[2023-06-07 19:05:32,689] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:05:32,697] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:05:32,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg81197d60-afd9-4328-ac24-b0f5bfcf09a3/dqc_reference
[2023-06-07 19:05:34,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:05:34,044] [INFO] Task started: Prodigal
[2023-06-07 19:05:34,045] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa7b92ed-5f36-49e5-b446-b494be87755a/GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna.gz | prodigal -d GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/cds.fna -a GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:05:38,446] [INFO] Task succeeded: Prodigal
[2023-06-07 19:05:38,447] [INFO] Task started: HMMsearch
[2023-06-07 19:05:38,447] [INFO] Running command: hmmsearch --tblout GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81197d60-afd9-4328-ac24-b0f5bfcf09a3/dqc_reference/reference_markers.hmm GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:05:38,709] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:05:38,712] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfa7b92ed-5f36-49e5-b446-b494be87755a/GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna.gz]
[2023-06-07 19:05:38,739] [INFO] Query marker FASTA was written to GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/markers.fasta
[2023-06-07 19:05:38,740] [INFO] Task started: Blastn
[2023-06-07 19:05:38,740] [INFO] Running command: blastn -query GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/markers.fasta -db /var/lib/cwl/stg81197d60-afd9-4328-ac24-b0f5bfcf09a3/dqc_reference/reference_markers.fasta -out GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:05:39,220] [INFO] Task succeeded: Blastn
[2023-06-07 19:05:39,224] [INFO] Selected 7 target genomes.
[2023-06-07 19:05:39,224] [INFO] Target genome list was writen to GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/target_genomes.txt
[2023-06-07 19:05:39,226] [INFO] Task started: fastANI
[2023-06-07 19:05:39,227] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa7b92ed-5f36-49e5-b446-b494be87755a/GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna.gz --refList GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/target_genomes.txt --output GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:05:41,869] [INFO] Task succeeded: fastANI
[2023-06-07 19:05:41,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81197d60-afd9-4328-ac24-b0f5bfcf09a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:05:41,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81197d60-afd9-4328-ac24-b0f5bfcf09a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:05:41,872] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:05:41,873] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 19:05:41,873] [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
--------------------------------------------------------------------------------
[2023-06-07 19:05:41,875] [INFO] DFAST Taxonomy check result was written to GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/tc_result.tsv
[2023-06-07 19:05:41,876] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:05:41,876] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:05:41,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81197d60-afd9-4328-ac24-b0f5bfcf09a3/dqc_reference/checkm_data
[2023-06-07 19:05:41,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:05:41,909] [INFO] Task started: CheckM
[2023-06-07 19:05:41,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/checkm_input GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/checkm_result
[2023-06-07 19:06:02,688] [INFO] Task succeeded: CheckM
[2023-06-07 19:06:02,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:06:02,711] [INFO] ===== Completeness check finished =====
[2023-06-07 19:06:02,712] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:06:02,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/markers.fasta)
[2023-06-07 19:06:02,713] [INFO] Task started: Blastn
[2023-06-07 19:06:02,713] [INFO] Running command: blastn -query GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/markers.fasta -db /var/lib/cwl/stg81197d60-afd9-4328-ac24-b0f5bfcf09a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:06:03,264] [INFO] Task succeeded: Blastn
[2023-06-07 19:06:03,270] [INFO] Selected 9 target genomes.
[2023-06-07 19:06:03,271] [INFO] Target genome list was writen to GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:06:03,276] [INFO] Task started: fastANI
[2023-06-07 19:06:03,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa7b92ed-5f36-49e5-b446-b494be87755a/GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna.gz --refList GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/target_genomes_gtdb.txt --output GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:06:07,272] [INFO] Task succeeded: fastANI
[2023-06-07 19:06:07,283] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 19:06:07,284] [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_900317795.1	s__UBA1213 sp900317795	93.1484	327	445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	97.97	97.34	0.76	0.68	10	-
GCA_002309275.1	s__UBA1213 sp002309275	87.2811	308	445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800005.1	s__UBA1213 sp902800005	82.5512	299	445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.32	99.32	0.91	0.91	2	-
GCA_902801715.1	s__UBA1213 sp902801715	82.5244	228	445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785555.1	s__UBA1213 sp902785555	81.4601	247	445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800065.1	s__UBA1213 sp902800065	81.3236	229	445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002350705.1	s__UBA1213 sp002350705	79.0256	145	445	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.87	99.87	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-07 19:06:07,286] [INFO] GTDB search result was written to GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/result_gtdb.tsv
[2023-06-07 19:06:07,289] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:06:07,292] [INFO] DFAST_QC result json was written to GCA_902793115.1_Rumen_uncultured_genome_RUG13836_genomic.fna/dqc_result.json
[2023-06-07 19:06:07,293] [INFO] DFAST_QC completed!
[2023-06-07 19:06:07,293] [INFO] Total running time: 0h0m35s