[2023-06-05 01:08:35,888] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:08:35,891] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:08:35,891] [INFO] DQC Reference Directory: /var/lib/cwl/stga7bfb74f-aaeb-48b7-a91d-7309dece1ed8/dqc_reference
[2023-06-05 01:08:37,211] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:08:37,212] [INFO] Task started: Prodigal
[2023-06-05 01:08:37,212] [INFO] Running command: gunzip -c /var/lib/cwl/stg80fef480-e8f2-45ed-a27d-d753192d1596/GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna.gz | prodigal -d GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/cds.fna -a GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:08:44,243] [INFO] Task succeeded: Prodigal
[2023-06-05 01:08:44,243] [INFO] Task started: HMMsearch
[2023-06-05 01:08:44,243] [INFO] Running command: hmmsearch --tblout GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7bfb74f-aaeb-48b7-a91d-7309dece1ed8/dqc_reference/reference_markers.hmm GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:08:44,522] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:08:44,524] [INFO] Found 6/6 markers.
[2023-06-05 01:08:44,557] [INFO] Query marker FASTA was written to GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/markers.fasta
[2023-06-05 01:08:44,557] [INFO] Task started: Blastn
[2023-06-05 01:08:44,557] [INFO] Running command: blastn -query GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/markers.fasta -db /var/lib/cwl/stga7bfb74f-aaeb-48b7-a91d-7309dece1ed8/dqc_reference/reference_markers.fasta -out GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:08:45,248] [INFO] Task succeeded: Blastn
[2023-06-05 01:08:45,252] [INFO] Selected 31 target genomes.
[2023-06-05 01:08:45,252] [INFO] Target genome list was writen to GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/target_genomes.txt
[2023-06-05 01:08:45,255] [INFO] Task started: fastANI
[2023-06-05 01:08:45,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg80fef480-e8f2-45ed-a27d-d753192d1596/GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna.gz --refList GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/target_genomes.txt --output GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:09:01,973] [INFO] Task succeeded: fastANI
[2023-06-05 01:09:01,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7bfb74f-aaeb-48b7-a91d-7309dece1ed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:09:01,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7bfb74f-aaeb-48b7-a91d-7309dece1ed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:09:01,977] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:09:01,977] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 01:09:01,977] [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 01:09:01,980] [INFO] DFAST Taxonomy check result was written to GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/tc_result.tsv
[2023-06-05 01:09:01,980] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:09:01,981] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:09:01,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7bfb74f-aaeb-48b7-a91d-7309dece1ed8/dqc_reference/checkm_data
[2023-06-05 01:09:01,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:09:02,016] [INFO] Task started: CheckM
[2023-06-05 01:09:02,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/checkm_input GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/checkm_result
[2023-06-05 01:09:28,473] [INFO] Task succeeded: CheckM
[2023-06-05 01:09:28,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:09:28,493] [INFO] ===== Completeness check finished =====
[2023-06-05 01:09:28,493] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:09:28,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/markers.fasta)
[2023-06-05 01:09:28,494] [INFO] Task started: Blastn
[2023-06-05 01:09:28,494] [INFO] Running command: blastn -query GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/markers.fasta -db /var/lib/cwl/stga7bfb74f-aaeb-48b7-a91d-7309dece1ed8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:09:29,764] [INFO] Task succeeded: Blastn
[2023-06-05 01:09:29,769] [INFO] Selected 15 target genomes.
[2023-06-05 01:09:29,769] [INFO] Target genome list was writen to GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:09:29,778] [INFO] Task started: fastANI
[2023-06-05 01:09:29,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg80fef480-e8f2-45ed-a27d-d753192d1596/GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna.gz --refList GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/target_genomes_gtdb.txt --output GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:09:38,542] [INFO] Task succeeded: fastANI
[2023-06-05 01:09:38,559] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:09:38,559] [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_902787715.1	s__ISDg sp902787715	98.0556	677	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	97.81	96.48	0.87	0.76	10	conclusive
GCA_902798585.1	s__ISDg sp902798585	83.3005	492	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	98.31	98.31	0.90	0.90	2	-
GCA_017617395.1	s__ISDg sp017617395	82.6683	462	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783725.1	s__ISDg sp902783725	82.4408	403	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	98.33	98.33	0.97	0.97	2	-
GCA_017561985.1	s__ISDg sp017561985	80.7977	211	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017441265.1	s__ISDg sp017441265	80.7267	344	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617545.1	s__ISDg sp017617545	80.2634	363	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002311665.1	s__ISDg sp002311665	79.9852	359	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	99.98	99.98	0.98	0.98	2	-
GCA_017551165.1	s__ISDg sp017551165	79.9813	345	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795625.1	s__ISDg sp902795625	79.4409	229	795	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__ISDg	95.0	97.87	97.87	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-05 01:09:38,561] [INFO] GTDB search result was written to GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/result_gtdb.tsv
[2023-06-05 01:09:38,562] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:09:38,565] [INFO] DFAST_QC result json was written to GCA_902792675.1_Rumen_uncultured_genome_RUG13801_genomic.fna/dqc_result.json
[2023-06-05 01:09:38,565] [INFO] DFAST_QC completed!
[2023-06-05 01:09:38,565] [INFO] Total running time: 0h1m3s