[2023-06-05 12:22:25,244] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:22:25,246] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:22:25,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg32ee6914-a3ab-4c0c-83bf-5e2e89427cf5/dqc_reference
[2023-06-05 12:22:28,779] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:22:28,780] [INFO] Task started: Prodigal
[2023-06-05 12:22:28,780] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c381d84-7924-4cc0-bca4-36b54168e749/GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna.gz | prodigal -d GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/cds.fna -a GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:22:34,013] [INFO] Task succeeded: Prodigal
[2023-06-05 12:22:34,013] [INFO] Task started: HMMsearch
[2023-06-05 12:22:34,013] [INFO] Running command: hmmsearch --tblout GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32ee6914-a3ab-4c0c-83bf-5e2e89427cf5/dqc_reference/reference_markers.hmm GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:22:34,303] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:22:34,304] [INFO] Found 6/6 markers.
[2023-06-05 12:22:34,330] [INFO] Query marker FASTA was written to GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/markers.fasta
[2023-06-05 12:22:34,331] [INFO] Task started: Blastn
[2023-06-05 12:22:34,331] [INFO] Running command: blastn -query GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/markers.fasta -db /var/lib/cwl/stg32ee6914-a3ab-4c0c-83bf-5e2e89427cf5/dqc_reference/reference_markers.fasta -out GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:22:35,638] [INFO] Task succeeded: Blastn
[2023-06-05 12:22:35,642] [INFO] Selected 17 target genomes.
[2023-06-05 12:22:35,642] [INFO] Target genome list was writen to GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/target_genomes.txt
[2023-06-05 12:22:35,647] [INFO] Task started: fastANI
[2023-06-05 12:22:35,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c381d84-7924-4cc0-bca4-36b54168e749/GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna.gz --refList GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/target_genomes.txt --output GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:22:47,124] [INFO] Task succeeded: fastANI
[2023-06-05 12:22:47,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32ee6914-a3ab-4c0c-83bf-5e2e89427cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:22:47,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32ee6914-a3ab-4c0c-83bf-5e2e89427cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:22:47,127] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:22:47,127] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 12:22:47,127] [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 12:22:47,129] [INFO] DFAST Taxonomy check result was written to GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/tc_result.tsv
[2023-06-05 12:22:47,130] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:22:47,130] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:22:47,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32ee6914-a3ab-4c0c-83bf-5e2e89427cf5/dqc_reference/checkm_data
[2023-06-05 12:22:47,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:22:47,162] [INFO] Task started: CheckM
[2023-06-05 12:22:47,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/checkm_input GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/checkm_result
[2023-06-05 12:23:10,321] [INFO] Task succeeded: CheckM
[2023-06-05 12:23:10,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 2.27%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:23:10,345] [INFO] ===== Completeness check finished =====
[2023-06-05 12:23:10,346] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:23:10,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/markers.fasta)
[2023-06-05 12:23:10,346] [INFO] Task started: Blastn
[2023-06-05 12:23:10,346] [INFO] Running command: blastn -query GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/markers.fasta -db /var/lib/cwl/stg32ee6914-a3ab-4c0c-83bf-5e2e89427cf5/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:23:11,191] [INFO] Task succeeded: Blastn
[2023-06-05 12:23:11,195] [INFO] Selected 15 target genomes.
[2023-06-05 12:23:11,195] [INFO] Target genome list was writen to GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:23:11,206] [INFO] Task started: fastANI
[2023-06-05 12:23:11,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c381d84-7924-4cc0-bca4-36b54168e749/GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna.gz --refList GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/target_genomes_gtdb.txt --output GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:23:19,028] [INFO] Task succeeded: fastANI
[2023-06-05 12:23:19,040] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:23:19,040] [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_902782235.1	s__Saccharofermentans sp902782235	100.0	731	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	98.76	98.60	0.85	0.82	8	conclusive
GCA_902801755.1	s__Saccharofermentans sp902801755	91.1158	473	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	98.05	98.05	0.82	0.82	2	-
GCA_016292155.1	s__Saccharofermentans sp016292155	88.9724	474	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017537905.1	s__Saccharofermentans sp017537905	87.2634	342	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780785.1	s__Saccharofermentans sp902780785	86.9767	586	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	98.16	98.16	0.93	0.93	2	-
GCA_003149065.1	s__Saccharofermentans sp003149065	86.1001	574	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	97.57	96.36	0.94	0.91	4	-
GCA_001604135.1	s__Saccharofermentans sp001604135	85.9884	585	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902764825.1	s__Saccharofermentans sp902764825	85.9024	600	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	97.58	96.60	0.94	0.88	6	-
GCA_016292145.1	s__Saccharofermentans sp016292145	85.5605	506	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	97.51	97.51	0.74	0.74	2	-
GCA_017509245.1	s__Saccharofermentans sp017509245	82.5097	387	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427465.1	s__Saccharofermentans sp017427465	82.2799	412	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	97.19	97.19	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-05 12:23:19,043] [INFO] GTDB search result was written to GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/result_gtdb.tsv
[2023-06-05 12:23:19,043] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:23:19,047] [INFO] DFAST_QC result json was written to GCA_902782235.1_Rumen_uncultured_genome_RUG12748_genomic.fna/dqc_result.json
[2023-06-05 12:23:19,048] [INFO] DFAST_QC completed!
[2023-06-05 12:23:19,048] [INFO] Total running time: 0h0m54s