[2023-06-04 21:25:23,718] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:25:23,728] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:25:23,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg652d6950-1d72-4831-890d-c4d00e8b80f7/dqc_reference
[2023-06-04 21:25:26,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:25:26,951] [INFO] Task started: Prodigal
[2023-06-04 21:25:26,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b708f7f-ca9e-48cd-8fbb-a5c614084496/GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna.gz | prodigal -d GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/cds.fna -a GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:25:35,738] [INFO] Task succeeded: Prodigal
[2023-06-04 21:25:35,738] [INFO] Task started: HMMsearch
[2023-06-04 21:25:35,739] [INFO] Running command: hmmsearch --tblout GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg652d6950-1d72-4831-890d-c4d00e8b80f7/dqc_reference/reference_markers.hmm GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:25:35,989] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:25:35,991] [INFO] Found 6/6 markers.
[2023-06-04 21:25:36,042] [INFO] Query marker FASTA was written to GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/markers.fasta
[2023-06-04 21:25:36,043] [INFO] Task started: Blastn
[2023-06-04 21:25:36,043] [INFO] Running command: blastn -query GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/markers.fasta -db /var/lib/cwl/stg652d6950-1d72-4831-890d-c4d00e8b80f7/dqc_reference/reference_markers.fasta -out GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:25:36,712] [INFO] Task succeeded: Blastn
[2023-06-04 21:25:36,717] [INFO] Selected 27 target genomes.
[2023-06-04 21:25:36,718] [INFO] Target genome list was writen to GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/target_genomes.txt
[2023-06-04 21:25:36,778] [INFO] Task started: fastANI
[2023-06-04 21:25:36,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b708f7f-ca9e-48cd-8fbb-a5c614084496/GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna.gz --refList GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/target_genomes.txt --output GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:25:54,356] [INFO] Task succeeded: fastANI
[2023-06-04 21:25:54,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg652d6950-1d72-4831-890d-c4d00e8b80f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:25:54,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg652d6950-1d72-4831-890d-c4d00e8b80f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:25:54,364] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:25:54,365] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 21:25:54,365] [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
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	77.2346	80	1023	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 21:25:54,367] [INFO] DFAST Taxonomy check result was written to GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/tc_result.tsv
[2023-06-04 21:25:54,368] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:25:54,368] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:25:54,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg652d6950-1d72-4831-890d-c4d00e8b80f7/dqc_reference/checkm_data
[2023-06-04 21:25:54,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:25:54,406] [INFO] Task started: CheckM
[2023-06-04 21:25:54,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/checkm_input GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/checkm_result
[2023-06-04 21:26:25,090] [INFO] Task succeeded: CheckM
[2023-06-04 21:26:25,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:26:25,126] [INFO] ===== Completeness check finished =====
[2023-06-04 21:26:25,127] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:26:25,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/markers.fasta)
[2023-06-04 21:26:25,127] [INFO] Task started: Blastn
[2023-06-04 21:26:25,128] [INFO] Running command: blastn -query GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/markers.fasta -db /var/lib/cwl/stg652d6950-1d72-4831-890d-c4d00e8b80f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:26:26,240] [INFO] Task succeeded: Blastn
[2023-06-04 21:26:26,248] [INFO] Selected 19 target genomes.
[2023-06-04 21:26:26,248] [INFO] Target genome list was writen to GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:26:26,282] [INFO] Task started: fastANI
[2023-06-04 21:26:26,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b708f7f-ca9e-48cd-8fbb-a5c614084496/GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna.gz --refList GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/target_genomes_gtdb.txt --output GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:26:34,778] [INFO] Task succeeded: fastANI
[2023-06-04 21:26:34,794] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:26:34,794] [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_900318875.1	s__CAG-791 sp900318875	98.8886	749	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.20	98.52	0.87	0.80	24	conclusive
GCA_900315055.1	s__CAG-791 sp900315055	79.1435	299	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.03	98.45	0.88	0.84	8	-
GCA_002353635.1	s__CAG-791 sp002353635	78.9545	143	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431495.1	s__CAG-791 sp000431495	77.6229	106	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.54	97.54	0.90	0.90	2	-
GCA_900107575.1	s__CAG-791 sp900107575	77.5377	167	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316855.1	s__CAG-791 sp900316855	77.438	168	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002372815.1	s__CAG-791 sp002372815	76.9621	86	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449745.1	s__CAG-791 sp017449745	76.9503	94	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781215.1	s__CAG-791 sp902781215	76.9157	113	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	96.36	96.36	0.81	0.81	2	-
GCA_002395235.1	s__CAG-791 sp002395235	76.5397	78	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766175.1	s__Stomatobaculum sp902766175	76.4825	52	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469935.1	s__CAG-791 sp017469935	76.3804	80	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002392385.1	s__CAG-791 sp002392385	76.3231	55	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796425.1	s__CAG-791 sp902796425	76.1999	93	1023	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 21:26:34,796] [INFO] GTDB search result was written to GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/result_gtdb.tsv
[2023-06-04 21:26:34,797] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:26:34,821] [INFO] DFAST_QC result json was written to GCA_902782075.1_Rumen_uncultured_genome_RUG12737_genomic.fna/dqc_result.json
[2023-06-04 21:26:34,821] [INFO] DFAST_QC completed!
[2023-06-04 21:26:34,821] [INFO] Total running time: 0h1m11s