[2024-01-25 20:17:50,717] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ed0307b-05c9-4e3d-bf22-07061c63961c/dqc_reference
[2024-01-25 20:17:51,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:51,871] [INFO] Task started: Prodigal
[2024-01-25 20:17:51,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg50ee4dd1-e450-49e9-be14-f87cadacb077/GCF_001029285.1_ASM102928v1_genomic.fna.gz | prodigal -d GCF_001029285.1_ASM102928v1_genomic.fna/cds.fna -a GCF_001029285.1_ASM102928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:00,428] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:00,428] [INFO] Task started: HMMsearch
[2024-01-25 20:18:00,428] [INFO] Running command: hmmsearch --tblout GCF_001029285.1_ASM102928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ed0307b-05c9-4e3d-bf22-07061c63961c/dqc_reference/reference_markers.hmm GCF_001029285.1_ASM102928v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:00,669] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:00,670] [INFO] Found 6/6 markers.
[2024-01-25 20:18:00,707] [INFO] Query marker FASTA was written to GCF_001029285.1_ASM102928v1_genomic.fna/markers.fasta
[2024-01-25 20:18:00,708] [INFO] Task started: Blastn
[2024-01-25 20:18:00,708] [INFO] Running command: blastn -query GCF_001029285.1_ASM102928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ed0307b-05c9-4e3d-bf22-07061c63961c/dqc_reference/reference_markers.fasta -out GCF_001029285.1_ASM102928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:01,228] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:01,231] [INFO] Selected 15 target genomes.
[2024-01-25 20:18:01,231] [INFO] Target genome list was writen to GCF_001029285.1_ASM102928v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:01,241] [INFO] Task started: fastANI
[2024-01-25 20:18:01,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ee4dd1-e450-49e9-be14-f87cadacb077/GCF_001029285.1_ASM102928v1_genomic.fna.gz --refList GCF_001029285.1_ASM102928v1_genomic.fna/target_genomes.txt --output GCF_001029285.1_ASM102928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:10,978] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:10,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ed0307b-05c9-4e3d-bf22-07061c63961c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:10,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ed0307b-05c9-4e3d-bf22-07061c63961c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:10,983] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:10,984] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:10,984] [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
Desulfosporosinus acididurans	strain=M1	GCA_001029285.1	476652	476652	type	True	100.0	1515	1519	95	conclusive
Desulfosporosinus acidiphilus	strain=SJ4	GCA_000255115.3	885581	885581	type	True	81.2692	820	1519	95	below_threshold
Desulfosporosinus youngiae	strain=DSM 17734	GCA_000244895.1	339862	339862	type	True	78.4191	210	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:10,985] [INFO] DFAST Taxonomy check result was written to GCF_001029285.1_ASM102928v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:10,985] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:10,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:10,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ed0307b-05c9-4e3d-bf22-07061c63961c/dqc_reference/checkm_data
[2024-01-25 20:18:10,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:11,031] [INFO] Task started: CheckM
[2024-01-25 20:18:11,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001029285.1_ASM102928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001029285.1_ASM102928v1_genomic.fna/checkm_input GCF_001029285.1_ASM102928v1_genomic.fna/checkm_result
[2024-01-25 20:18:40,613] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:40,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:40,633] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:40,633] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:40,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001029285.1_ASM102928v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:40,634] [INFO] Task started: Blastn
[2024-01-25 20:18:40,634] [INFO] Running command: blastn -query GCF_001029285.1_ASM102928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ed0307b-05c9-4e3d-bf22-07061c63961c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001029285.1_ASM102928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:41,412] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:41,414] [INFO] Selected 13 target genomes.
[2024-01-25 20:18:41,415] [INFO] Target genome list was writen to GCF_001029285.1_ASM102928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:41,424] [INFO] Task started: fastANI
[2024-01-25 20:18:41,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ee4dd1-e450-49e9-be14-f87cadacb077/GCF_001029285.1_ASM102928v1_genomic.fna.gz --refList GCF_001029285.1_ASM102928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001029285.1_ASM102928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:51,436] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:51,441] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:51,442] [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_001029285.1	s__Desulfosporosinus acididurans	100.0	1515	1519	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	96.53	96.53	0.82	0.82	2	conclusive
GCF_002196705.1	s__Desulfosporosinus sp002196705	91.2515	1145	1519	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000255115.2	s__Desulfosporosinus acidiphilus	81.3119	811	1519	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224515.1	s__Desulfosporosinus sp000224515	78.189	224	1519	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004766055.1	s__Desulfosporosinus sp004766055	77.91	212	1519	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:51,443] [INFO] GTDB search result was written to GCF_001029285.1_ASM102928v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:51,444] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:51,446] [INFO] DFAST_QC result json was written to GCF_001029285.1_ASM102928v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:51,446] [INFO] DFAST_QC completed!
[2024-01-25 20:18:51,446] [INFO] Total running time: 0h1m1s