[2023-06-13 07:44:42,184] [INFO] DFAST_QC pipeline started.
[2023-06-13 07:44:42,187] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 07:44:42,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg25b6bee6-cec8-4cde-a71c-d8de98c13949/dqc_reference
[2023-06-13 07:44:43,396] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 07:44:43,397] [INFO] Task started: Prodigal
[2023-06-13 07:44:43,397] [INFO] Running command: gunzip -c /var/lib/cwl/stgb682513d-fb85-446a-8004-4406e00ce8c6/GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 07:44:45,368] [INFO] Task succeeded: Prodigal
[2023-06-13 07:44:45,368] [INFO] Task started: HMMsearch
[2023-06-13 07:44:45,369] [INFO] Running command: hmmsearch --tblout GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25b6bee6-cec8-4cde-a71c-d8de98c13949/dqc_reference/reference_markers.hmm GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 07:44:45,572] [INFO] Task succeeded: HMMsearch
[2023-06-13 07:44:45,573] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb682513d-fb85-446a-8004-4406e00ce8c6/GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 07:44:45,597] [INFO] Query marker FASTA was written to GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 07:44:45,597] [INFO] Task started: Blastn
[2023-06-13 07:44:45,597] [INFO] Running command: blastn -query GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg25b6bee6-cec8-4cde-a71c-d8de98c13949/dqc_reference/reference_markers.fasta -out GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:44:46,746] [INFO] Task succeeded: Blastn
[2023-06-13 07:44:46,750] [INFO] Selected 18 target genomes.
[2023-06-13 07:44:46,750] [INFO] Target genome list was writen to GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 07:44:46,753] [INFO] Task started: fastANI
[2023-06-13 07:44:46,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgb682513d-fb85-446a-8004-4406e00ce8c6/GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 07:44:53,723] [INFO] Task succeeded: fastANI
[2023-06-13 07:44:53,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25b6bee6-cec8-4cde-a71c-d8de98c13949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 07:44:53,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25b6bee6-cec8-4cde-a71c-d8de98c13949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 07:44:53,726] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 07:44:53,726] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 07:44:53,726] [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 07:44:53,728] [INFO] DFAST Taxonomy check result was written to GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 07:44:53,729] [INFO] ===== Taxonomy check completed =====
[2023-06-13 07:44:53,729] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 07:44:53,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25b6bee6-cec8-4cde-a71c-d8de98c13949/dqc_reference/checkm_data
[2023-06-13 07:44:53,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 07:44:53,748] [INFO] Task started: CheckM
[2023-06-13 07:44:53,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 07:45:07,946] [INFO] Task succeeded: CheckM
[2023-06-13 07:45:07,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 07:45:07,967] [INFO] ===== Completeness check finished =====
[2023-06-13 07:45:07,967] [INFO] ===== Start GTDB Search =====
[2023-06-13 07:45:07,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 07:45:07,968] [INFO] Task started: Blastn
[2023-06-13 07:45:07,968] [INFO] Running command: blastn -query GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg25b6bee6-cec8-4cde-a71c-d8de98c13949/dqc_reference/reference_markers_gtdb.fasta -out GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:45:08,965] [INFO] Task succeeded: Blastn
[2023-06-13 07:45:08,970] [INFO] Selected 18 target genomes.
[2023-06-13 07:45:08,970] [INFO] Target genome list was writen to GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 07:45:08,977] [INFO] Task started: fastANI
[2023-06-13 07:45:08,977] [INFO] Running command: fastANI --query /var/lib/cwl/stgb682513d-fb85-446a-8004-4406e00ce8c6/GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 07:45:12,546] [INFO] Task succeeded: fastANI
[2023-06-13 07:45:12,553] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 07:45:12,554] [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_900545735.1	s__UMGS687 sp900545735	97.4793	218	308	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UMGS687	95.0	97.93	97.92	0.87	0.87	3	conclusive
GCA_900551705.1	s__UMGS687 sp900551705	82.1333	204	308	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UMGS687	95.0	98.42	96.85	0.93	0.91	3	-
GCA_900544595.1	s__UMGS687 sp900544595	77.8621	58	308	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__UMGS687	95.0	96.41	95.32	0.93	0.91	4	-
--------------------------------------------------------------------------------
[2023-06-13 07:45:12,556] [INFO] GTDB search result was written to GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 07:45:12,556] [INFO] ===== GTDB Search completed =====
[2023-06-13 07:45:12,559] [INFO] DFAST_QC result json was written to GCA_938016345.1_ERR414289_bin.63_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 07:45:12,559] [INFO] DFAST_QC completed!
[2023-06-13 07:45:12,559] [INFO] Total running time: 0h0m30s