[2024-01-24 12:06:11,868] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:11,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:11,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg3281ebe1-d3cf-4fcc-acf1-7a0886fa2994/dqc_reference
[2024-01-24 12:06:13,146] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,147] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,147] [INFO] Running command: gunzip -c /var/lib/cwl/stgf04ae14e-88e9-4fce-ba77-8a68fea493b3/GCF_014764365.1_ASM1476436v1_genomic.fna.gz | prodigal -d GCF_014764365.1_ASM1476436v1_genomic.fna/cds.fna -a GCF_014764365.1_ASM1476436v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:27,043] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:27,043] [INFO] Task started: HMMsearch
[2024-01-24 12:06:27,044] [INFO] Running command: hmmsearch --tblout GCF_014764365.1_ASM1476436v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3281ebe1-d3cf-4fcc-acf1-7a0886fa2994/dqc_reference/reference_markers.hmm GCF_014764365.1_ASM1476436v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:27,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:27,379] [INFO] Found 6/6 markers.
[2024-01-24 12:06:27,420] [INFO] Query marker FASTA was written to GCF_014764365.1_ASM1476436v1_genomic.fna/markers.fasta
[2024-01-24 12:06:27,420] [INFO] Task started: Blastn
[2024-01-24 12:06:27,420] [INFO] Running command: blastn -query GCF_014764365.1_ASM1476436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3281ebe1-d3cf-4fcc-acf1-7a0886fa2994/dqc_reference/reference_markers.fasta -out GCF_014764365.1_ASM1476436v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:28,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:28,194] [INFO] Selected 8 target genomes.
[2024-01-24 12:06:28,194] [INFO] Target genome list was writen to GCF_014764365.1_ASM1476436v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:28,198] [INFO] Task started: fastANI
[2024-01-24 12:06:28,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgf04ae14e-88e9-4fce-ba77-8a68fea493b3/GCF_014764365.1_ASM1476436v1_genomic.fna.gz --refList GCF_014764365.1_ASM1476436v1_genomic.fna/target_genomes.txt --output GCF_014764365.1_ASM1476436v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:37,892] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:37,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3281ebe1-d3cf-4fcc-acf1-7a0886fa2994/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:37,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3281ebe1-d3cf-4fcc-acf1-7a0886fa2994/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:37,900] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:37,901] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:37,901] [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
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	100.0	1401	1402	95	conclusive
Roseococcus suduntuyensis	strain=DSM 19979	GCA_014196305.1	455361	455361	type	True	94.4996	1266	1402	95	below_threshold
Roseococcus suduntuyensis	strain=SHET	GCA_017311525.1	455361	455361	type	True	94.4826	1267	1402	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	94.0489	1224	1402	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	80.4288	765	1402	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	79.8264	710	1402	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	79.3764	708	1402	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	78.0023	519	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:37,902] [INFO] DFAST Taxonomy check result was written to GCF_014764365.1_ASM1476436v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:37,903] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:37,903] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:37,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3281ebe1-d3cf-4fcc-acf1-7a0886fa2994/dqc_reference/checkm_data
[2024-01-24 12:06:37,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:37,948] [INFO] Task started: CheckM
[2024-01-24 12:06:37,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014764365.1_ASM1476436v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014764365.1_ASM1476436v1_genomic.fna/checkm_input GCF_014764365.1_ASM1476436v1_genomic.fna/checkm_result
[2024-01-24 12:08:15,460] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:15,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:15,486] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:15,486] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:15,486] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014764365.1_ASM1476436v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:15,487] [INFO] Task started: Blastn
[2024-01-24 12:08:15,487] [INFO] Running command: blastn -query GCF_014764365.1_ASM1476436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3281ebe1-d3cf-4fcc-acf1-7a0886fa2994/dqc_reference/reference_markers_gtdb.fasta -out GCF_014764365.1_ASM1476436v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:16,641] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:16,646] [INFO] Selected 9 target genomes.
[2024-01-24 12:08:16,646] [INFO] Target genome list was writen to GCF_014764365.1_ASM1476436v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:16,660] [INFO] Task started: fastANI
[2024-01-24 12:08:16,661] [INFO] Running command: fastANI --query /var/lib/cwl/stgf04ae14e-88e9-4fce-ba77-8a68fea493b3/GCF_014764365.1_ASM1476436v1_genomic.fna.gz --refList GCF_014764365.1_ASM1476436v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014764365.1_ASM1476436v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:26,938] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:26,947] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:26,947] [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_014764365.1	s__Roseococcus sp014764365	100.0	1400	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014196305.1	s__Roseococcus suduntuyensis	94.4996	1266	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017311575.1	s__Roseococcus thiosulfatophilus	94.0489	1224	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129145.1	s__Roseococcus sp007129145	83.7371	433	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425365.1	s__Roseococcus flocculans	83.1636	873	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083995.1	s__Roseococcus sp019083995	82.2326	921	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004336745.1	s__Roseococcus sp004336745	80.887	817	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355885.1	s__Roseococcus sp017355885	80.4916	697	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003604215.1	s__Roseomonas vastitatis	77.9885	521	1402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:26,948] [INFO] GTDB search result was written to GCF_014764365.1_ASM1476436v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:26,950] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:26,953] [INFO] DFAST_QC result json was written to GCF_014764365.1_ASM1476436v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:26,953] [INFO] DFAST_QC completed!
[2024-01-24 12:08:26,954] [INFO] Total running time: 0h2m15s