[2023-06-05 00:14:07,983] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:14:07,984] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:14:07,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg483a6e2f-7b0a-4762-9cca-6630032e3742/dqc_reference
[2023-06-05 00:14:09,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:14:09,270] [INFO] Task started: Prodigal
[2023-06-05 00:14:09,271] [INFO] Running command: gunzip -c /var/lib/cwl/stgbefee4c0-e16f-4522-86cb-9a4454baa5dc/GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna.gz | prodigal -d GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/cds.fna -a GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:14:14,640] [INFO] Task succeeded: Prodigal
[2023-06-05 00:14:14,641] [INFO] Task started: HMMsearch
[2023-06-05 00:14:14,641] [INFO] Running command: hmmsearch --tblout GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg483a6e2f-7b0a-4762-9cca-6630032e3742/dqc_reference/reference_markers.hmm GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:14:14,861] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:14:14,862] [INFO] Found 6/6 markers.
[2023-06-05 00:14:14,884] [INFO] Query marker FASTA was written to GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/markers.fasta
[2023-06-05 00:14:14,884] [INFO] Task started: Blastn
[2023-06-05 00:14:14,884] [INFO] Running command: blastn -query GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/markers.fasta -db /var/lib/cwl/stg483a6e2f-7b0a-4762-9cca-6630032e3742/dqc_reference/reference_markers.fasta -out GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:15,521] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:15,524] [INFO] Selected 25 target genomes.
[2023-06-05 00:14:15,525] [INFO] Target genome list was writen to GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/target_genomes.txt
[2023-06-05 00:14:15,531] [INFO] Task started: fastANI
[2023-06-05 00:14:15,531] [INFO] Running command: fastANI --query /var/lib/cwl/stgbefee4c0-e16f-4522-86cb-9a4454baa5dc/GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna.gz --refList GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/target_genomes.txt --output GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:14:32,374] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:32,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg483a6e2f-7b0a-4762-9cca-6630032e3742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:14:32,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg483a6e2f-7b0a-4762-9cca-6630032e3742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:14:32,380] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:14:32,381] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:14:32,381] [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
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	76.3719	64	684	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:14:32,383] [INFO] DFAST Taxonomy check result was written to GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/tc_result.tsv
[2023-06-05 00:14:32,384] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:14:32,384] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:14:32,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg483a6e2f-7b0a-4762-9cca-6630032e3742/dqc_reference/checkm_data
[2023-06-05 00:14:32,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:14:32,411] [INFO] Task started: CheckM
[2023-06-05 00:14:32,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/checkm_input GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/checkm_result
[2023-06-05 00:14:54,110] [INFO] Task succeeded: CheckM
[2023-06-05 00:14:54,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:14:54,127] [INFO] ===== Completeness check finished =====
[2023-06-05 00:14:54,127] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:14:54,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/markers.fasta)
[2023-06-05 00:14:54,128] [INFO] Task started: Blastn
[2023-06-05 00:14:54,128] [INFO] Running command: blastn -query GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/markers.fasta -db /var/lib/cwl/stg483a6e2f-7b0a-4762-9cca-6630032e3742/dqc_reference/reference_markers_gtdb.fasta -out GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:55,042] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:55,045] [INFO] Selected 18 target genomes.
[2023-06-05 00:14:55,045] [INFO] Target genome list was writen to GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:14:55,101] [INFO] Task started: fastANI
[2023-06-05 00:14:55,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgbefee4c0-e16f-4522-86cb-9a4454baa5dc/GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna.gz --refList GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/target_genomes_gtdb.txt --output GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:15:02,487] [INFO] Task succeeded: fastANI
[2023-06-05 00:15:02,508] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:15:02,508] [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_900317045.1	s__UBA1066 sp900317045	99.5669	631	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.33	98.92	0.88	0.76	8	conclusive
GCA_900315305.1	s__UBA1066 sp900315305	77.7714	144	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.26	98.90	0.90	0.82	11	-
GCA_002350625.1	s__UBA1066 sp002350625	77.4552	151	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.93	99.93	0.93	0.93	2	-
GCA_900320575.1	s__UBA1066 sp900320575	77.4271	95	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.66	99.66	0.99	0.99	2	-
GCA_902766945.1	s__UBA1066 sp902766945	77.269	123	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773195.1	s__UBA1066 sp902773195	77.1394	139	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766955.1	s__UBA1066 sp902766955	76.9948	118	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.96	97.96	0.75	0.75	2	-
GCA_902783935.1	s__UBA1066 sp902783935	76.9294	65	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369495.1	s__UBA1066 sp002369495	76.7887	63	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.09	98.09	0.78	0.78	2	-
GCA_017430765.1	s__UBA1066 sp017430765	76.6872	66	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797025.1	s__Bilifractor sp902797025	75.7674	51	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:15:02,510] [INFO] GTDB search result was written to GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/result_gtdb.tsv
[2023-06-05 00:15:02,511] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:15:02,513] [INFO] DFAST_QC result json was written to GCA_902790645.1_Rumen_uncultured_genome_RUG13589_genomic.fna/dqc_result.json
[2023-06-05 00:15:02,514] [INFO] DFAST_QC completed!
[2023-06-05 00:15:02,514] [INFO] Total running time: 0h0m55s