[2023-06-07 19:05:02,303] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:05:02,308] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:05:02,308] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdb8c571-a622-4ec5-9187-e9a2c701acba/dqc_reference
[2023-06-07 19:05:03,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:05:03,685] [INFO] Task started: Prodigal
[2023-06-07 19:05:03,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c79d519-0913-4aca-9e2f-0d2f8ef36b5a/GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna.gz | prodigal -d GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/cds.fna -a GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:05:09,963] [INFO] Task succeeded: Prodigal
[2023-06-07 19:05:09,964] [INFO] Task started: HMMsearch
[2023-06-07 19:05:09,964] [INFO] Running command: hmmsearch --tblout GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdb8c571-a622-4ec5-9187-e9a2c701acba/dqc_reference/reference_markers.hmm GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:05:10,233] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:05:10,235] [INFO] Found 6/6 markers.
[2023-06-07 19:05:10,268] [INFO] Query marker FASTA was written to GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/markers.fasta
[2023-06-07 19:05:10,268] [INFO] Task started: Blastn
[2023-06-07 19:05:10,268] [INFO] Running command: blastn -query GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdb8c571-a622-4ec5-9187-e9a2c701acba/dqc_reference/reference_markers.fasta -out GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:05:10,875] [INFO] Task succeeded: Blastn
[2023-06-07 19:05:10,880] [INFO] Selected 25 target genomes.
[2023-06-07 19:05:10,880] [INFO] Target genome list was writen to GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/target_genomes.txt
[2023-06-07 19:05:10,911] [INFO] Task started: fastANI
[2023-06-07 19:05:10,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c79d519-0913-4aca-9e2f-0d2f8ef36b5a/GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna.gz --refList GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/target_genomes.txt --output GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:05:29,299] [INFO] Task succeeded: fastANI
[2023-06-07 19:05:29,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdb8c571-a622-4ec5-9187-e9a2c701acba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:05:29,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdb8c571-a622-4ec5-9187-e9a2c701acba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:05:29,303] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:05:29,303] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 19:05:29,303] [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
--------------------------------------------------------------------------------
[2023-06-07 19:05:29,308] [INFO] DFAST Taxonomy check result was written to GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/tc_result.tsv
[2023-06-07 19:05:29,309] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:05:29,309] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:05:29,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdb8c571-a622-4ec5-9187-e9a2c701acba/dqc_reference/checkm_data
[2023-06-07 19:05:29,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:05:29,344] [INFO] Task started: CheckM
[2023-06-07 19:05:29,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/checkm_input GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/checkm_result
[2023-06-07 19:05:53,288] [INFO] Task succeeded: CheckM
[2023-06-07 19:05:53,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:05:53,319] [INFO] ===== Completeness check finished =====
[2023-06-07 19:05:53,320] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:05:53,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/markers.fasta)
[2023-06-07 19:05:53,320] [INFO] Task started: Blastn
[2023-06-07 19:05:53,321] [INFO] Running command: blastn -query GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdb8c571-a622-4ec5-9187-e9a2c701acba/dqc_reference/reference_markers_gtdb.fasta -out GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:05:54,134] [INFO] Task succeeded: Blastn
[2023-06-07 19:05:54,139] [INFO] Selected 13 target genomes.
[2023-06-07 19:05:54,140] [INFO] Target genome list was writen to GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:05:54,151] [INFO] Task started: fastANI
[2023-06-07 19:05:54,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c79d519-0913-4aca-9e2f-0d2f8ef36b5a/GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna.gz --refList GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/target_genomes_gtdb.txt --output GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:06:00,272] [INFO] Task succeeded: fastANI
[2023-06-07 19:06:00,280] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 19:06:00,280] [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_002448475.1	s__UBA3636 sp002448475	97.2806	540	604	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	97.08	96.88	0.80	0.71	3	conclusive
GCA_017476965.1	s__UBA3636 sp017476965	78.9427	133	604	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	95.60	95.60	0.67	0.67	2	-
GCA_902761575.1	s__UBA3636 sp902761575	78.301	162	604	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	96.69	96.69	0.81	0.81	2	-
GCA_017413145.1	s__UBA3636 sp017413145	77.8051	130	604	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793555.1	s__UBA3636 sp902793555	77.6491	164	604	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017457625.1	s__UBA3636 sp017457625	77.6105	147	604	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017450425.1	s__UBA3636 sp017450425	76.8799	87	604	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 19:06:00,282] [INFO] GTDB search result was written to GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/result_gtdb.tsv
[2023-06-07 19:06:00,283] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:06:00,286] [INFO] DFAST_QC result json was written to GCA_902772875.1_Rumen_uncultured_genome_RUG11812_genomic.fna/dqc_result.json
[2023-06-07 19:06:00,286] [INFO] DFAST_QC completed!
[2023-06-07 19:06:00,286] [INFO] Total running time: 0h0m58s