[2023-06-19 09:08:52,257] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:08:52,261] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:08:52,262] [INFO] DQC Reference Directory: /var/lib/cwl/stg44a71fc2-aa9a-4aba-a370-0dbd9bd44b6d/dqc_reference
[2023-06-19 09:08:53,465] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:08:53,465] [INFO] Task started: Prodigal
[2023-06-19 09:08:53,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg884fa95b-8979-45fc-92f0-2728c0bf8606/GCA_018367315.1_ASM1836731v1_genomic.fna.gz | prodigal -d GCA_018367315.1_ASM1836731v1_genomic.fna/cds.fna -a GCA_018367315.1_ASM1836731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:08:55,910] [INFO] Task succeeded: Prodigal
[2023-06-19 09:08:55,910] [INFO] Task started: HMMsearch
[2023-06-19 09:08:55,910] [INFO] Running command: hmmsearch --tblout GCA_018367315.1_ASM1836731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44a71fc2-aa9a-4aba-a370-0dbd9bd44b6d/dqc_reference/reference_markers.hmm GCA_018367315.1_ASM1836731v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:08:56,121] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:08:56,122] [INFO] Found 6/6 markers.
[2023-06-19 09:08:56,145] [INFO] Query marker FASTA was written to GCA_018367315.1_ASM1836731v1_genomic.fna/markers.fasta
[2023-06-19 09:08:56,145] [INFO] Task started: Blastn
[2023-06-19 09:08:56,145] [INFO] Running command: blastn -query GCA_018367315.1_ASM1836731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44a71fc2-aa9a-4aba-a370-0dbd9bd44b6d/dqc_reference/reference_markers.fasta -out GCA_018367315.1_ASM1836731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:08:56,720] [INFO] Task succeeded: Blastn
[2023-06-19 09:08:56,730] [INFO] Selected 10 target genomes.
[2023-06-19 09:08:56,731] [INFO] Target genome list was writen to GCA_018367315.1_ASM1836731v1_genomic.fna/target_genomes.txt
[2023-06-19 09:08:56,733] [INFO] Task started: fastANI
[2023-06-19 09:08:56,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg884fa95b-8979-45fc-92f0-2728c0bf8606/GCA_018367315.1_ASM1836731v1_genomic.fna.gz --refList GCA_018367315.1_ASM1836731v1_genomic.fna/target_genomes.txt --output GCA_018367315.1_ASM1836731v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:09:01,001] [INFO] Task succeeded: fastANI
[2023-06-19 09:09:01,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44a71fc2-aa9a-4aba-a370-0dbd9bd44b6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:09:01,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44a71fc2-aa9a-4aba-a370-0dbd9bd44b6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:09:01,013] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:09:01,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:09:01,013] [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
Gemella haemolysans	strain=ATCC 10379	GCA_000173915.1	1379	1379	suspected-type	True	93.9605	460	535	95	below_threshold
Gemella haemolysans	strain=CCUG 37985T	GCA_008692995.1	1379	1379	suspected-type	True	93.9217	464	535	95	below_threshold
Gemella sanguinis	strain=ATCC 700632	GCA_000701685.1	84135	84135	type	True	80.9804	305	535	95	below_threshold
Gemella morbillorum	strain=NCTC11323	GCA_900476045.1	29391	29391	type	True	80.6834	289	535	95	below_threshold
Gemella morbillorum	strain=FDAARGOS_1501	GCA_020097435.1	29391	29391	type	True	80.6364	292	535	95	below_threshold
Gemella cuniculi	strain=DSM 15828	GCA_000425665.1	150240	150240	type	True	79.3798	245	535	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:09:01,015] [INFO] DFAST Taxonomy check result was written to GCA_018367315.1_ASM1836731v1_genomic.fna/tc_result.tsv
[2023-06-19 09:09:01,016] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:09:01,016] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:09:01,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44a71fc2-aa9a-4aba-a370-0dbd9bd44b6d/dqc_reference/checkm_data
[2023-06-19 09:09:01,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:09:01,041] [INFO] Task started: CheckM
[2023-06-19 09:09:01,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018367315.1_ASM1836731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018367315.1_ASM1836731v1_genomic.fna/checkm_input GCA_018367315.1_ASM1836731v1_genomic.fna/checkm_result
[2023-06-19 09:09:16,413] [INFO] Task succeeded: CheckM
[2023-06-19 09:09:16,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:09:16,439] [INFO] ===== Completeness check finished =====
[2023-06-19 09:09:16,439] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:09:16,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018367315.1_ASM1836731v1_genomic.fna/markers.fasta)
[2023-06-19 09:09:16,440] [INFO] Task started: Blastn
[2023-06-19 09:09:16,440] [INFO] Running command: blastn -query GCA_018367315.1_ASM1836731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44a71fc2-aa9a-4aba-a370-0dbd9bd44b6d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018367315.1_ASM1836731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:09:17,259] [INFO] Task succeeded: Blastn
[2023-06-19 09:09:17,264] [INFO] Selected 6 target genomes.
[2023-06-19 09:09:17,265] [INFO] Target genome list was writen to GCA_018367315.1_ASM1836731v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:09:17,266] [INFO] Task started: fastANI
[2023-06-19 09:09:17,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg884fa95b-8979-45fc-92f0-2728c0bf8606/GCA_018367315.1_ASM1836731v1_genomic.fna.gz --refList GCA_018367315.1_ASM1836731v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018367315.1_ASM1836731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:09:20,449] [INFO] Task succeeded: fastANI
[2023-06-19 09:09:20,462] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:09:20,462] [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
GCF_001553035.1	s__Gemella haemolysans_B	97.7169	468	535	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	97.70	97.59	0.85	0.81	4	conclusive
GCF_000173915.1	s__Gemella haemolysans	93.9605	460	535	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.96	99.96	0.99	0.99	3	-
GCA_900766305.1	s__Gemella sp900766305	93.1923	434	535	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002871655.1	s__Gemella sp002871655	87.8361	446	535	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	98.42	98.42	0.93	0.93	2	-
GCF_901873445.1	s__Gemella haemolysans_C	87.5696	435	535	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012273215.1	s__Gemella haemolysans_A	87.1701	449	535	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-19 09:09:20,465] [INFO] GTDB search result was written to GCA_018367315.1_ASM1836731v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:09:20,465] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:09:20,468] [INFO] DFAST_QC result json was written to GCA_018367315.1_ASM1836731v1_genomic.fna/dqc_result.json
[2023-06-19 09:09:20,468] [INFO] DFAST_QC completed!
[2023-06-19 09:09:20,468] [INFO] Total running time: 0h0m28s