[2023-06-08 02:39:55,976] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:39:55,980] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:39:55,980] [INFO] DQC Reference Directory: /var/lib/cwl/stgef381c62-2180-458e-ac21-1a50002b8b69/dqc_reference
[2023-06-08 02:39:57,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:39:57,537] [INFO] Task started: Prodigal
[2023-06-08 02:39:57,538] [INFO] Running command: gunzip -c /var/lib/cwl/stg8598421c-57be-43e7-a48a-98a43c1c8801/GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna.gz | prodigal -d GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/cds.fna -a GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:40:05,537] [INFO] Task succeeded: Prodigal
[2023-06-08 02:40:05,538] [INFO] Task started: HMMsearch
[2023-06-08 02:40:05,538] [INFO] Running command: hmmsearch --tblout GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef381c62-2180-458e-ac21-1a50002b8b69/dqc_reference/reference_markers.hmm GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:40:05,786] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:40:05,787] [INFO] Found 6/6 markers.
[2023-06-08 02:40:05,805] [INFO] Query marker FASTA was written to GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/markers.fasta
[2023-06-08 02:40:05,805] [INFO] Task started: Blastn
[2023-06-08 02:40:05,805] [INFO] Running command: blastn -query GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/markers.fasta -db /var/lib/cwl/stgef381c62-2180-458e-ac21-1a50002b8b69/dqc_reference/reference_markers.fasta -out GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:40:06,439] [INFO] Task succeeded: Blastn
[2023-06-08 02:40:06,442] [INFO] Selected 24 target genomes.
[2023-06-08 02:40:06,443] [INFO] Target genome list was writen to GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/target_genomes.txt
[2023-06-08 02:40:06,445] [INFO] Task started: fastANI
[2023-06-08 02:40:06,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg8598421c-57be-43e7-a48a-98a43c1c8801/GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna.gz --refList GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/target_genomes.txt --output GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:40:20,524] [INFO] Task succeeded: fastANI
[2023-06-08 02:40:20,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef381c62-2180-458e-ac21-1a50002b8b69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:40:20,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef381c62-2180-458e-ac21-1a50002b8b69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:40:20,527] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:40:20,527] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 02:40:20,527] [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
--------------------------------------------------------------------------------
[2023-06-08 02:40:20,529] [INFO] DFAST Taxonomy check result was written to GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/tc_result.tsv
[2023-06-08 02:40:20,530] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:40:20,530] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:40:20,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef381c62-2180-458e-ac21-1a50002b8b69/dqc_reference/checkm_data
[2023-06-08 02:40:20,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:40:20,559] [INFO] Task started: CheckM
[2023-06-08 02:40:20,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/checkm_input GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/checkm_result
[2023-06-08 02:40:47,835] [INFO] Task succeeded: CheckM
[2023-06-08 02:40:47,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:40:47,857] [INFO] ===== Completeness check finished =====
[2023-06-08 02:40:47,858] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:40:47,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/markers.fasta)
[2023-06-08 02:40:47,858] [INFO] Task started: Blastn
[2023-06-08 02:40:47,858] [INFO] Running command: blastn -query GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/markers.fasta -db /var/lib/cwl/stgef381c62-2180-458e-ac21-1a50002b8b69/dqc_reference/reference_markers_gtdb.fasta -out GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:40:48,652] [INFO] Task succeeded: Blastn
[2023-06-08 02:40:48,656] [INFO] Selected 14 target genomes.
[2023-06-08 02:40:48,656] [INFO] Target genome list was writen to GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:40:48,661] [INFO] Task started: fastANI
[2023-06-08 02:40:48,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg8598421c-57be-43e7-a48a-98a43c1c8801/GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna.gz --refList GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/target_genomes_gtdb.txt --output GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:40:53,764] [INFO] Task succeeded: fastANI
[2023-06-08 02:40:53,781] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 02:40:53,782] [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_902774045.1	s__Cryptobacteroides sp902774045	100.0	547	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017459075.1	s__Cryptobacteroides sp017459075	79.1668	183	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316675.1	s__Cryptobacteroides sp900316675	79.0307	200	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.02	0.91	0.85	9	-
GCA_900314395.1	s__Cryptobacteroides sp900314395	78.9768	185	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.48	98.95	0.92	0.85	3	-
GCA_017443025.1	s__Cryptobacteroides sp017443025	78.5529	107	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.45	98.45	0.86	0.86	2	-
GCA_900319855.1	s__Cryptobacteroides sp900319855	77.1833	56	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.60	97.81	0.89	0.84	6	-
GCA_017960545.1	s__Cryptobacteroides sp017960545	76.5905	51	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017477465.1	s__Cryptobacteroides sp017477465	76.5826	55	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794615.1	s__Cryptobacteroides sp902794615	76.5012	58	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.63	96.28	0.79	0.72	4	-
--------------------------------------------------------------------------------
[2023-06-08 02:40:53,784] [INFO] GTDB search result was written to GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/result_gtdb.tsv
[2023-06-08 02:40:53,785] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:40:53,789] [INFO] DFAST_QC result json was written to GCA_902774045.1_Rumen_uncultured_genome_RUG11933_genomic.fna/dqc_result.json
[2023-06-08 02:40:53,789] [INFO] DFAST_QC completed!
[2023-06-08 02:40:53,789] [INFO] Total running time: 0h0m58s