[2023-06-13 06:33:10,230] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:33:10,233] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:33:10,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg95996625-8bdb-438b-a45d-0ee0da2f48cc/dqc_reference
[2023-06-13 06:33:11,429] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:33:11,429] [INFO] Task started: Prodigal
[2023-06-13 06:33:11,430] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb251948-2f54-4446-9c06-eb801e7180a7/GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:33:16,716] [INFO] Task succeeded: Prodigal
[2023-06-13 06:33:16,717] [INFO] Task started: HMMsearch
[2023-06-13 06:33:16,717] [INFO] Running command: hmmsearch --tblout GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95996625-8bdb-438b-a45d-0ee0da2f48cc/dqc_reference/reference_markers.hmm GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:33:16,927] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:33:16,929] [INFO] Found 6/6 markers.
[2023-06-13 06:33:16,954] [INFO] Query marker FASTA was written to GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 06:33:16,955] [INFO] Task started: Blastn
[2023-06-13 06:33:16,955] [INFO] Running command: blastn -query GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg95996625-8bdb-438b-a45d-0ee0da2f48cc/dqc_reference/reference_markers.fasta -out GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:33:17,521] [INFO] Task succeeded: Blastn
[2023-06-13 06:33:17,544] [INFO] Selected 17 target genomes.
[2023-06-13 06:33:17,545] [INFO] Target genome list was writen to GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 06:33:17,548] [INFO] Task started: fastANI
[2023-06-13 06:33:17,548] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb251948-2f54-4446-9c06-eb801e7180a7/GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:33:25,867] [INFO] Task succeeded: fastANI
[2023-06-13 06:33:25,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95996625-8bdb-438b-a45d-0ee0da2f48cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:33:25,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95996625-8bdb-438b-a45d-0ee0da2f48cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:33:25,870] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 06:33:25,870] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 06:33:25,870] [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
--------------------------------------------------------------------------------
[2023-06-13 06:33:25,872] [INFO] DFAST Taxonomy check result was written to GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 06:33:25,873] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:33:25,873] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:33:25,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95996625-8bdb-438b-a45d-0ee0da2f48cc/dqc_reference/checkm_data
[2023-06-13 06:33:25,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:33:25,905] [INFO] Task started: CheckM
[2023-06-13 06:33:25,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 06:33:47,826] [INFO] Task succeeded: CheckM
[2023-06-13 06:33:47,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:33:47,848] [INFO] ===== Completeness check finished =====
[2023-06-13 06:33:47,848] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:33:47,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 06:33:47,849] [INFO] Task started: Blastn
[2023-06-13 06:33:47,849] [INFO] Running command: blastn -query GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg95996625-8bdb-438b-a45d-0ee0da2f48cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:33:48,566] [INFO] Task succeeded: Blastn
[2023-06-13 06:33:48,571] [INFO] Selected 22 target genomes.
[2023-06-13 06:33:48,571] [INFO] Target genome list was writen to GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:33:48,579] [INFO] Task started: fastANI
[2023-06-13 06:33:48,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb251948-2f54-4446-9c06-eb801e7180a7/GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:33:56,544] [INFO] Task succeeded: fastANI
[2023-06-13 06:33:56,551] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:33:56,551] [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_900550805.1	s__UMGS1338 sp900550805	98.3033	383	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__QALW01;g__UMGS1338	95.0	98.41	98.08	0.89	0.86	3	conclusive
GCA_017516345.1	s__UMGS1338 sp017516345	77.1515	79	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__QALW01;g__UMGS1338	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 06:33:56,553] [INFO] GTDB search result was written to GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 06:33:56,554] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:33:56,556] [INFO] DFAST_QC result json was written to GCA_938040355.1_ERR589771_bin.64_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 06:33:56,556] [INFO] DFAST_QC completed!
[2023-06-13 06:33:56,556] [INFO] Total running time: 0h0m46s