[2023-06-08 11:22:31,568] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:22:31,570] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:22:31,570] [INFO] DQC Reference Directory: /var/lib/cwl/stge255f6bd-3b60-431c-af57-b94550776f1b/dqc_reference
[2023-06-08 11:22:32,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:22:32,867] [INFO] Task started: Prodigal
[2023-06-08 11:22:32,867] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cc2dd6c-925e-448e-8756-ba3403870f57/GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna.gz | prodigal -d GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/cds.fna -a GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:22:42,114] [INFO] Task succeeded: Prodigal
[2023-06-08 11:22:42,114] [INFO] Task started: HMMsearch
[2023-06-08 11:22:42,114] [INFO] Running command: hmmsearch --tblout GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge255f6bd-3b60-431c-af57-b94550776f1b/dqc_reference/reference_markers.hmm GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:22:42,398] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:22:42,403] [INFO] Found 6/6 markers.
[2023-06-08 11:22:42,453] [INFO] Query marker FASTA was written to GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/markers.fasta
[2023-06-08 11:22:42,454] [INFO] Task started: Blastn
[2023-06-08 11:22:42,454] [INFO] Running command: blastn -query GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/markers.fasta -db /var/lib/cwl/stge255f6bd-3b60-431c-af57-b94550776f1b/dqc_reference/reference_markers.fasta -out GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:22:43,080] [INFO] Task succeeded: Blastn
[2023-06-08 11:22:43,088] [INFO] Selected 25 target genomes.
[2023-06-08 11:22:43,088] [INFO] Target genome list was writen to GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/target_genomes.txt
[2023-06-08 11:22:43,090] [INFO] Task started: fastANI
[2023-06-08 11:22:43,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cc2dd6c-925e-448e-8756-ba3403870f57/GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna.gz --refList GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/target_genomes.txt --output GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:22:55,676] [INFO] Task succeeded: fastANI
[2023-06-08 11:22:55,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge255f6bd-3b60-431c-af57-b94550776f1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:22:55,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge255f6bd-3b60-431c-af57-b94550776f1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:22:55,679] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:22:55,679] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:22:55,679] [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 11:22:55,682] [INFO] DFAST Taxonomy check result was written to GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/tc_result.tsv
[2023-06-08 11:22:55,683] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:22:55,683] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:22:55,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge255f6bd-3b60-431c-af57-b94550776f1b/dqc_reference/checkm_data
[2023-06-08 11:22:55,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:22:55,726] [INFO] Task started: CheckM
[2023-06-08 11:22:55,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/checkm_input GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/checkm_result
[2023-06-08 11:23:27,514] [INFO] Task succeeded: CheckM
[2023-06-08 11:23:27,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:23:27,541] [INFO] ===== Completeness check finished =====
[2023-06-08 11:23:27,541] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:23:27,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/markers.fasta)
[2023-06-08 11:23:27,542] [INFO] Task started: Blastn
[2023-06-08 11:23:27,542] [INFO] Running command: blastn -query GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/markers.fasta -db /var/lib/cwl/stge255f6bd-3b60-431c-af57-b94550776f1b/dqc_reference/reference_markers_gtdb.fasta -out GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:23:28,382] [INFO] Task succeeded: Blastn
[2023-06-08 11:23:28,386] [INFO] Selected 10 target genomes.
[2023-06-08 11:23:28,386] [INFO] Target genome list was writen to GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:23:28,390] [INFO] Task started: fastANI
[2023-06-08 11:23:28,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cc2dd6c-925e-448e-8756-ba3403870f57/GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna.gz --refList GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/target_genomes_gtdb.txt --output GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:23:35,230] [INFO] Task succeeded: fastANI
[2023-06-08 11:23:35,241] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:23:35,241] [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_900320485.1	s__Acetatifactor sp900320485	99.6405	840	1116	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.34	98.92	0.92	0.92	3	conclusive
GCA_017527205.1	s__Acetatifactor sp017527205	81.0764	442	1116	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	97.89	95.83	0.86	0.78	5	-
GCA_015056795.1	s__Acetatifactor sp015056795	80.1733	452	1116	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017552985.1	s__Acetatifactor sp017552985	80.0188	465	1116	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290775.1	s__Acetatifactor sp016290775	79.8541	381	1116	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	96.79	96.42	0.91	0.89	5	-
GCA_017400965.1	s__Acetatifactor sp017400965	79.8117	303	1116	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.43	98.28	0.80	0.76	3	-
GCA_016293615.1	s__Acetatifactor sp016293615	77.4555	110	1116	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:23:35,243] [INFO] GTDB search result was written to GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/result_gtdb.tsv
[2023-06-08 11:23:35,244] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:23:35,246] [INFO] DFAST_QC result json was written to GCA_902793475.1_Rumen_uncultured_genome_RUG13871_genomic.fna/dqc_result.json
[2023-06-08 11:23:35,246] [INFO] DFAST_QC completed!
[2023-06-08 11:23:35,246] [INFO] Total running time: 0h1m4s