[2023-06-05 18:01:52,112] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:01:52,125] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:01:52,125] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2151e66-9163-4f27-8d4f-d63e8ccf8078/dqc_reference
[2023-06-05 18:01:53,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:01:53,360] [INFO] Task started: Prodigal
[2023-06-05 18:01:53,360] [INFO] Running command: gunzip -c /var/lib/cwl/stg53f13457-15e4-4ea2-a1aa-c7332fce6838/GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna.gz | prodigal -d GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/cds.fna -a GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:01:59,019] [INFO] Task succeeded: Prodigal
[2023-06-05 18:01:59,019] [INFO] Task started: HMMsearch
[2023-06-05 18:01:59,019] [INFO] Running command: hmmsearch --tblout GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2151e66-9163-4f27-8d4f-d63e8ccf8078/dqc_reference/reference_markers.hmm GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:01:59,429] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:01:59,431] [INFO] Found 6/6 markers.
[2023-06-05 18:01:59,463] [INFO] Query marker FASTA was written to GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/markers.fasta
[2023-06-05 18:01:59,463] [INFO] Task started: Blastn
[2023-06-05 18:01:59,463] [INFO] Running command: blastn -query GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2151e66-9163-4f27-8d4f-d63e8ccf8078/dqc_reference/reference_markers.fasta -out GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:00,617] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:00,621] [INFO] Selected 34 target genomes.
[2023-06-05 18:02:00,621] [INFO] Target genome list was writen to GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/target_genomes.txt
[2023-06-05 18:02:00,634] [INFO] Task started: fastANI
[2023-06-05 18:02:00,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg53f13457-15e4-4ea2-a1aa-c7332fce6838/GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna.gz --refList GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/target_genomes.txt --output GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:02:20,102] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:20,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2151e66-9163-4f27-8d4f-d63e8ccf8078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:02:20,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2151e66-9163-4f27-8d4f-d63e8ccf8078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:02:20,106] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:02:20,106] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:02:20,106] [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 18:02:20,121] [INFO] DFAST Taxonomy check result was written to GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/tc_result.tsv
[2023-06-05 18:02:20,123] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:02:20,123] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:02:20,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2151e66-9163-4f27-8d4f-d63e8ccf8078/dqc_reference/checkm_data
[2023-06-05 18:02:20,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:02:20,155] [INFO] Task started: CheckM
[2023-06-05 18:02:20,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/checkm_input GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/checkm_result
[2023-06-05 18:02:43,795] [INFO] Task succeeded: CheckM
[2023-06-05 18:02:43,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:02:43,850] [INFO] ===== Completeness check finished =====
[2023-06-05 18:02:43,850] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:02:43,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/markers.fasta)
[2023-06-05 18:02:43,852] [INFO] Task started: Blastn
[2023-06-05 18:02:43,852] [INFO] Running command: blastn -query GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2151e66-9163-4f27-8d4f-d63e8ccf8078/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:45,059] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:45,064] [INFO] Selected 16 target genomes.
[2023-06-05 18:02:45,064] [INFO] Target genome list was writen to GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:02:45,079] [INFO] Task started: fastANI
[2023-06-05 18:02:45,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg53f13457-15e4-4ea2-a1aa-c7332fce6838/GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna.gz --refList GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/target_genomes_gtdb.txt --output GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:02:52,619] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:52,637] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:02:52,637] [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_900315305.1	s__UBA1066 sp900315305	98.9871	595	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.26	98.90	0.90	0.82	11	conclusive
GCA_900320615.1	s__UBA1066 sp900320615	89.0472	474	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.42	99.12	0.88	0.79	4	-
GCA_900317045.1	s__UBA1066 sp900317045	77.5259	112	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.33	98.92	0.88	0.76	8	-
GCA_900317515.1	s__UBA1066 sp900317515	77.2612	87	658	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_002350625.1	s__UBA1066 sp002350625	77.2	93	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.93	99.93	0.93	0.93	2	-
GCA_900314565.1	s__UBA1066 sp900314565	77.0586	67	658	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.26	96.12	0.90	0.66	19	-
GCA_902766945.1	s__UBA1066 sp902766945	77.0291	73	658	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_902773195.1	s__UBA1066 sp902773195	76.8041	78	658	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	76.7759	79	658	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_002371465.1	s__UBA1066 sp002371465	76.6441	69	658	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_902766955.1	s__UBA1066 sp902766955	76.6287	77	658	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_902783325.1	s__UBA1066 sp902783325	76.0529	62	658	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 18:02:52,640] [INFO] GTDB search result was written to GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/result_gtdb.tsv
[2023-06-05 18:02:52,640] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:02:52,644] [INFO] DFAST_QC result json was written to GCA_902771765.1_Rumen_uncultured_genome_RUG11702_genomic.fna/dqc_result.json
[2023-06-05 18:02:52,644] [INFO] DFAST_QC completed!
[2023-06-05 18:02:52,644] [INFO] Total running time: 0h1m1s