[2023-06-05 00:53:12,722] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:53:12,727] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:53:12,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg7331e7a3-11da-4f94-973f-c8ecb183a8d8/dqc_reference
[2023-06-05 00:53:14,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:53:14,063] [INFO] Task started: Prodigal
[2023-06-05 00:53:14,064] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3200bb6-4574-4539-a1d5-e5f536a43b65/GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna.gz | prodigal -d GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/cds.fna -a GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:53:18,482] [INFO] Task succeeded: Prodigal
[2023-06-05 00:53:18,482] [INFO] Task started: HMMsearch
[2023-06-05 00:53:18,482] [INFO] Running command: hmmsearch --tblout GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7331e7a3-11da-4f94-973f-c8ecb183a8d8/dqc_reference/reference_markers.hmm GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:53:18,761] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:53:18,763] [INFO] Found 6/6 markers.
[2023-06-05 00:53:18,791] [INFO] Query marker FASTA was written to GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/markers.fasta
[2023-06-05 00:53:18,791] [INFO] Task started: Blastn
[2023-06-05 00:53:18,791] [INFO] Running command: blastn -query GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/markers.fasta -db /var/lib/cwl/stg7331e7a3-11da-4f94-973f-c8ecb183a8d8/dqc_reference/reference_markers.fasta -out GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:53:19,437] [INFO] Task succeeded: Blastn
[2023-06-05 00:53:19,441] [INFO] Selected 30 target genomes.
[2023-06-05 00:53:19,441] [INFO] Target genome list was writen to GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/target_genomes.txt
[2023-06-05 00:53:19,443] [INFO] Task started: fastANI
[2023-06-05 00:53:19,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3200bb6-4574-4539-a1d5-e5f536a43b65/GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna.gz --refList GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/target_genomes.txt --output GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:53:36,631] [INFO] Task succeeded: fastANI
[2023-06-05 00:53:36,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7331e7a3-11da-4f94-973f-c8ecb183a8d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:53:36,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7331e7a3-11da-4f94-973f-c8ecb183a8d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:53:36,635] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:53:36,635] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:53:36,635] [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 00:53:36,638] [INFO] DFAST Taxonomy check result was written to GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/tc_result.tsv
[2023-06-05 00:53:36,638] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:53:36,639] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:53:36,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7331e7a3-11da-4f94-973f-c8ecb183a8d8/dqc_reference/checkm_data
[2023-06-05 00:53:36,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:53:36,672] [INFO] Task started: CheckM
[2023-06-05 00:53:36,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/checkm_input GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/checkm_result
[2023-06-05 00:53:58,274] [INFO] Task succeeded: CheckM
[2023-06-05 00:53:58,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.13%
Contamintation: 7.29%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 00:53:58,299] [INFO] ===== Completeness check finished =====
[2023-06-05 00:53:58,300] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:53:58,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/markers.fasta)
[2023-06-05 00:53:58,301] [INFO] Task started: Blastn
[2023-06-05 00:53:58,301] [INFO] Running command: blastn -query GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/markers.fasta -db /var/lib/cwl/stg7331e7a3-11da-4f94-973f-c8ecb183a8d8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:53:59,307] [INFO] Task succeeded: Blastn
[2023-06-05 00:53:59,312] [INFO] Selected 16 target genomes.
[2023-06-05 00:53:59,312] [INFO] Target genome list was writen to GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:53:59,637] [INFO] Task started: fastANI
[2023-06-05 00:53:59,637] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3200bb6-4574-4539-a1d5-e5f536a43b65/GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna.gz --refList GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/target_genomes_gtdb.txt --output GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:54:06,613] [INFO] Task succeeded: fastANI
[2023-06-05 00:54:06,623] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:54:06,623] [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_900316165.1	s__Weimeria sp900316165	97.5147	610	710	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Weimeria	95.0	98.03	96.72	0.87	0.80	4	conclusive
GCA_900317825.1	s__Weimeria sp900317825	80.7486	337	710	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Weimeria	95.0	98.68	98.26	0.87	0.76	11	-
GCA_003862155.1	s__Weimeria bifida	80.3926	321	710	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Weimeria	95.0	99.80	99.80	0.99	0.99	2	-
GCA_900315505.1	s__Weimeria sp900315505	79.3698	205	710	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Weimeria	95.0	97.28	95.87	0.90	0.84	6	-
GCA_002480925.1	s__Weimeria sp002480925	78.1801	168	710	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Weimeria	95.0	99.74	98.63	0.96	0.92	7	-
--------------------------------------------------------------------------------
[2023-06-05 00:54:06,625] [INFO] GTDB search result was written to GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/result_gtdb.tsv
[2023-06-05 00:54:06,625] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:54:06,628] [INFO] DFAST_QC result json was written to GCA_902773985.1_Rumen_uncultured_genome_RUG11920_genomic.fna/dqc_result.json
[2023-06-05 00:54:06,628] [INFO] DFAST_QC completed!
[2023-06-05 00:54:06,628] [INFO] Total running time: 0h0m54s