[2023-06-19 08:29:17,984] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:29:17,985] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:29:17,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg9beea2f6-dd26-4e67-8243-f29f0746bb04/dqc_reference
[2023-06-19 08:29:19,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:29:19,167] [INFO] Task started: Prodigal
[2023-06-19 08:29:19,167] [INFO] Running command: gunzip -c /var/lib/cwl/stgfecaf5f6-ed11-4ad8-9afe-77ddd44c6f6e/GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:29:21,055] [INFO] Task succeeded: Prodigal
[2023-06-19 08:29:21,055] [INFO] Task started: HMMsearch
[2023-06-19 08:29:21,056] [INFO] Running command: hmmsearch --tblout GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9beea2f6-dd26-4e67-8243-f29f0746bb04/dqc_reference/reference_markers.hmm GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:29:21,193] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:29:21,194] [INFO] Found 6/6 markers.
[2023-06-19 08:29:21,209] [INFO] Query marker FASTA was written to GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 08:29:21,210] [INFO] Task started: Blastn
[2023-06-19 08:29:21,210] [INFO] Running command: blastn -query GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9beea2f6-dd26-4e67-8243-f29f0746bb04/dqc_reference/reference_markers.fasta -out GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:29:21,775] [INFO] Task succeeded: Blastn
[2023-06-19 08:29:21,783] [INFO] Selected 12 target genomes.
[2023-06-19 08:29:21,783] [INFO] Target genome list was writen to GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 08:29:21,785] [INFO] Task started: fastANI
[2023-06-19 08:29:21,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgfecaf5f6-ed11-4ad8-9afe-77ddd44c6f6e/GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:29:25,991] [INFO] Task succeeded: fastANI
[2023-06-19 08:29:25,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9beea2f6-dd26-4e67-8243-f29f0746bb04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:29:25,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9beea2f6-dd26-4e67-8243-f29f0746bb04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:29:25,993] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:29:25,993] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:29:25,993] [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
--------------------------------------------------------------------------------
[2023-06-19 08:29:25,995] [INFO] DFAST Taxonomy check result was written to GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 08:29:25,995] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:29:25,995] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:29:25,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9beea2f6-dd26-4e67-8243-f29f0746bb04/dqc_reference/checkm_data
[2023-06-19 08:29:25,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:29:26,025] [INFO] Task started: CheckM
[2023-06-19 08:29:26,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 08:29:38,902] [INFO] Task succeeded: CheckM
[2023-06-19 08:29:38,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:29:38,926] [INFO] ===== Completeness check finished =====
[2023-06-19 08:29:38,926] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:29:38,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 08:29:38,927] [INFO] Task started: Blastn
[2023-06-19 08:29:38,927] [INFO] Running command: blastn -query GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9beea2f6-dd26-4e67-8243-f29f0746bb04/dqc_reference/reference_markers_gtdb.fasta -out GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:29:39,692] [INFO] Task succeeded: Blastn
[2023-06-19 08:29:39,695] [INFO] Selected 18 target genomes.
[2023-06-19 08:29:39,696] [INFO] Target genome list was writen to GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:29:39,700] [INFO] Task started: fastANI
[2023-06-19 08:29:39,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgfecaf5f6-ed11-4ad8-9afe-77ddd44c6f6e/GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:29:41,861] [INFO] Task succeeded: fastANI
[2023-06-19 08:29:41,864] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 08:29:41,864] [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_018061865.1	s__JAGOTH01 sp018061865	83.7934	92	126	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__JAGOTH01	95.0	99.88	99.79	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2023-06-19 08:29:41,866] [INFO] GTDB search result was written to GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 08:29:41,867] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:29:41,871] [INFO] DFAST_QC result json was written to GCA_937895685.1_SRR6231139_bin.96_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 08:29:41,872] [INFO] DFAST_QC completed!
[2023-06-19 08:29:41,872] [INFO] Total running time: 0h0m24s