[2023-06-08 05:04:32,252] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:04:32,266] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:04:32,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgf75bbd27-16f4-40b5-a6e3-3dcd6cc07a86/dqc_reference
[2023-06-08 05:04:34,075] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:04:34,076] [INFO] Task started: Prodigal
[2023-06-08 05:04:34,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c444ab3-07d3-44ab-84fa-c52c7a9c1571/GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna.gz | prodigal -d GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/cds.fna -a GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:04:39,969] [INFO] Task succeeded: Prodigal
[2023-06-08 05:04:39,969] [INFO] Task started: HMMsearch
[2023-06-08 05:04:39,969] [INFO] Running command: hmmsearch --tblout GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf75bbd27-16f4-40b5-a6e3-3dcd6cc07a86/dqc_reference/reference_markers.hmm GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:04:40,157] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:04:40,159] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5c444ab3-07d3-44ab-84fa-c52c7a9c1571/GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna.gz]
[2023-06-08 05:04:40,191] [INFO] Query marker FASTA was written to GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/markers.fasta
[2023-06-08 05:04:40,192] [INFO] Task started: Blastn
[2023-06-08 05:04:40,192] [INFO] Running command: blastn -query GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/markers.fasta -db /var/lib/cwl/stgf75bbd27-16f4-40b5-a6e3-3dcd6cc07a86/dqc_reference/reference_markers.fasta -out GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:04:40,749] [INFO] Task succeeded: Blastn
[2023-06-08 05:04:40,752] [INFO] Selected 27 target genomes.
[2023-06-08 05:04:40,753] [INFO] Target genome list was writen to GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/target_genomes.txt
[2023-06-08 05:04:40,754] [INFO] Task started: fastANI
[2023-06-08 05:04:40,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c444ab3-07d3-44ab-84fa-c52c7a9c1571/GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna.gz --refList GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/target_genomes.txt --output GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:04:54,885] [INFO] Task succeeded: fastANI
[2023-06-08 05:04:54,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf75bbd27-16f4-40b5-a6e3-3dcd6cc07a86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:04:54,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf75bbd27-16f4-40b5-a6e3-3dcd6cc07a86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:04:54,893] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 05:04:54,894] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 05:04:54,894] [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
Porcincola intestinalis	strain=Oil+RF-744-WCA-WT-11	GCA_009696445.1	2606632	2606632	type	True	95.0454	464	662	95	conclusive
--------------------------------------------------------------------------------
[2023-06-08 05:04:54,896] [INFO] DFAST Taxonomy check result was written to GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/tc_result.tsv
[2023-06-08 05:04:54,896] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:04:54,896] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:04:54,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf75bbd27-16f4-40b5-a6e3-3dcd6cc07a86/dqc_reference/checkm_data
[2023-06-08 05:04:54,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:04:54,927] [INFO] Task started: CheckM
[2023-06-08 05:04:54,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/checkm_input GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/checkm_result
[2023-06-08 05:05:18,727] [INFO] Task succeeded: CheckM
[2023-06-08 05:05:18,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.19%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-08 05:05:18,744] [INFO] ===== Completeness check finished =====
[2023-06-08 05:05:18,744] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:05:18,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/markers.fasta)
[2023-06-08 05:05:18,744] [INFO] Task started: Blastn
[2023-06-08 05:05:18,745] [INFO] Running command: blastn -query GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/markers.fasta -db /var/lib/cwl/stgf75bbd27-16f4-40b5-a6e3-3dcd6cc07a86/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:05:19,577] [INFO] Task succeeded: Blastn
[2023-06-08 05:05:19,581] [INFO] Selected 19 target genomes.
[2023-06-08 05:05:19,581] [INFO] Target genome list was writen to GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:05:19,583] [INFO] Task started: fastANI
[2023-06-08 05:05:19,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c444ab3-07d3-44ab-84fa-c52c7a9c1571/GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna.gz --refList GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/target_genomes_gtdb.txt --output GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:05:28,522] [INFO] Task succeeded: fastANI
[2023-06-08 05:05:28,529] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-08 05:05:28,529] [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_902761585.1	s__Porcincola sp902800805	97.8791	428	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	98.06	97.58	0.81	0.65	18	inconclusive
GCF_009696445.1	s__Porcincola intestinalis	95.0454	464	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	97.03	96.19	0.86	0.71	6	inconclusive
GCA_900555005.1	s__Porcincola sp900555005	90.5413	311	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	99.94	99.94	0.95	0.95	2	-
GCA_002482005.1	s__Porcincola sp002482005	79.2396	195	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781455.1	s__Porcincola sp902781455	78.145	59	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797665.1	s__Porcincola sp902797665	77.3469	60	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235415.1	s__Porcincola sp905235415	76.6981	74	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 05:05:28,531] [INFO] GTDB search result was written to GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/result_gtdb.tsv
[2023-06-08 05:05:28,532] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:05:28,534] [INFO] DFAST_QC result json was written to GCA_902800235.1_Rumen_uncultured_genome_RUG14553_genomic.fna/dqc_result.json
[2023-06-08 05:05:28,534] [INFO] DFAST_QC completed!
[2023-06-08 05:05:28,534] [INFO] Total running time: 0h0m56s