[2023-06-04 23:25:27,830] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:25:27,832] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:25:27,833] [INFO] DQC Reference Directory: /var/lib/cwl/stgc52655f2-5783-45e4-83a8-0c94f31ad2c9/dqc_reference
[2023-06-04 23:25:29,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:25:29,699] [INFO] Task started: Prodigal
[2023-06-04 23:25:29,699] [INFO] Running command: gunzip -c /var/lib/cwl/stga42c4aa0-4220-4bfd-915a-5f3a0557fa60/GCA_934434945.1_ERR7745858_bin.243_genomic.fna.gz | prodigal -d GCA_934434945.1_ERR7745858_bin.243_genomic.fna/cds.fna -a GCA_934434945.1_ERR7745858_bin.243_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:25:34,596] [INFO] Task succeeded: Prodigal
[2023-06-04 23:25:34,597] [INFO] Task started: HMMsearch
[2023-06-04 23:25:34,597] [INFO] Running command: hmmsearch --tblout GCA_934434945.1_ERR7745858_bin.243_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc52655f2-5783-45e4-83a8-0c94f31ad2c9/dqc_reference/reference_markers.hmm GCA_934434945.1_ERR7745858_bin.243_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:25:34,888] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:25:34,889] [INFO] Found 6/6 markers.
[2023-06-04 23:25:34,911] [INFO] Query marker FASTA was written to GCA_934434945.1_ERR7745858_bin.243_genomic.fna/markers.fasta
[2023-06-04 23:25:34,911] [INFO] Task started: Blastn
[2023-06-04 23:25:34,911] [INFO] Running command: blastn -query GCA_934434945.1_ERR7745858_bin.243_genomic.fna/markers.fasta -db /var/lib/cwl/stgc52655f2-5783-45e4-83a8-0c94f31ad2c9/dqc_reference/reference_markers.fasta -out GCA_934434945.1_ERR7745858_bin.243_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:25:35,511] [INFO] Task succeeded: Blastn
[2023-06-04 23:25:35,526] [INFO] Selected 20 target genomes.
[2023-06-04 23:25:35,526] [INFO] Target genome list was writen to GCA_934434945.1_ERR7745858_bin.243_genomic.fna/target_genomes.txt
[2023-06-04 23:25:35,532] [INFO] Task started: fastANI
[2023-06-04 23:25:35,532] [INFO] Running command: fastANI --query /var/lib/cwl/stga42c4aa0-4220-4bfd-915a-5f3a0557fa60/GCA_934434945.1_ERR7745858_bin.243_genomic.fna.gz --refList GCA_934434945.1_ERR7745858_bin.243_genomic.fna/target_genomes.txt --output GCA_934434945.1_ERR7745858_bin.243_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:25:50,393] [INFO] Task succeeded: fastANI
[2023-06-04 23:25:50,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc52655f2-5783-45e4-83a8-0c94f31ad2c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:25:50,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc52655f2-5783-45e4-83a8-0c94f31ad2c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:25:50,396] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:25:50,396] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 23:25:50,396] [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
--------------------------------------------------------------------------------
[2023-06-04 23:25:50,398] [INFO] DFAST Taxonomy check result was written to GCA_934434945.1_ERR7745858_bin.243_genomic.fna/tc_result.tsv
[2023-06-04 23:25:50,399] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:25:50,399] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:25:50,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc52655f2-5783-45e4-83a8-0c94f31ad2c9/dqc_reference/checkm_data
[2023-06-04 23:25:50,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:25:50,427] [INFO] Task started: CheckM
[2023-06-04 23:25:50,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934434945.1_ERR7745858_bin.243_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934434945.1_ERR7745858_bin.243_genomic.fna/checkm_input GCA_934434945.1_ERR7745858_bin.243_genomic.fna/checkm_result
[2023-06-04 23:26:12,326] [INFO] Task succeeded: CheckM
[2023-06-04 23:26:12,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:26:12,348] [INFO] ===== Completeness check finished =====
[2023-06-04 23:26:12,348] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:26:12,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934434945.1_ERR7745858_bin.243_genomic.fna/markers.fasta)
[2023-06-04 23:26:12,349] [INFO] Task started: Blastn
[2023-06-04 23:26:12,349] [INFO] Running command: blastn -query GCA_934434945.1_ERR7745858_bin.243_genomic.fna/markers.fasta -db /var/lib/cwl/stgc52655f2-5783-45e4-83a8-0c94f31ad2c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_934434945.1_ERR7745858_bin.243_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:26:13,095] [INFO] Task succeeded: Blastn
[2023-06-04 23:26:13,100] [INFO] Selected 14 target genomes.
[2023-06-04 23:26:13,100] [INFO] Target genome list was writen to GCA_934434945.1_ERR7745858_bin.243_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:26:13,177] [INFO] Task started: fastANI
[2023-06-04 23:26:13,178] [INFO] Running command: fastANI --query /var/lib/cwl/stga42c4aa0-4220-4bfd-915a-5f3a0557fa60/GCA_934434945.1_ERR7745858_bin.243_genomic.fna.gz --refList GCA_934434945.1_ERR7745858_bin.243_genomic.fna/target_genomes_gtdb.txt --output GCA_934434945.1_ERR7745858_bin.243_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:26:18,675] [INFO] Task succeeded: fastANI
[2023-06-04 23:26:18,686] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:26:18,687] [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_905201285.1	s__UMGS1820 sp905201285	99.1652	479	714	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820	95.0	98.99	98.99	0.93	0.93	2	conclusive
GCA_902797885.1	s__UMGS1820 sp902797885	93.8855	470	714	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555375.1	s__UMGS1820 sp900555375	80.9589	195	714	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820	95.0	98.83	97.66	0.90	0.83	3	-
GCA_900545865.1	s__UMGS1820 sp900545865	80.6186	210	714	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820	95.0	98.20	97.57	0.85	0.76	4	-
GCA_902766745.1	s__UMGS1820 sp902766745	78.1787	115	714	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777435.1	s__UMGS1820 sp902777435	77.7591	77	714	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:26:18,689] [INFO] GTDB search result was written to GCA_934434945.1_ERR7745858_bin.243_genomic.fna/result_gtdb.tsv
[2023-06-04 23:26:18,689] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:26:18,693] [INFO] DFAST_QC result json was written to GCA_934434945.1_ERR7745858_bin.243_genomic.fna/dqc_result.json
[2023-06-04 23:26:18,693] [INFO] DFAST_QC completed!
[2023-06-04 23:26:18,694] [INFO] Total running time: 0h0m51s