[2024-01-25 19:59:50,388] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:50,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:50,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg09a4b2c8-1963-4c0e-84e2-1f287f468b64/dqc_reference
[2024-01-25 19:59:51,535] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:51,536] [INFO] Task started: Prodigal
[2024-01-25 19:59:51,536] [INFO] Running command: gunzip -c /var/lib/cwl/stgb34f871e-e080-4ea9-9c17-f0bbeab542c2/GCF_002000125.1_ASM200012v1_genomic.fna.gz | prodigal -d GCF_002000125.1_ASM200012v1_genomic.fna/cds.fna -a GCF_002000125.1_ASM200012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:55,717] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:55,717] [INFO] Task started: HMMsearch
[2024-01-25 19:59:55,717] [INFO] Running command: hmmsearch --tblout GCF_002000125.1_ASM200012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09a4b2c8-1963-4c0e-84e2-1f287f468b64/dqc_reference/reference_markers.hmm GCF_002000125.1_ASM200012v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:55,904] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:55,905] [INFO] Found 6/6 markers.
[2024-01-25 19:59:55,927] [INFO] Query marker FASTA was written to GCF_002000125.1_ASM200012v1_genomic.fna/markers.fasta
[2024-01-25 19:59:55,927] [INFO] Task started: Blastn
[2024-01-25 19:59:55,927] [INFO] Running command: blastn -query GCF_002000125.1_ASM200012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09a4b2c8-1963-4c0e-84e2-1f287f468b64/dqc_reference/reference_markers.fasta -out GCF_002000125.1_ASM200012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:56,547] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:56,550] [INFO] Selected 14 target genomes.
[2024-01-25 19:59:56,550] [INFO] Target genome list was writen to GCF_002000125.1_ASM200012v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:56,569] [INFO] Task started: fastANI
[2024-01-25 19:59:56,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgb34f871e-e080-4ea9-9c17-f0bbeab542c2/GCF_002000125.1_ASM200012v1_genomic.fna.gz --refList GCF_002000125.1_ASM200012v1_genomic.fna/target_genomes.txt --output GCF_002000125.1_ASM200012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:03,811] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:03,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09a4b2c8-1963-4c0e-84e2-1f287f468b64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:03,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09a4b2c8-1963-4c0e-84e2-1f287f468b64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:03,819] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:03,819] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:03,819] [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
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	100.0	662	663	95	conclusive
Rodentibacter rarus	strain=CCUG 17206	GCA_001998965.1	1908260	1908260	type	True	91.9883	497	663	95	below_threshold
Rodentibacter trehalosifermentans	strain=H1987082031	GCA_002000545.1	1908263	1908263	type	True	88.0655	520	663	95	below_threshold
Rodentibacter ratti	strain=F75	GCA_002000485.1	1906745	1906745	type	True	84.5562	479	663	95	below_threshold
Rodentibacter mrazii	strain=Ppn418	GCA_001998825.1	1908257	1908257	type	True	83.1659	470	663	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	83.0655	497	663	95	below_threshold
Rodentibacter pneumotropicus	strain=DSM 21403	GCA_000379905.1	758	758	type	True	83.0585	501	663	95	below_threshold
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	80.5637	430	663	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.7549	416	663	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	78.8898	290	663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:03,824] [INFO] DFAST Taxonomy check result was written to GCF_002000125.1_ASM200012v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:03,824] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:03,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:03,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09a4b2c8-1963-4c0e-84e2-1f287f468b64/dqc_reference/checkm_data
[2024-01-25 20:00:03,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:03,851] [INFO] Task started: CheckM
[2024-01-25 20:00:03,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002000125.1_ASM200012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002000125.1_ASM200012v1_genomic.fna/checkm_input GCF_002000125.1_ASM200012v1_genomic.fna/checkm_result
[2024-01-25 20:00:22,848] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:22,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:22,876] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:22,876] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:22,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002000125.1_ASM200012v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:22,877] [INFO] Task started: Blastn
[2024-01-25 20:00:22,877] [INFO] Running command: blastn -query GCF_002000125.1_ASM200012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09a4b2c8-1963-4c0e-84e2-1f287f468b64/dqc_reference/reference_markers_gtdb.fasta -out GCF_002000125.1_ASM200012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:23,939] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:23,948] [INFO] Selected 11 target genomes.
[2024-01-25 20:00:23,949] [INFO] Target genome list was writen to GCF_002000125.1_ASM200012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:23,980] [INFO] Task started: fastANI
[2024-01-25 20:00:23,980] [INFO] Running command: fastANI --query /var/lib/cwl/stgb34f871e-e080-4ea9-9c17-f0bbeab542c2/GCF_002000125.1_ASM200012v1_genomic.fna.gz --refList GCF_002000125.1_ASM200012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002000125.1_ASM200012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:29,749] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:29,756] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:29,756] [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_002000125.1	s__Rodentibacter heidelbergensis	100.0	662	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001998965.1	s__Rodentibacter rarus	91.998	497	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	99.19	99.19	0.90	0.90	2	-
GCF_002000545.1	s__Rodentibacter trehalosifermentans	88.0655	520	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.00	97.91	0.88	0.88	3	-
GCF_002000485.1	s__Rodentibacter ratti	84.5354	480	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	96.24	96.11	0.85	0.81	4	-
GCF_001999285.1	s__Rodentibacter sp001999285	83.4975	514	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	97.96	97.96	0.90	0.90	3	-
GCF_001998825.1	s__Rodentibacter mrazii	83.1619	470	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	95.11	95.11	0.86	0.86	2	-
GCF_000379905.1	s__Rodentibacter pneumotropicus	83.0661	499	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.90	97.98	0.93	0.87	18	-
GCF_001999425.1	s__Rodentibacter sp001999425	81.7555	477	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999335.1	s__Rodentibacter sp001999335	81.7469	443	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999305.1	s__Rodentibacter myodis	80.614	426	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356115.1	s__Rodentibacter sp015356115	79.7303	418	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:29,762] [INFO] GTDB search result was written to GCF_002000125.1_ASM200012v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:29,762] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:29,766] [INFO] DFAST_QC result json was written to GCF_002000125.1_ASM200012v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:29,766] [INFO] DFAST_QC completed!
[2024-01-25 20:00:29,767] [INFO] Total running time: 0h0m39s