[2023-06-08 10:25:16,929] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:25:16,931] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:25:16,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8983f24-9222-4568-a0d8-f06e1835e631/dqc_reference
[2023-06-08 10:25:18,191] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:25:18,192] [INFO] Task started: Prodigal
[2023-06-08 10:25:18,192] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0959172-8da7-4f09-b5a7-f514850a79bb/GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna.gz | prodigal -d GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/cds.fna -a GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:25:23,047] [INFO] Task succeeded: Prodigal
[2023-06-08 10:25:23,047] [INFO] Task started: HMMsearch
[2023-06-08 10:25:23,047] [INFO] Running command: hmmsearch --tblout GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8983f24-9222-4568-a0d8-f06e1835e631/dqc_reference/reference_markers.hmm GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:25:23,297] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:25:23,298] [INFO] Found 6/6 markers.
[2023-06-08 10:25:23,327] [INFO] Query marker FASTA was written to GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/markers.fasta
[2023-06-08 10:25:23,328] [INFO] Task started: Blastn
[2023-06-08 10:25:23,328] [INFO] Running command: blastn -query GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8983f24-9222-4568-a0d8-f06e1835e631/dqc_reference/reference_markers.fasta -out GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:25:23,908] [INFO] Task succeeded: Blastn
[2023-06-08 10:25:23,913] [INFO] Selected 22 target genomes.
[2023-06-08 10:25:23,913] [INFO] Target genome list was writen to GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/target_genomes.txt
[2023-06-08 10:25:23,916] [INFO] Task started: fastANI
[2023-06-08 10:25:23,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0959172-8da7-4f09-b5a7-f514850a79bb/GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna.gz --refList GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/target_genomes.txt --output GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:25:34,745] [INFO] Task succeeded: fastANI
[2023-06-08 10:25:34,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8983f24-9222-4568-a0d8-f06e1835e631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:25:34,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8983f24-9222-4568-a0d8-f06e1835e631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:25:34,751] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:25:34,751] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 10:25:34,752] [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
Butyrivibrio proteoclasticus	strain=B316	GCA_000145035.1	43305	43305	type	True	77.3437	51	681	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 10:25:34,753] [INFO] DFAST Taxonomy check result was written to GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/tc_result.tsv
[2023-06-08 10:25:34,754] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:25:34,754] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:25:34,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8983f24-9222-4568-a0d8-f06e1835e631/dqc_reference/checkm_data
[2023-06-08 10:25:34,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:25:34,779] [INFO] Task started: CheckM
[2023-06-08 10:25:34,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/checkm_input GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/checkm_result
[2023-06-08 10:25:57,165] [INFO] Task succeeded: CheckM
[2023-06-08 10:25:57,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 7.41%
Strain heterogeneity: 12.50%
--------------------------------------------------------------------------------
[2023-06-08 10:25:57,205] [INFO] ===== Completeness check finished =====
[2023-06-08 10:25:57,205] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:25:57,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/markers.fasta)
[2023-06-08 10:25:57,206] [INFO] Task started: Blastn
[2023-06-08 10:25:57,206] [INFO] Running command: blastn -query GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8983f24-9222-4568-a0d8-f06e1835e631/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:25:58,020] [INFO] Task succeeded: Blastn
[2023-06-08 10:25:58,023] [INFO] Selected 18 target genomes.
[2023-06-08 10:25:58,024] [INFO] Target genome list was writen to GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:25:58,035] [INFO] Task started: fastANI
[2023-06-08 10:25:58,035] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0959172-8da7-4f09-b5a7-f514850a79bb/GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna.gz --refList GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/target_genomes_gtdb.txt --output GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:26:04,971] [INFO] Task succeeded: fastANI
[2023-06-08 10:26:04,986] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:26:04,986] [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_902779505.1	s__UBA1712 sp902779505	98.0379	544	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	98.45	98.04	0.85	0.80	3	conclusive
GCA_018056665.1	s__UBA1712 sp018056665	78.4556	100	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	98.04	97.91	0.92	0.92	3	-
GCA_900766815.1	s__UBA1712 sp900766815	78.4207	92	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	98.38	98.38	0.86	0.86	2	-
GCA_018064425.1	s__UBA1712 sp018064425	78.3526	106	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789785.1	s__UBA1712 sp902789785	78.3032	65	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	97.67	97.20	0.85	0.79	3	-
GCA_902778165.1	s__UBA1712 sp902778165	78.1696	128	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	97.58	97.58	0.88	0.88	2	-
GCA_002317245.1	s__UBA1712 sp002317245	78.0896	87	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540355.1	s__UBA1712 sp017540355	77.445	102	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	97.99	97.99	0.85	0.85	2	-
GCA_905235845.1	s__UBA1712 sp905235845	77.2083	76	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424265.1	s__Butyrivibrio sp000424265	77.0902	57	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002393095.1	s__UBA1712 sp002393095	76.9068	56	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	99.62	99.62	0.88	0.88	2	-
GCA_017961385.1	s__UBA1712 sp017961385	76.8146	53	681	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	98.30	98.30	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-08 10:26:04,988] [INFO] GTDB search result was written to GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/result_gtdb.tsv
[2023-06-08 10:26:04,988] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:26:04,992] [INFO] DFAST_QC result json was written to GCA_902778465.1_Rumen_uncultured_genome_RUG12370_genomic.fna/dqc_result.json
[2023-06-08 10:26:04,992] [INFO] DFAST_QC completed!
[2023-06-08 10:26:04,992] [INFO] Total running time: 0h0m48s