[2023-06-30 00:38:04,846] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:38:04,848] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:38:04,848] [INFO] DQC Reference Directory: /var/lib/cwl/stge89097be-92fa-44de-95a2-11e88336ccb0/dqc_reference
[2023-06-30 00:38:06,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:38:06,075] [INFO] Task started: Prodigal
[2023-06-30 00:38:06,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg552f527c-80e8-4c20-a528-cf0ef68eabc4/GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna.gz | prodigal -d GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/cds.fna -a GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:38:09,383] [INFO] Task succeeded: Prodigal
[2023-06-30 00:38:09,384] [INFO] Task started: HMMsearch
[2023-06-30 00:38:09,384] [INFO] Running command: hmmsearch --tblout GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge89097be-92fa-44de-95a2-11e88336ccb0/dqc_reference/reference_markers.hmm GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:38:09,555] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:38:09,556] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg552f527c-80e8-4c20-a528-cf0ef68eabc4/GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna.gz]
[2023-06-30 00:38:09,576] [INFO] Query marker FASTA was written to GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/markers.fasta
[2023-06-30 00:38:09,577] [INFO] Task started: Blastn
[2023-06-30 00:38:09,577] [INFO] Running command: blastn -query GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/markers.fasta -db /var/lib/cwl/stge89097be-92fa-44de-95a2-11e88336ccb0/dqc_reference/reference_markers.fasta -out GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:38:10,147] [INFO] Task succeeded: Blastn
[2023-06-30 00:38:10,171] [INFO] Selected 10 target genomes.
[2023-06-30 00:38:10,172] [INFO] Target genome list was writen to GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/target_genomes.txt
[2023-06-30 00:38:10,175] [INFO] Task started: fastANI
[2023-06-30 00:38:10,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg552f527c-80e8-4c20-a528-cf0ef68eabc4/GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna.gz --refList GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/target_genomes.txt --output GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:38:16,211] [INFO] Task succeeded: fastANI
[2023-06-30 00:38:16,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge89097be-92fa-44de-95a2-11e88336ccb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:38:16,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge89097be-92fa-44de-95a2-11e88336ccb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:38:16,214] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:38:16,214] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:38:16,215] [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 00:38:16,217] [INFO] DFAST Taxonomy check result was written to GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/tc_result.tsv
[2023-06-30 00:38:16,218] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:38:16,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:38:16,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge89097be-92fa-44de-95a2-11e88336ccb0/dqc_reference/checkm_data
[2023-06-30 00:38:16,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:38:16,243] [INFO] Task started: CheckM
[2023-06-30 00:38:16,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/checkm_input GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/checkm_result
[2023-06-30 00:38:33,291] [INFO] Task succeeded: CheckM
[2023-06-30 00:38:33,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 00:38:33,314] [INFO] ===== Completeness check finished =====
[2023-06-30 00:38:33,315] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:38:33,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/markers.fasta)
[2023-06-30 00:38:33,315] [INFO] Task started: Blastn
[2023-06-30 00:38:33,316] [INFO] Running command: blastn -query GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/markers.fasta -db /var/lib/cwl/stge89097be-92fa-44de-95a2-11e88336ccb0/dqc_reference/reference_markers_gtdb.fasta -out GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:38:34,089] [INFO] Task succeeded: Blastn
[2023-06-30 00:38:34,093] [INFO] Selected 9 target genomes.
[2023-06-30 00:38:34,093] [INFO] Target genome list was writen to GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:38:34,101] [INFO] Task started: fastANI
[2023-06-30 00:38:34,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg552f527c-80e8-4c20-a528-cf0ef68eabc4/GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna.gz --refList GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/target_genomes_gtdb.txt --output GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:38:37,380] [INFO] Task succeeded: fastANI
[2023-06-30 00:38:37,385] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:38:37,386] [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_002292895.1	s__UBA966 sp002292895	91.6129	101	116	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	99.22	99.02	0.83	0.82	3	-
--------------------------------------------------------------------------------
[2023-06-30 00:38:37,409] [INFO] GTDB search result was written to GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/result_gtdb.tsv
[2023-06-30 00:38:37,410] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:38:37,413] [INFO] DFAST_QC result json was written to GCA_903834335.1_freshwater_MAG_---_UppL5_bin-1563_genomic.fna/dqc_result.json
[2023-06-30 00:38:37,413] [INFO] DFAST_QC completed!
[2023-06-30 00:38:37,413] [INFO] Total running time: 0h0m33s