[2023-06-05 02:43:09,258] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:43:09,263] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:43:09,264] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2476953-d283-43c8-829f-44ea42965e32/dqc_reference
[2023-06-05 02:43:10,590] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:43:10,591] [INFO] Task started: Prodigal
[2023-06-05 02:43:10,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg88e701f2-8124-4efd-844a-54a72e1c6886/GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna.gz | prodigal -d GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/cds.fna -a GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:43:14,484] [INFO] Task succeeded: Prodigal
[2023-06-05 02:43:14,485] [INFO] Task started: HMMsearch
[2023-06-05 02:43:14,485] [INFO] Running command: hmmsearch --tblout GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2476953-d283-43c8-829f-44ea42965e32/dqc_reference/reference_markers.hmm GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:43:14,747] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:43:14,748] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg88e701f2-8124-4efd-844a-54a72e1c6886/GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna.gz]
[2023-06-05 02:43:14,766] [INFO] Query marker FASTA was written to GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/markers.fasta
[2023-06-05 02:43:14,766] [INFO] Task started: Blastn
[2023-06-05 02:43:14,767] [INFO] Running command: blastn -query GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2476953-d283-43c8-829f-44ea42965e32/dqc_reference/reference_markers.fasta -out GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:43:15,383] [INFO] Task succeeded: Blastn
[2023-06-05 02:43:15,387] [INFO] Selected 28 target genomes.
[2023-06-05 02:43:15,388] [INFO] Target genome list was writen to GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/target_genomes.txt
[2023-06-05 02:43:15,390] [INFO] Task started: fastANI
[2023-06-05 02:43:15,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg88e701f2-8124-4efd-844a-54a72e1c6886/GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna.gz --refList GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/target_genomes.txt --output GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:43:34,735] [INFO] Task succeeded: fastANI
[2023-06-05 02:43:34,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2476953-d283-43c8-829f-44ea42965e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:43:34,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2476953-d283-43c8-829f-44ea42965e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:43:34,739] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:43:34,739] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:43:34,739] [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 02:43:34,741] [INFO] DFAST Taxonomy check result was written to GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/tc_result.tsv
[2023-06-05 02:43:34,742] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:43:34,743] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:43:34,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2476953-d283-43c8-829f-44ea42965e32/dqc_reference/checkm_data
[2023-06-05 02:43:34,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:43:34,772] [INFO] Task started: CheckM
[2023-06-05 02:43:34,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/checkm_input GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/checkm_result
[2023-06-05 02:43:54,286] [INFO] Task succeeded: CheckM
[2023-06-05 02:43:54,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:43:54,313] [INFO] ===== Completeness check finished =====
[2023-06-05 02:43:54,313] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:43:54,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/markers.fasta)
[2023-06-05 02:43:54,314] [INFO] Task started: Blastn
[2023-06-05 02:43:54,314] [INFO] Running command: blastn -query GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2476953-d283-43c8-829f-44ea42965e32/dqc_reference/reference_markers_gtdb.fasta -out GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:43:55,196] [INFO] Task succeeded: Blastn
[2023-06-05 02:43:55,200] [INFO] Selected 17 target genomes.
[2023-06-05 02:43:55,200] [INFO] Target genome list was writen to GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:43:55,205] [INFO] Task started: fastANI
[2023-06-05 02:43:55,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg88e701f2-8124-4efd-844a-54a72e1c6886/GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna.gz --refList GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/target_genomes_gtdb.txt --output GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:44:02,821] [INFO] Task succeeded: fastANI
[2023-06-05 02:44:02,842] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:44:02,843] [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_900314565.1	s__UBA1066 sp900314565	99.0535	480	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.26	96.12	0.90	0.66	19	conclusive
GCA_902785985.1	s__UBA1066 sp902785985	89.5104	384	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788035.1	s__UBA1066 sp902788035	78.6666	112	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.60	97.29	0.74	0.68	4	-
GCA_900317515.1	s__UBA1066 sp900317515	78.6643	118	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.06	96.06	0.86	0.79	9	-
GCA_017514845.1	s__UBA1066 sp017514845	78.3821	93	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315305.1	s__UBA1066 sp900315305	78.014	69	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.26	98.90	0.90	0.82	11	-
GCA_002369495.1	s__UBA1066 sp002369495	77.4766	90	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.09	98.09	0.78	0.78	2	-
GCA_003446335.1	s__UBA1066 sp003446335	76.9377	66	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320575.1	s__UBA1066 sp900320575	76.84	58	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.66	99.66	0.99	0.99	2	-
GCA_902766955.1	s__UBA1066 sp902766955	76.4665	52	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.96	97.96	0.75	0.75	2	-
GCA_902766655.1	s__UBA1066 sp902766655	76.4392	55	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773435.1	s__UBA1066 sp902773435	76.4286	50	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:44:02,845] [INFO] GTDB search result was written to GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/result_gtdb.tsv
[2023-06-05 02:44:02,846] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:44:02,849] [INFO] DFAST_QC result json was written to GCA_902781085.1_Rumen_uncultured_genome_RUG12641_genomic.fna/dqc_result.json
[2023-06-05 02:44:02,849] [INFO] DFAST_QC completed!
[2023-06-05 02:44:02,849] [INFO] Total running time: 0h0m54s