[2023-06-08 00:54:26,928] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:54:26,931] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:54:26,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cf72d99-df67-4212-a97b-1c84d39d78a6/dqc_reference
[2023-06-08 00:54:28,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:54:28,280] [INFO] Task started: Prodigal
[2023-06-08 00:54:28,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d99b8db-f2ad-4544-941b-abe5fbd00cbe/GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna.gz | prodigal -d GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/cds.fna -a GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:54:32,219] [INFO] Task succeeded: Prodigal
[2023-06-08 00:54:32,220] [INFO] Task started: HMMsearch
[2023-06-08 00:54:32,220] [INFO] Running command: hmmsearch --tblout GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cf72d99-df67-4212-a97b-1c84d39d78a6/dqc_reference/reference_markers.hmm GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:54:32,450] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:54:32,451] [INFO] Found 6/6 markers.
[2023-06-08 00:54:32,478] [INFO] Query marker FASTA was written to GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/markers.fasta
[2023-06-08 00:54:32,478] [INFO] Task started: Blastn
[2023-06-08 00:54:32,479] [INFO] Running command: blastn -query GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cf72d99-df67-4212-a97b-1c84d39d78a6/dqc_reference/reference_markers.fasta -out GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:54:33,127] [INFO] Task succeeded: Blastn
[2023-06-08 00:54:33,131] [INFO] Selected 17 target genomes.
[2023-06-08 00:54:33,132] [INFO] Target genome list was writen to GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/target_genomes.txt
[2023-06-08 00:54:33,136] [INFO] Task started: fastANI
[2023-06-08 00:54:33,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d99b8db-f2ad-4544-941b-abe5fbd00cbe/GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna.gz --refList GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/target_genomes.txt --output GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:54:46,965] [INFO] Task succeeded: fastANI
[2023-06-08 00:54:46,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cf72d99-df67-4212-a97b-1c84d39d78a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:54:46,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cf72d99-df67-4212-a97b-1c84d39d78a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:54:46,968] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:54:46,968] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:54:46,968] [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 00:54:46,970] [INFO] DFAST Taxonomy check result was written to GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/tc_result.tsv
[2023-06-08 00:54:46,970] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:54:46,971] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:54:46,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cf72d99-df67-4212-a97b-1c84d39d78a6/dqc_reference/checkm_data
[2023-06-08 00:54:46,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:54:46,998] [INFO] Task started: CheckM
[2023-06-08 00:54:46,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/checkm_input GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/checkm_result
[2023-06-08 00:55:05,899] [INFO] Task succeeded: CheckM
[2023-06-08 00:55:05,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:55:05,920] [INFO] ===== Completeness check finished =====
[2023-06-08 00:55:05,920] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:55:05,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/markers.fasta)
[2023-06-08 00:55:05,921] [INFO] Task started: Blastn
[2023-06-08 00:55:05,921] [INFO] Running command: blastn -query GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cf72d99-df67-4212-a97b-1c84d39d78a6/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:55:06,769] [INFO] Task succeeded: Blastn
[2023-06-08 00:55:06,773] [INFO] Selected 11 target genomes.
[2023-06-08 00:55:06,773] [INFO] Target genome list was writen to GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:55:06,782] [INFO] Task started: fastANI
[2023-06-08 00:55:06,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d99b8db-f2ad-4544-941b-abe5fbd00cbe/GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna.gz --refList GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/target_genomes_gtdb.txt --output GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:55:10,071] [INFO] Task succeeded: fastANI
[2023-06-08 00:55:10,086] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:55:10,086] [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_002329395.1	s__UBA1436 sp002329395	98.6859	365	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	98.64	98.61	0.87	0.85	4	conclusive
GCF_002159705.1	s__UBA1436 sp002159705	82.7884	330	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576915.1	s__UBA1436 sp910576915	82.2214	319	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	97.08	97.03	0.93	0.92	3	-
GCA_002432025.1	s__UBA1436 sp002432025	80.6489	281	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	98.20	97.76	0.93	0.89	3	-
GCA_900541355.1	s__UBA1436 sp900541355	80.037	238	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	97.39	97.24	0.88	0.86	4	-
GCA_019120455.1	s__Avelusimicrobium excrementipullorum	79.2617	201	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__Avelusimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315795.1	s__UBA1436 sp900315795	78.5433	159	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	98.45	96.90	0.94	0.89	3	-
GCA_902766765.1	s__UBA1436 sp902766765	77.3779	108	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017961295.1	s__UBA1436 sp017961295	77.2596	62	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767385.1	s__UBA1436 sp902767385	77.019	78	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235355.1	s__Avelusimicrobium sp905235355	76.989	89	434	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__Avelusimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 00:55:10,089] [INFO] GTDB search result was written to GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/result_gtdb.tsv
[2023-06-08 00:55:10,090] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:55:10,093] [INFO] DFAST_QC result json was written to GCA_902461635.1_UHGG-TPA_MGYG-HGUT-00358_genomic.fna/dqc_result.json
[2023-06-08 00:55:10,094] [INFO] DFAST_QC completed!
[2023-06-08 00:55:10,094] [INFO] Total running time: 0h0m43s