBA12481	95.0	99.86	99.79	0.93	0.92	3	conclusive
GCA_903832165.1	s__UBA12481 sp903832165	80.7416	620	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12481;g__UBA12481	95.0	99.74	99.74	0.90	0.90	2	-
GCA_903919065.1	s__UBA12481 sp903919065	80.5694	728	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12481;g__UBA12481	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280905.1	s__UBA12481 sp007280905	78.099	327	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12481;g__UBA12481	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919925.1	s__UBA12481 sp903919925	77.9311	297	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12481;g__UBA12481	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 19:55:10,908] [INFO] GTDB search result was written to GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/result_gtdb.tsv
[2023-06-30 19:55:10,908] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:55:10,911] [INFO] DFAST_QC result json was written to GCA_903844595.1_freshwater_MAG_---_MJ-time_bin-3892_genomic.fna/dqc_result.json
[2023-06-30 19:55:10,911] [INFO] DFAST_QC completed!
[2023-06-30 19:55:10,911] [INFO] Total running time: 0h1m54s