[2023-06-05 13:29:57,780] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:29:57,784] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:29:57,785] [INFO] DQC Reference Directory: /var/lib/cwl/stgd95acc9f-dde5-4b24-9554-1542a9de2a6d/dqc_reference
[2023-06-05 13:29:59,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:29:59,208] [INFO] Task started: Prodigal
[2023-06-05 13:29:59,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg454d572f-3776-49f9-910e-6b03daf0433c/GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna.gz | prodigal -d GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/cds.fna -a GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:30:03,252] [INFO] Task succeeded: Prodigal
[2023-06-05 13:30:03,253] [INFO] Task started: HMMsearch
[2023-06-05 13:30:03,253] [INFO] Running command: hmmsearch --tblout GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd95acc9f-dde5-4b24-9554-1542a9de2a6d/dqc_reference/reference_markers.hmm GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:30:03,462] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:30:03,463] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg454d572f-3776-49f9-910e-6b03daf0433c/GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna.gz]
[2023-06-05 13:30:03,485] [INFO] Query marker FASTA was written to GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/markers.fasta
[2023-06-05 13:30:03,486] [INFO] Task started: Blastn
[2023-06-05 13:30:03,486] [INFO] Running command: blastn -query GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/markers.fasta -db /var/lib/cwl/stgd95acc9f-dde5-4b24-9554-1542a9de2a6d/dqc_reference/reference_markers.fasta -out GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:30:04,149] [INFO] Task succeeded: Blastn
[2023-06-05 13:30:04,153] [INFO] Selected 28 target genomes.
[2023-06-05 13:30:04,153] [INFO] Target genome list was writen to GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/target_genomes.txt
[2023-06-05 13:30:04,181] [INFO] Task started: fastANI
[2023-06-05 13:30:04,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg454d572f-3776-49f9-910e-6b03daf0433c/GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna.gz --refList GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/target_genomes.txt --output GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:30:18,388] [INFO] Task succeeded: fastANI
[2023-06-05 13:30:18,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd95acc9f-dde5-4b24-9554-1542a9de2a6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:30:18,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd95acc9f-dde5-4b24-9554-1542a9de2a6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:30:18,392] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:30:18,392] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:30:18,392] [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
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	76.7359	56	626	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:30:18,394] [INFO] DFAST Taxonomy check result was written to GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/tc_result.tsv
[2023-06-05 13:30:18,395] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:30:18,395] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:30:18,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd95acc9f-dde5-4b24-9554-1542a9de2a6d/dqc_reference/checkm_data
[2023-06-05 13:30:18,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:30:18,420] [INFO] Task started: CheckM
[2023-06-05 13:30:18,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/checkm_input GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/checkm_result
[2023-06-05 13:30:37,881] [INFO] Task succeeded: CheckM
[2023-06-05 13:30:37,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:30:37,899] [INFO] ===== Completeness check finished =====
[2023-06-05 13:30:37,900] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:30:37,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/markers.fasta)
[2023-06-05 13:30:37,900] [INFO] Task started: Blastn
[2023-06-05 13:30:37,900] [INFO] Running command: blastn -query GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/markers.fasta -db /var/lib/cwl/stgd95acc9f-dde5-4b24-9554-1542a9de2a6d/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:30:38,762] [INFO] Task succeeded: Blastn
[2023-06-05 13:30:38,767] [INFO] Selected 23 target genomes.
[2023-06-05 13:30:38,767] [INFO] Target genome list was writen to GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:30:38,774] [INFO] Task started: fastANI
[2023-06-05 13:30:38,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg454d572f-3776-49f9-910e-6b03daf0433c/GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna.gz --refList GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/target_genomes_gtdb.txt --output GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:30:49,085] [INFO] Task succeeded: fastANI
[2023-06-05 13:30:49,094] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:30:49,095] [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_002349525.1	s__V9D3004 sp002349525	99.8793	603	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__V9D3004	95.0	99.26	98.90	0.94	0.92	4	conclusive
GCA_015057405.1	s__V9D3004 sp015057405	77.8002	117	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__V9D3004	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760345.1	s__V9D3004 sp900760345	77.7571	108	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__V9D3004	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057375.1	s__V9D3004 sp015057375	77.6681	126	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__V9D3004	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766825.1	s__RUG11200 sp902766825	77.1251	59	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11200	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000621985.1	s__V9D3004 sp000621985	76.9832	98	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__V9D3004	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902763335.1	s__UBA2821 sp902763335	76.884	53	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918265.1	s__Falcatimonas sp018918265	76.7543	71	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_001414325.1	s__Butyribacter intestini	76.6177	64	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	98.53	97.85	0.90	0.84	10	-
GCA_002351535.1	s__UBA2821 sp002351535	76.5741	65	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-05 13:30:49,097] [INFO] GTDB search result was written to GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/result_gtdb.tsv
[2023-06-05 13:30:49,097] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:30:49,100] [INFO] DFAST_QC result json was written to GCA_902767105.1_Rumen_uncultured_genome_RUG11226_genomic.fna/dqc_result.json
[2023-06-05 13:30:49,100] [INFO] DFAST_QC completed!
[2023-06-05 13:30:49,100] [INFO] Total running time: 0h0m51s