[2024-01-24 11:51:50,357] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,358] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgefe51729-e9cf-4903-afec-9a182f48b7fc/dqc_reference
[2024-01-24 11:51:51,578] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,578] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,579] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4ae58ea-54cf-436f-809d-7e7ba9c6e85f/GCF_015689335.1_ASM1568933v1_genomic.fna.gz | prodigal -d GCF_015689335.1_ASM1568933v1_genomic.fna/cds.fna -a GCF_015689335.1_ASM1568933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:20,089] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:20,089] [INFO] Task started: HMMsearch
[2024-01-24 11:52:20,089] [INFO] Running command: hmmsearch --tblout GCF_015689335.1_ASM1568933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefe51729-e9cf-4903-afec-9a182f48b7fc/dqc_reference/reference_markers.hmm GCF_015689335.1_ASM1568933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:20,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:20,423] [INFO] Found 6/6 markers.
[2024-01-24 11:52:20,493] [INFO] Query marker FASTA was written to GCF_015689335.1_ASM1568933v1_genomic.fna/markers.fasta
[2024-01-24 11:52:20,493] [INFO] Task started: Blastn
[2024-01-24 11:52:20,494] [INFO] Running command: blastn -query GCF_015689335.1_ASM1568933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefe51729-e9cf-4903-afec-9a182f48b7fc/dqc_reference/reference_markers.fasta -out GCF_015689335.1_ASM1568933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:21,504] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:21,509] [INFO] Selected 10 target genomes.
[2024-01-24 11:52:21,510] [INFO] Target genome list was writen to GCF_015689335.1_ASM1568933v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:21,517] [INFO] Task started: fastANI
[2024-01-24 11:52:21,517] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ae58ea-54cf-436f-809d-7e7ba9c6e85f/GCF_015689335.1_ASM1568933v1_genomic.fna.gz --refList GCF_015689335.1_ASM1568933v1_genomic.fna/target_genomes.txt --output GCF_015689335.1_ASM1568933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:38,447] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:38,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefe51729-e9cf-4903-afec-9a182f48b7fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:38,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefe51729-e9cf-4903-afec-9a182f48b7fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:38,466] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:38,467] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:38,467] [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
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	92.5249	2084	2477	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	91.4502	1973	2477	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	89.305	1866	2477	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	89.1899	1929	2477	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	89.0403	1846	2477	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	82.2286	926	2477	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	82.0586	1013	2477	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.5347	1005	2477	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.4464	989	2477	95	below_threshold
Massilia aurea	strain=JCM 13879	GCA_024753205.1	373040	373040	type	True	80.2633	862	2477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:38,469] [INFO] DFAST Taxonomy check result was written to GCF_015689335.1_ASM1568933v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:38,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:38,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:38,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefe51729-e9cf-4903-afec-9a182f48b7fc/dqc_reference/checkm_data
[2024-01-24 11:52:38,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:38,538] [INFO] Task started: CheckM
[2024-01-24 11:52:38,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015689335.1_ASM1568933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015689335.1_ASM1568933v1_genomic.fna/checkm_input GCF_015689335.1_ASM1568933v1_genomic.fna/checkm_result
[2024-01-24 11:54:02,697] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:02,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:02,725] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:02,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:02,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015689335.1_ASM1568933v1_genomic.fna/markers.fasta)
[2024-01-24 11:54:02,726] [INFO] Task started: Blastn
[2024-01-24 11:54:02,726] [INFO] Running command: blastn -query GCF_015689335.1_ASM1568933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefe51729-e9cf-4903-afec-9a182f48b7fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_015689335.1_ASM1568933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:04,684] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:04,689] [INFO] Selected 7 target genomes.
[2024-01-24 11:54:04,689] [INFO] Target genome list was writen to GCF_015689335.1_ASM1568933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:04,696] [INFO] Task started: fastANI
[2024-01-24 11:54:04,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ae58ea-54cf-436f-809d-7e7ba9c6e85f/GCF_015689335.1_ASM1568933v1_genomic.fna.gz --refList GCF_015689335.1_ASM1568933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015689335.1_ASM1568933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:20,538] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:20,545] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:20,546] [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_015689335.1	s__Massilia sp001485665	100.0	2471	2477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	97.10	97.10	0.90	0.90	3	conclusive
GCF_011682175.1	s__Massilia frigida	92.5303	2083	2477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752675.1	s__Massilia violaceinigra	91.4495	1973	2477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682145.1	s__Massilia mucilaginosa	89.2973	1867	2477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682065.1	s__Massilia rubra	89.1882	1929	2477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_003953935.1	s__Massilia atriviolacea	89.0519	1845	2477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682045.1	s__Massilia aquatica	88.8769	1856	2477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:20,547] [INFO] GTDB search result was written to GCF_015689335.1_ASM1568933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:20,548] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:20,552] [INFO] DFAST_QC result json was written to GCF_015689335.1_ASM1568933v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:20,552] [INFO] DFAST_QC completed!
[2024-01-24 11:54:20,552] [INFO] Total running time: 0h2m30s