[2023-06-05 01:17:59,292] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:17:59,295] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:17:59,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg537a3a8d-6e03-4190-966f-dce18857c599/dqc_reference
[2023-06-05 01:18:00,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:18:00,609] [INFO] Task started: Prodigal
[2023-06-05 01:18:00,609] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dcc6c05-6bac-48e4-bd07-7cdae4341e33/GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna.gz | prodigal -d GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/cds.fna -a GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:18:06,886] [INFO] Task succeeded: Prodigal
[2023-06-05 01:18:06,887] [INFO] Task started: HMMsearch
[2023-06-05 01:18:06,887] [INFO] Running command: hmmsearch --tblout GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg537a3a8d-6e03-4190-966f-dce18857c599/dqc_reference/reference_markers.hmm GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:18:07,144] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:18:07,146] [INFO] Found 6/6 markers.
[2023-06-05 01:18:07,170] [INFO] Query marker FASTA was written to GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/markers.fasta
[2023-06-05 01:18:07,171] [INFO] Task started: Blastn
[2023-06-05 01:18:07,171] [INFO] Running command: blastn -query GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/markers.fasta -db /var/lib/cwl/stg537a3a8d-6e03-4190-966f-dce18857c599/dqc_reference/reference_markers.fasta -out GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:07,848] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:07,853] [INFO] Selected 31 target genomes.
[2023-06-05 01:18:07,853] [INFO] Target genome list was writen to GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/target_genomes.txt
[2023-06-05 01:18:07,882] [INFO] Task started: fastANI
[2023-06-05 01:18:07,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dcc6c05-6bac-48e4-bd07-7cdae4341e33/GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna.gz --refList GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/target_genomes.txt --output GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:18:25,212] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:25,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg537a3a8d-6e03-4190-966f-dce18857c599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:18:25,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg537a3a8d-6e03-4190-966f-dce18857c599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:18:25,217] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:18:25,217] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:18:25,217] [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	77.9054	88	763	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:18:25,219] [INFO] DFAST Taxonomy check result was written to GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/tc_result.tsv
[2023-06-05 01:18:25,219] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:18:25,220] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:18:25,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg537a3a8d-6e03-4190-966f-dce18857c599/dqc_reference/checkm_data
[2023-06-05 01:18:25,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:18:25,246] [INFO] Task started: CheckM
[2023-06-05 01:18:25,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/checkm_input GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/checkm_result
[2023-06-05 01:18:50,888] [INFO] Task succeeded: CheckM
[2023-06-05 01:18:50,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 12.50%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-06-05 01:18:50,915] [INFO] ===== Completeness check finished =====
[2023-06-05 01:18:50,916] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:18:50,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/markers.fasta)
[2023-06-05 01:18:50,917] [INFO] Task started: Blastn
[2023-06-05 01:18:50,917] [INFO] Running command: blastn -query GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/markers.fasta -db /var/lib/cwl/stg537a3a8d-6e03-4190-966f-dce18857c599/dqc_reference/reference_markers_gtdb.fasta -out GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:52,013] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:52,018] [INFO] Selected 14 target genomes.
[2023-06-05 01:18:52,018] [INFO] Target genome list was writen to GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:18:52,023] [INFO] Task started: fastANI
[2023-06-05 01:18:52,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dcc6c05-6bac-48e4-bd07-7cdae4341e33/GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna.gz --refList GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/target_genomes_gtdb.txt --output GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:18:58,068] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:58,083] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:18:58,083] [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_902781455.1	s__Porcincola sp902781455	100.0	760	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902799015.1	s__Porcincola sp902799015	80.9827	358	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	98.95	98.88	0.78	0.76	3	-
GCA_900321365.1	s__Porcincola sp900321365	79.7479	266	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	100.00	100.00	0.98	0.98	2	-
GCA_002371345.1	s__Porcincola sp002371345	79.2819	254	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	98.87	98.75	0.86	0.84	4	-
GCA_905236545.1	s__Porcincola sp905236545	79.1397	251	763	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_902767065.1	s__Porcincola sp902767065	79.0373	196	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	98.57	98.57	0.82	0.82	2	-
GCA_902765725.1	s__Porcincola sp002350685	78.3919	198	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	99.96	99.96	0.96	0.96	2	-
GCA_902801515.1	s__Porcincola sp902801515	78.3317	183	763	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	78.2171	191	763	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_900313765.1	s__Porcincola sp900313765	78.1671	146	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	98.06	96.12	0.84	0.70	3	-
GCA_902803155.1	s__Porcincola sp902803155	77.3074	138	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:18:58,085] [INFO] GTDB search result was written to GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/result_gtdb.tsv
[2023-06-05 01:18:58,085] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:18:58,095] [INFO] DFAST_QC result json was written to GCA_902781455.1_Rumen_uncultured_genome_RUG12671_genomic.fna/dqc_result.json
[2023-06-05 01:18:58,095] [INFO] DFAST_QC completed!
[2023-06-05 01:18:58,095] [INFO] Total running time: 0h0m59s