[2023-06-08 01:36:48,000] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:36:48,003] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:36:48,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg01943838-6b8e-4c9a-b3d0-b20ad2c15ed2/dqc_reference
[2023-06-08 01:36:50,236] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:36:50,237] [INFO] Task started: Prodigal
[2023-06-08 01:36:50,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg76bc9872-9a57-48de-8cb0-17fd88e2b6b3/GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna.gz | prodigal -d GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/cds.fna -a GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:36:56,670] [INFO] Task succeeded: Prodigal
[2023-06-08 01:36:56,670] [INFO] Task started: HMMsearch
[2023-06-08 01:36:56,671] [INFO] Running command: hmmsearch --tblout GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01943838-6b8e-4c9a-b3d0-b20ad2c15ed2/dqc_reference/reference_markers.hmm GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:36:56,897] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:36:56,898] [INFO] Found 6/6 markers.
[2023-06-08 01:36:56,932] [INFO] Query marker FASTA was written to GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/markers.fasta
[2023-06-08 01:36:56,933] [INFO] Task started: Blastn
[2023-06-08 01:36:56,933] [INFO] Running command: blastn -query GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/markers.fasta -db /var/lib/cwl/stg01943838-6b8e-4c9a-b3d0-b20ad2c15ed2/dqc_reference/reference_markers.fasta -out GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:36:57,514] [INFO] Task succeeded: Blastn
[2023-06-08 01:36:57,519] [INFO] Selected 17 target genomes.
[2023-06-08 01:36:57,519] [INFO] Target genome list was writen to GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/target_genomes.txt
[2023-06-08 01:36:57,522] [INFO] Task started: fastANI
[2023-06-08 01:36:57,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg76bc9872-9a57-48de-8cb0-17fd88e2b6b3/GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna.gz --refList GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/target_genomes.txt --output GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:37:08,209] [INFO] Task succeeded: fastANI
[2023-06-08 01:37:08,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01943838-6b8e-4c9a-b3d0-b20ad2c15ed2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:37:08,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01943838-6b8e-4c9a-b3d0-b20ad2c15ed2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:37:08,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 01:37:08,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 01:37:08,212] [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 01:37:08,215] [INFO] DFAST Taxonomy check result was written to GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/tc_result.tsv
[2023-06-08 01:37:08,215] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:37:08,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:37:08,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01943838-6b8e-4c9a-b3d0-b20ad2c15ed2/dqc_reference/checkm_data
[2023-06-08 01:37:08,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:37:08,250] [INFO] Task started: CheckM
[2023-06-08 01:37:08,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/checkm_input GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/checkm_result
[2023-06-08 01:37:34,247] [INFO] Task succeeded: CheckM
[2023-06-08 01:37:34,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 21.88%
Strain heterogeneity: 52.94%
--------------------------------------------------------------------------------
[2023-06-08 01:37:34,274] [INFO] ===== Completeness check finished =====
[2023-06-08 01:37:34,274] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:37:34,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/markers.fasta)
[2023-06-08 01:37:34,275] [INFO] Task started: Blastn
[2023-06-08 01:37:34,275] [INFO] Running command: blastn -query GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/markers.fasta -db /var/lib/cwl/stg01943838-6b8e-4c9a-b3d0-b20ad2c15ed2/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:37:35,070] [INFO] Task succeeded: Blastn
[2023-06-08 01:37:35,077] [INFO] Selected 15 target genomes.
[2023-06-08 01:37:35,077] [INFO] Target genome list was writen to GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:37:35,086] [INFO] Task started: fastANI
[2023-06-08 01:37:35,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg76bc9872-9a57-48de-8cb0-17fd88e2b6b3/GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna.gz --refList GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/target_genomes_gtdb.txt --output GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:37:43,830] [INFO] Task succeeded: fastANI
[2023-06-08 01:37:43,842] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 01:37:43,842] [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_900321785.1	s__CAG-791 sp900321785	99.0353	502	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.92	97.67	0.83	0.75	9	conclusive
GCA_902780385.1	s__CAG-791 sp902780385	82.1251	412	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.16	97.16	0.72	0.72	2	-
GCA_002390025.1	s__CAG-791 sp002390025	81.8949	380	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318375.1	s__CAG-791 sp900318375	81.691	410	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.93	99.93	0.92	0.92	2	-
GCA_902777355.1	s__CAG-791 sp902777355	80.0928	309	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781215.1	s__CAG-791 sp902781215	80.0637	287	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	96.36	96.36	0.81	0.81	2	-
GCA_017513005.1	s__CAG-791 sp017513005	79.5933	220	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.02	99.02	0.89	0.89	2	-
GCF_900101015.1	s__CAG-791 sp900101015	79.4645	265	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.38	97.83	0.92	0.75	35	-
GCA_002394525.1	s__CAG-791 sp002394525	79.3231	213	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.96	97.96	0.79	0.79	2	-
GCA_002358875.1	s__CAG-791 sp002358875	78.6747	205	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801415.1	s__CAG-791 sp902801415	78.3236	107	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.60	97.44	0.77	0.76	3	-
--------------------------------------------------------------------------------
[2023-06-08 01:37:43,844] [INFO] GTDB search result was written to GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/result_gtdb.tsv
[2023-06-08 01:37:43,844] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:37:43,847] [INFO] DFAST_QC result json was written to GCA_902778435.1_Rumen_uncultured_genome_RUG12369_genomic.fna/dqc_result.json
[2023-06-08 01:37:43,848] [INFO] DFAST_QC completed!
[2023-06-08 01:37:43,848] [INFO] Total running time: 0h0m56s