[2023-06-08 00:54:29,188] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:54:29,190] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:54:29,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b45d796-ca47-4a84-a274-c88ab3d7db92/dqc_reference
[2023-06-08 00:54:30,442] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:54:30,442] [INFO] Task started: Prodigal
[2023-06-08 00:54:30,443] [INFO] Running command: gunzip -c /var/lib/cwl/stg44e00119-0e53-43d2-9ceb-86958608fb58/GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna.gz | prodigal -d GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/cds.fna -a GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:54:45,512] [INFO] Task succeeded: Prodigal
[2023-06-08 00:54:45,512] [INFO] Task started: HMMsearch
[2023-06-08 00:54:45,513] [INFO] Running command: hmmsearch --tblout GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b45d796-ca47-4a84-a274-c88ab3d7db92/dqc_reference/reference_markers.hmm GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:54:45,764] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:54:45,766] [INFO] Found 6/6 markers.
[2023-06-08 00:54:45,795] [INFO] Query marker FASTA was written to GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/markers.fasta
[2023-06-08 00:54:45,796] [INFO] Task started: Blastn
[2023-06-08 00:54:45,796] [INFO] Running command: blastn -query GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b45d796-ca47-4a84-a274-c88ab3d7db92/dqc_reference/reference_markers.fasta -out GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:54:46,394] [INFO] Task succeeded: Blastn
[2023-06-08 00:54:46,398] [INFO] Selected 26 target genomes.
[2023-06-08 00:54:46,398] [INFO] Target genome list was writen to GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/target_genomes.txt
[2023-06-08 00:54:46,403] [INFO] Task started: fastANI
[2023-06-08 00:54:46,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg44e00119-0e53-43d2-9ceb-86958608fb58/GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna.gz --refList GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/target_genomes.txt --output GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:55:02,286] [INFO] Task succeeded: fastANI
[2023-06-08 00:55:02,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b45d796-ca47-4a84-a274-c88ab3d7db92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:55:02,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b45d796-ca47-4a84-a274-c88ab3d7db92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:55:02,291] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:55:02,291] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 00:55:02,291] [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
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	76.94	52	940	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:55:02,293] [INFO] DFAST Taxonomy check result was written to GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/tc_result.tsv
[2023-06-08 00:55:02,294] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:55:02,294] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:55:02,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b45d796-ca47-4a84-a274-c88ab3d7db92/dqc_reference/checkm_data
[2023-06-08 00:55:02,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:55:02,331] [INFO] Task started: CheckM
[2023-06-08 00:55:02,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/checkm_input GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/checkm_result
[2023-06-08 00:55:47,998] [INFO] Task succeeded: CheckM
[2023-06-08 00:55:48,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:55:48,019] [INFO] ===== Completeness check finished =====
[2023-06-08 00:55:48,019] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:55:48,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/markers.fasta)
[2023-06-08 00:55:48,020] [INFO] Task started: Blastn
[2023-06-08 00:55:48,020] [INFO] Running command: blastn -query GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b45d796-ca47-4a84-a274-c88ab3d7db92/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:55:48,831] [INFO] Task succeeded: Blastn
[2023-06-08 00:55:48,835] [INFO] Selected 16 target genomes.
[2023-06-08 00:55:48,836] [INFO] Target genome list was writen to GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:55:48,840] [INFO] Task started: fastANI
[2023-06-08 00:55:48,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg44e00119-0e53-43d2-9ceb-86958608fb58/GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna.gz --refList GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/target_genomes_gtdb.txt --output GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:55:56,276] [INFO] Task succeeded: fastANI
[2023-06-08 00:55:56,300] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:55:56,300] [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_001701295.1	s__CAG-485 sp001701295	98.2256	695	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.35	97.87	0.80	0.76	5	conclusive
GCA_009775355.1	s__CAG-485 sp009775355	79.4364	345	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.73	98.73	0.89	0.89	2	-
GCA_014867205.1	s__CAG-485 sp014867205	79.3988	244	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578385.1	s__CAG-485 sp910578385	79.0128	283	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584125.1	s__CAG-485 sp910584125	78.4175	208	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214735.1	s__CAG-485 sp905214735	78.0217	152	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586175.1	s__CAG-485 sp910586175	77.9727	133	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584185.1	s__CAG-485 sp910584185	77.9166	148	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760815.1	s__CAG-485 sp900760815	77.8948	144	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.28	97.28	0.85	0.85	2	-
GCA_900766975.1	s__CAG-485 sp900766975	77.7227	119	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361155.1	s__CAG-485 sp002361155	77.6266	91	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.36	98.51	0.82	0.74	7	-
GCA_910585285.1	s__CAG-485 sp910585285	77.3028	95	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003762615.1	s__CAG-485 sp002493045	77.247	80	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.48	99.22	0.95	0.91	14	-
GCA_014800785.1	s__CAG-485 sp014800785	76.8479	80	940	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.26	97.26	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-08 00:55:56,303] [INFO] GTDB search result was written to GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/result_gtdb.tsv
[2023-06-08 00:55:56,303] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:55:56,306] [INFO] DFAST_QC result json was written to GCA_902461595.1_UHGG-TPA_MGYG-HGUT-00354_genomic.fna/dqc_result.json
[2023-06-08 00:55:56,307] [INFO] DFAST_QC completed!
[2023-06-08 00:55:56,307] [INFO] Total running time: 0h1m27s