[2023-06-28 19:04:10,194] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:04:10,197] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:04:10,197] [INFO] DQC Reference Directory: /var/lib/cwl/stg67d227ad-deeb-4ee0-9c69-596ed11a411c/dqc_reference
[2023-06-28 19:04:11,585] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:04:11,586] [INFO] Task started: Prodigal
[2023-06-28 19:04:11,586] [INFO] Running command: gunzip -c /var/lib/cwl/stg298cdc60-62fd-434e-87c6-18c7a60bb4ff/GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:04:21,137] [INFO] Task succeeded: Prodigal
[2023-06-28 19:04:21,138] [INFO] Task started: HMMsearch
[2023-06-28 19:04:21,138] [INFO] Running command: hmmsearch --tblout GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67d227ad-deeb-4ee0-9c69-596ed11a411c/dqc_reference/reference_markers.hmm GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:04:21,415] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:04:21,416] [INFO] Found 6/6 markers.
[2023-06-28 19:04:21,452] [INFO] Query marker FASTA was written to GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 19:04:21,452] [INFO] Task started: Blastn
[2023-06-28 19:04:21,452] [INFO] Running command: blastn -query GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg67d227ad-deeb-4ee0-9c69-596ed11a411c/dqc_reference/reference_markers.fasta -out GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:22,137] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:22,141] [INFO] Selected 29 target genomes.
[2023-06-28 19:04:22,142] [INFO] Target genome list was writen to GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 19:04:22,178] [INFO] Task started: fastANI
[2023-06-28 19:04:22,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg298cdc60-62fd-434e-87c6-18c7a60bb4ff/GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:04:44,056] [INFO] Task succeeded: fastANI
[2023-06-28 19:04:44,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67d227ad-deeb-4ee0-9c69-596ed11a411c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:04:44,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67d227ad-deeb-4ee0-9c69-596ed11a411c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:04:44,059] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:04:44,059] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:04:44,059] [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
--------------------------------------------------------------------------------
[2023-06-28 19:04:44,061] [INFO] DFAST Taxonomy check result was written to GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 19:04:44,062] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:04:44,062] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:04:44,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67d227ad-deeb-4ee0-9c69-596ed11a411c/dqc_reference/checkm_data
[2023-06-28 19:04:44,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:04:44,113] [INFO] Task started: CheckM
[2023-06-28 19:04:44,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 19:05:17,070] [INFO] Task succeeded: CheckM
[2023-06-28 19:05:17,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:05:17,097] [INFO] ===== Completeness check finished =====
[2023-06-28 19:05:17,097] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:05:17,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 19:05:17,098] [INFO] Task started: Blastn
[2023-06-28 19:05:17,098] [INFO] Running command: blastn -query GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg67d227ad-deeb-4ee0-9c69-596ed11a411c/dqc_reference/reference_markers_gtdb.fasta -out GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:05:18,125] [INFO] Task succeeded: Blastn
[2023-06-28 19:05:18,129] [INFO] Selected 25 target genomes.
[2023-06-28 19:05:18,129] [INFO] Target genome list was writen to GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:05:18,144] [INFO] Task started: fastANI
[2023-06-28 19:05:18,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg298cdc60-62fd-434e-87c6-18c7a60bb4ff/GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:05:33,126] [INFO] Task succeeded: fastANI
[2023-06-28 19:05:33,132] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:05:33,133] [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_003452295.1	s__UBA7455 sp003452295	99.6056	861	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7455	95.0	99.39	99.39	0.69	0.69	2	conclusive
GCA_002712135.1	s__UBA7455 sp002712135	81.9769	609	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7455	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:05:33,135] [INFO] GTDB search result was written to GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 19:05:33,136] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:05:33,138] [INFO] DFAST_QC result json was written to GCA_913045175.1_ERR599094_bin.30_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 19:05:33,138] [INFO] DFAST_QC completed!
[2023-06-28 19:05:33,138] [INFO] Total running time: 0h1m23s