[2023-06-05 09:25:44,649] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:25:44,651] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:25:44,651] [INFO] DQC Reference Directory: /var/lib/cwl/stge7dbfaea-e1f0-4baf-a81a-3395678a6ee9/dqc_reference
[2023-06-05 09:25:46,790] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:25:46,792] [INFO] Task started: Prodigal
[2023-06-05 09:25:46,793] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1aced1b-5869-4b25-b931-2625418e5281/GCA_004554855.1_ASM455485v1_genomic.fna.gz | prodigal -d GCA_004554855.1_ASM455485v1_genomic.fna/cds.fna -a GCA_004554855.1_ASM455485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:25:52,345] [INFO] Task succeeded: Prodigal
[2023-06-05 09:25:52,345] [INFO] Task started: HMMsearch
[2023-06-05 09:25:52,345] [INFO] Running command: hmmsearch --tblout GCA_004554855.1_ASM455485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7dbfaea-e1f0-4baf-a81a-3395678a6ee9/dqc_reference/reference_markers.hmm GCA_004554855.1_ASM455485v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:25:52,589] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:25:52,590] [INFO] Found 6/6 markers.
[2023-06-05 09:25:52,618] [INFO] Query marker FASTA was written to GCA_004554855.1_ASM455485v1_genomic.fna/markers.fasta
[2023-06-05 09:25:52,618] [INFO] Task started: Blastn
[2023-06-05 09:25:52,618] [INFO] Running command: blastn -query GCA_004554855.1_ASM455485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7dbfaea-e1f0-4baf-a81a-3395678a6ee9/dqc_reference/reference_markers.fasta -out GCA_004554855.1_ASM455485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:53,286] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:53,290] [INFO] Selected 30 target genomes.
[2023-06-05 09:25:53,291] [INFO] Target genome list was writen to GCA_004554855.1_ASM455485v1_genomic.fna/target_genomes.txt
[2023-06-05 09:25:53,297] [INFO] Task started: fastANI
[2023-06-05 09:25:53,298] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1aced1b-5869-4b25-b931-2625418e5281/GCA_004554855.1_ASM455485v1_genomic.fna.gz --refList GCA_004554855.1_ASM455485v1_genomic.fna/target_genomes.txt --output GCA_004554855.1_ASM455485v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:26:08,901] [INFO] Task succeeded: fastANI
[2023-06-05 09:26:08,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7dbfaea-e1f0-4baf-a81a-3395678a6ee9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:26:08,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7dbfaea-e1f0-4baf-a81a-3395678a6ee9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:26:08,915] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:26:08,916] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:26:08,916] [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 09:26:08,919] [INFO] DFAST Taxonomy check result was written to GCA_004554855.1_ASM455485v1_genomic.fna/tc_result.tsv
[2023-06-05 09:26:08,919] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:26:08,920] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:26:08,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7dbfaea-e1f0-4baf-a81a-3395678a6ee9/dqc_reference/checkm_data
[2023-06-05 09:26:08,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:26:08,952] [INFO] Task started: CheckM
[2023-06-05 09:26:08,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004554855.1_ASM455485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004554855.1_ASM455485v1_genomic.fna/checkm_input GCA_004554855.1_ASM455485v1_genomic.fna/checkm_result
[2023-06-05 09:26:31,518] [INFO] Task succeeded: CheckM
[2023-06-05 09:26:31,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:26:31,541] [INFO] ===== Completeness check finished =====
[2023-06-05 09:26:31,541] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:26:31,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004554855.1_ASM455485v1_genomic.fna/markers.fasta)
[2023-06-05 09:26:31,542] [INFO] Task started: Blastn
[2023-06-05 09:26:31,542] [INFO] Running command: blastn -query GCA_004554855.1_ASM455485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7dbfaea-e1f0-4baf-a81a-3395678a6ee9/dqc_reference/reference_markers_gtdb.fasta -out GCA_004554855.1_ASM455485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:26:32,689] [INFO] Task succeeded: Blastn
[2023-06-05 09:26:32,694] [INFO] Selected 26 target genomes.
[2023-06-05 09:26:32,694] [INFO] Target genome list was writen to GCA_004554855.1_ASM455485v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:26:32,710] [INFO] Task started: fastANI
[2023-06-05 09:26:32,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1aced1b-5869-4b25-b931-2625418e5281/GCA_004554855.1_ASM455485v1_genomic.fna.gz --refList GCA_004554855.1_ASM455485v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004554855.1_ASM455485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:26:42,271] [INFO] Task succeeded: fastANI
[2023-06-05 09:26:42,280] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:26:42,280] [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_900548115.1	s__UMGS1052 sp900548115	98.1502	547	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UMGS1052	95.0	98.21	98.21	0.82	0.82	2	conclusive
GCA_015063785.1	s__UMGS1052 sp015063785	77.6081	111	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UMGS1052	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549365.1	s__UMGS1052 sp017549365	77.0092	108	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UMGS1052	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549405.1	s__UMGS1052 sp017549405	76.7883	53	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UMGS1052	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757905.1	s__UMGS882 sp900757905	76.4557	70	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UMGS882	95.0	99.82	99.82	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-05 09:26:42,282] [INFO] GTDB search result was written to GCA_004554855.1_ASM455485v1_genomic.fna/result_gtdb.tsv
[2023-06-05 09:26:42,283] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:26:42,285] [INFO] DFAST_QC result json was written to GCA_004554855.1_ASM455485v1_genomic.fna/dqc_result.json
[2023-06-05 09:26:42,286] [INFO] DFAST_QC completed!
[2023-06-05 09:26:42,286] [INFO] Total running time: 0h0m58s