[2023-06-18 17:28:54,670] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:28:54,672] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:28:54,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg24f2e219-631e-4f58-b83a-7fc65f3e9f33/dqc_reference
[2023-06-18 17:28:55,771] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:28:55,771] [INFO] Task started: Prodigal
[2023-06-18 17:28:55,772] [INFO] Running command: gunzip -c /var/lib/cwl/stgeba762ed-3b19-4c72-a72a-5f04d959c2b7/GCA_013139765.1_ASM1313976v1_genomic.fna.gz | prodigal -d GCA_013139765.1_ASM1313976v1_genomic.fna/cds.fna -a GCA_013139765.1_ASM1313976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:28:59,473] [INFO] Task succeeded: Prodigal
[2023-06-18 17:28:59,473] [INFO] Task started: HMMsearch
[2023-06-18 17:28:59,473] [INFO] Running command: hmmsearch --tblout GCA_013139765.1_ASM1313976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24f2e219-631e-4f58-b83a-7fc65f3e9f33/dqc_reference/reference_markers.hmm GCA_013139765.1_ASM1313976v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:28:59,645] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:28:59,646] [INFO] Found 6/6 markers.
[2023-06-18 17:28:59,665] [INFO] Query marker FASTA was written to GCA_013139765.1_ASM1313976v1_genomic.fna/markers.fasta
[2023-06-18 17:28:59,666] [INFO] Task started: Blastn
[2023-06-18 17:28:59,666] [INFO] Running command: blastn -query GCA_013139765.1_ASM1313976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24f2e219-631e-4f58-b83a-7fc65f3e9f33/dqc_reference/reference_markers.fasta -out GCA_013139765.1_ASM1313976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:29:00,199] [INFO] Task succeeded: Blastn
[2023-06-18 17:29:00,206] [INFO] Selected 35 target genomes.
[2023-06-18 17:29:00,206] [INFO] Target genome list was writen to GCA_013139765.1_ASM1313976v1_genomic.fna/target_genomes.txt
[2023-06-18 17:29:00,209] [INFO] Task started: fastANI
[2023-06-18 17:29:00,210] [INFO] Running command: fastANI --query /var/lib/cwl/stgeba762ed-3b19-4c72-a72a-5f04d959c2b7/GCA_013139765.1_ASM1313976v1_genomic.fna.gz --refList GCA_013139765.1_ASM1313976v1_genomic.fna/target_genomes.txt --output GCA_013139765.1_ASM1313976v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:29:11,365] [INFO] Task succeeded: fastANI
[2023-06-18 17:29:11,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24f2e219-631e-4f58-b83a-7fc65f3e9f33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:29:11,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24f2e219-631e-4f58-b83a-7fc65f3e9f33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:29:11,369] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:29:11,369] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:29:11,369] [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
Sulfurovum lithotrophicum	strain=ATCC BAA-797	GCA_000987835.1	206403	206403	type	True	76.2846	57	598	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:29:11,370] [INFO] DFAST Taxonomy check result was written to GCA_013139765.1_ASM1313976v1_genomic.fna/tc_result.tsv
[2023-06-18 17:29:11,373] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:29:11,374] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:29:11,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24f2e219-631e-4f58-b83a-7fc65f3e9f33/dqc_reference/checkm_data
[2023-06-18 17:29:11,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:29:11,400] [INFO] Task started: CheckM
[2023-06-18 17:29:11,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013139765.1_ASM1313976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013139765.1_ASM1313976v1_genomic.fna/checkm_input GCA_013139765.1_ASM1313976v1_genomic.fna/checkm_result
[2023-06-18 17:29:28,399] [INFO] Task succeeded: CheckM
[2023-06-18 17:29:28,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.96%
Contamintation: 20.83%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 17:29:28,423] [INFO] ===== Completeness check finished =====
[2023-06-18 17:29:28,423] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:29:28,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013139765.1_ASM1313976v1_genomic.fna/markers.fasta)
[2023-06-18 17:29:28,424] [INFO] Task started: Blastn
[2023-06-18 17:29:28,424] [INFO] Running command: blastn -query GCA_013139765.1_ASM1313976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24f2e219-631e-4f58-b83a-7fc65f3e9f33/dqc_reference/reference_markers_gtdb.fasta -out GCA_013139765.1_ASM1313976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:29:29,201] [INFO] Task succeeded: Blastn
[2023-06-18 17:29:29,206] [INFO] Selected 12 target genomes.
[2023-06-18 17:29:29,206] [INFO] Target genome list was writen to GCA_013139765.1_ASM1313976v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:29:29,211] [INFO] Task started: fastANI
[2023-06-18 17:29:29,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgeba762ed-3b19-4c72-a72a-5f04d959c2b7/GCA_013139765.1_ASM1313976v1_genomic.fna.gz --refList GCA_013139765.1_ASM1313976v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013139765.1_ASM1313976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:29:33,573] [INFO] Task succeeded: fastANI
[2023-06-18 17:29:33,581] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:29:33,581] [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_013139765.1	s__Sulfurovum sp013139765	100.0	593	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013607775.1	s__Sulfurovum sp013607775	79.1417	199	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330645.1	s__Sulfurovum sp011330645	78.8006	162	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661535.1	s__Sulfurovum sp015661535	78.3717	161	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744875.1	s__Sulfurovum sp016744875	78.279	191	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727855.1	s__Sulfurovum sp902727855	78.0501	178	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646505.1	s__Sulfurovum sp003646505	78.0164	139	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733355.1	s__Sulfurovum sp002733355	77.9575	148	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004377245.1	s__Sulfurovum sp004377245	77.8566	67	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296775.1	s__Sulfurovum sp000296775	77.698	147	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978375.1	s__Sulfurovum sp003978375	77.586	99	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727995.1	s__UBA1140 sp902727995	76.7958	62	598	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:29:33,583] [INFO] GTDB search result was written to GCA_013139765.1_ASM1313976v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:29:33,583] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:29:33,587] [INFO] DFAST_QC result json was written to GCA_013139765.1_ASM1313976v1_genomic.fna/dqc_result.json
[2023-06-18 17:29:33,588] [INFO] DFAST_QC completed!
[2023-06-18 17:29:33,588] [INFO] Total running time: 0h0m39s