[2023-06-30 10:51:31,728] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:51:31,732] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:51:31,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f3d547a-3d42-4b4b-84d5-b4fd96614da8/dqc_reference
[2023-06-30 10:51:33,615] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:51:33,616] [INFO] Task started: Prodigal
[2023-06-30 10:51:33,617] [INFO] Running command: gunzip -c /var/lib/cwl/stg407c0d65-49f5-496d-a1bc-a9f4c628d4b2/GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna.gz | prodigal -d GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/cds.fna -a GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:51:37,772] [INFO] Task succeeded: Prodigal
[2023-06-30 10:51:37,772] [INFO] Task started: HMMsearch
[2023-06-30 10:51:37,772] [INFO] Running command: hmmsearch --tblout GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f3d547a-3d42-4b4b-84d5-b4fd96614da8/dqc_reference/reference_markers.hmm GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:51:37,912] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:51:37,913] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg407c0d65-49f5-496d-a1bc-a9f4c628d4b2/GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna.gz]
[2023-06-30 10:51:37,924] [INFO] Query marker FASTA was written to GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/markers.fasta
[2023-06-30 10:51:37,924] [INFO] Task started: Blastn
[2023-06-30 10:51:37,924] [INFO] Running command: blastn -query GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f3d547a-3d42-4b4b-84d5-b4fd96614da8/dqc_reference/reference_markers.fasta -out GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:51:38,397] [INFO] Task succeeded: Blastn
[2023-06-30 10:51:38,401] [INFO] Selected 13 target genomes.
[2023-06-30 10:51:38,401] [INFO] Target genome list was writen to GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/target_genomes.txt
[2023-06-30 10:51:38,403] [INFO] Task started: fastANI
[2023-06-30 10:51:38,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg407c0d65-49f5-496d-a1bc-a9f4c628d4b2/GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna.gz --refList GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/target_genomes.txt --output GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:51:44,713] [INFO] Task succeeded: fastANI
[2023-06-30 10:51:44,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f3d547a-3d42-4b4b-84d5-b4fd96614da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:51:44,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f3d547a-3d42-4b4b-84d5-b4fd96614da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:51:44,716] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:51:44,716] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:51:44,716] [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 10:51:44,718] [INFO] DFAST Taxonomy check result was written to GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/tc_result.tsv
[2023-06-30 10:51:44,718] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:51:44,719] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:51:44,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f3d547a-3d42-4b4b-84d5-b4fd96614da8/dqc_reference/checkm_data
[2023-06-30 10:51:44,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:51:44,732] [INFO] Task started: CheckM
[2023-06-30 10:51:44,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/checkm_input GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/checkm_result
[2023-06-30 10:52:02,507] [INFO] Task succeeded: CheckM
[2023-06-30 10:52:02,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.15%
Contamintation: 3.12%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 10:52:02,526] [INFO] ===== Completeness check finished =====
[2023-06-30 10:52:02,527] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:52:02,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/markers.fasta)
[2023-06-30 10:52:02,527] [INFO] Task started: Blastn
[2023-06-30 10:52:02,527] [INFO] Running command: blastn -query GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f3d547a-3d42-4b4b-84d5-b4fd96614da8/dqc_reference/reference_markers_gtdb.fasta -out GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:52:03,006] [INFO] Task succeeded: Blastn
[2023-06-30 10:52:03,010] [INFO] Selected 10 target genomes.
[2023-06-30 10:52:03,010] [INFO] Target genome list was writen to GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:52:03,015] [INFO] Task started: fastANI
[2023-06-30 10:52:03,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg407c0d65-49f5-496d-a1bc-a9f4c628d4b2/GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna.gz --refList GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/target_genomes_gtdb.txt --output GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:52:04,354] [INFO] Task succeeded: fastANI
[2023-06-30 10:52:04,357] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:52:04,357] [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_903878285.1	s__GWA1-54-10 sp903878285	99.9514	165	167	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__SBAW01;g__GWA1-54-10	95.0	99.97	99.95	0.98	0.97	8	conclusive
GCA_903819895.1	s__GWA1-54-10 sp903819895	83.4444	119	167	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__SBAW01;g__GWA1-54-10	95.0	99.89	99.81	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-30 10:52:04,359] [INFO] GTDB search result was written to GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/result_gtdb.tsv
[2023-06-30 10:52:04,360] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:52:04,362] [INFO] DFAST_QC result json was written to GCA_903945425.1_freshwater_MAG_---_I-3_bin-005_genomic.fna/dqc_result.json
[2023-06-30 10:52:04,362] [INFO] DFAST_QC completed!
[2023-06-30 10:52:04,362] [INFO] Total running time: 0h0m33s