[2023-06-05 02:54:30,623] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:54:30,631] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:54:30,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg21c8ebd9-abd1-41cd-865b-adc96a6c9370/dqc_reference
[2023-06-05 02:54:31,873] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:54:31,873] [INFO] Task started: Prodigal
[2023-06-05 02:54:31,874] [INFO] Running command: gunzip -c /var/lib/cwl/stg404c0da5-cda3-4792-8970-f54e81a43601/GCA_902836945.1_MGYG-HGUT-04900_genomic.fna.gz | prodigal -d GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/cds.fna -a GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:54:34,517] [INFO] Task succeeded: Prodigal
[2023-06-05 02:54:34,517] [INFO] Task started: HMMsearch
[2023-06-05 02:54:34,518] [INFO] Running command: hmmsearch --tblout GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21c8ebd9-abd1-41cd-865b-adc96a6c9370/dqc_reference/reference_markers.hmm GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:54:34,733] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:54:34,734] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg404c0da5-cda3-4792-8970-f54e81a43601/GCA_902836945.1_MGYG-HGUT-04900_genomic.fna.gz]
[2023-06-05 02:54:34,761] [INFO] Query marker FASTA was written to GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/markers.fasta
[2023-06-05 02:54:34,762] [INFO] Task started: Blastn
[2023-06-05 02:54:34,762] [INFO] Running command: blastn -query GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/markers.fasta -db /var/lib/cwl/stg21c8ebd9-abd1-41cd-865b-adc96a6c9370/dqc_reference/reference_markers.fasta -out GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:54:36,506] [INFO] Task succeeded: Blastn
[2023-06-05 02:54:36,510] [INFO] Selected 25 target genomes.
[2023-06-05 02:54:36,510] [INFO] Target genome list was writen to GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/target_genomes.txt
[2023-06-05 02:54:36,514] [INFO] Task started: fastANI
[2023-06-05 02:54:36,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg404c0da5-cda3-4792-8970-f54e81a43601/GCA_902836945.1_MGYG-HGUT-04900_genomic.fna.gz --refList GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/target_genomes.txt --output GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:54:47,136] [INFO] Task succeeded: fastANI
[2023-06-05 02:54:47,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21c8ebd9-abd1-41cd-865b-adc96a6c9370/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:54:47,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21c8ebd9-abd1-41cd-865b-adc96a6c9370/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:54:47,139] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:54:47,139] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:54:47,140] [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
--------------------------------------------------------------------------------
[2023-06-05 02:54:47,142] [INFO] DFAST Taxonomy check result was written to GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/tc_result.tsv
[2023-06-05 02:54:47,143] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:54:47,143] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:54:47,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21c8ebd9-abd1-41cd-865b-adc96a6c9370/dqc_reference/checkm_data
[2023-06-05 02:54:47,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:54:47,167] [INFO] Task started: CheckM
[2023-06-05 02:54:47,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/checkm_input GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/checkm_result
[2023-06-05 02:55:03,655] [INFO] Task succeeded: CheckM
[2023-06-05 02:55:03,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:55:03,675] [INFO] ===== Completeness check finished =====
[2023-06-05 02:55:03,675] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:55:03,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/markers.fasta)
[2023-06-05 02:55:03,676] [INFO] Task started: Blastn
[2023-06-05 02:55:03,676] [INFO] Running command: blastn -query GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/markers.fasta -db /var/lib/cwl/stg21c8ebd9-abd1-41cd-865b-adc96a6c9370/dqc_reference/reference_markers_gtdb.fasta -out GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:55:04,499] [INFO] Task succeeded: Blastn
[2023-06-05 02:55:04,503] [INFO] Selected 15 target genomes.
[2023-06-05 02:55:04,504] [INFO] Target genome list was writen to GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:55:04,605] [INFO] Task started: fastANI
[2023-06-05 02:55:04,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg404c0da5-cda3-4792-8970-f54e81a43601/GCA_902836945.1_MGYG-HGUT-04900_genomic.fna.gz --refList GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/target_genomes_gtdb.txt --output GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:55:09,186] [INFO] Task succeeded: fastANI
[2023-06-05 02:55:09,194] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 02:55:09,194] [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_000435675.1	s__CAG-1427 sp000435675	94.0094	81	100	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	95.82	95.24	0.91	0.83	9	-
GCA_900538545.1	s__CAG-1427 sp900538545	93.7417	89	100	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	95.97	95.36	0.90	0.87	4	-
GCA_900542525.1	s__CAG-1427 sp900542525	88.5532	82	100	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAG-1427	95.0	99.99	99.99	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-05 02:55:09,196] [INFO] GTDB search result was written to GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/result_gtdb.tsv
[2023-06-05 02:55:09,197] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:55:09,200] [INFO] DFAST_QC result json was written to GCA_902836945.1_MGYG-HGUT-04900_genomic.fna/dqc_result.json
[2023-06-05 02:55:09,200] [INFO] DFAST_QC completed!
[2023-06-05 02:55:09,200] [INFO] Total running time: 0h0m39s