[2024-01-24 13:17:05,657] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg00271a62-be9a-4df0-be24-15dd3490060c/dqc_reference
[2024-01-24 13:17:07,015] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:07,016] [INFO] Task started: Prodigal
[2024-01-24 13:17:07,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f2ffac7-e3ca-4dc3-ac88-18f785140971/GCF_003011895.2_ASM301189v2_genomic.fna.gz | prodigal -d GCF_003011895.2_ASM301189v2_genomic.fna/cds.fna -a GCF_003011895.2_ASM301189v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:27,160] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:27,161] [INFO] Task started: HMMsearch
[2024-01-24 13:17:27,161] [INFO] Running command: hmmsearch --tblout GCF_003011895.2_ASM301189v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00271a62-be9a-4df0-be24-15dd3490060c/dqc_reference/reference_markers.hmm GCF_003011895.2_ASM301189v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:27,610] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:27,611] [INFO] Found 6/6 markers.
[2024-01-24 13:17:27,668] [INFO] Query marker FASTA was written to GCF_003011895.2_ASM301189v2_genomic.fna/markers.fasta
[2024-01-24 13:17:27,669] [INFO] Task started: Blastn
[2024-01-24 13:17:27,669] [INFO] Running command: blastn -query GCF_003011895.2_ASM301189v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg00271a62-be9a-4df0-be24-15dd3490060c/dqc_reference/reference_markers.fasta -out GCF_003011895.2_ASM301189v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:28,829] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:28,833] [INFO] Selected 20 target genomes.
[2024-01-24 13:17:28,833] [INFO] Target genome list was writen to GCF_003011895.2_ASM301189v2_genomic.fna/target_genomes.txt
[2024-01-24 13:17:28,841] [INFO] Task started: fastANI
[2024-01-24 13:17:28,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f2ffac7-e3ca-4dc3-ac88-18f785140971/GCF_003011895.2_ASM301189v2_genomic.fna.gz --refList GCF_003011895.2_ASM301189v2_genomic.fna/target_genomes.txt --output GCF_003011895.2_ASM301189v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:57,845] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:57,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00271a62-be9a-4df0-be24-15dd3490060c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:57,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00271a62-be9a-4df0-be24-15dd3490060c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:57,863] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:57,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:57,864] [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 glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	100.0	1931	1945	95	conclusive
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	82.5394	971	1945	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	82.2541	1041	1945	95	below_threshold
Massilia psychrophila	strain=CGMCC 1.15196	GCA_014641415.1	1603353	1603353	type	True	82.059	835	1945	95	below_threshold
Massilia psychrophila	strain=JCM 30813	GCA_002760665.1	1603353	1603353	type	True	82.0354	845	1945	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	81.888	1044	1945	95	below_threshold
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	81.8715	843	1945	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	81.8505	1013	1945	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	81.8403	982	1945	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	81.8078	1050	1945	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.7222	836	1945	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	81.649	888	1945	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	81.2874	894	1945	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	81.116	841	1945	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	80.9501	911	1945	95	below_threshold
Massilia horti	strain=ONC3	GCA_004614195.1	2562153	2562153	type	True	80.9113	807	1945	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	80.8679	839	1945	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	80.8396	848	1945	95	below_threshold
Massilia timonae	strain=CCUG 45783	GCA_000315425.1	47229	47229	type	True	80.7414	897	1945	95	below_threshold
Massilia aromaticivorans	strain=ML15P13	GCA_013003915.1	2725995	2725995	type	True	80.6807	850	1945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:57,865] [INFO] DFAST Taxonomy check result was written to GCF_003011895.2_ASM301189v2_genomic.fna/tc_result.tsv
[2024-01-24 13:17:57,866] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:57,866] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:57,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00271a62-be9a-4df0-be24-15dd3490060c/dqc_reference/checkm_data
[2024-01-24 13:17:57,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:57,927] [INFO] Task started: CheckM
[2024-01-24 13:17:57,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003011895.2_ASM301189v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003011895.2_ASM301189v2_genomic.fna/checkm_input GCF_003011895.2_ASM301189v2_genomic.fna/checkm_result
[2024-01-24 13:18:51,000] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:51,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:51,025] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:51,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:51,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003011895.2_ASM301189v2_genomic.fna/markers.fasta)
[2024-01-24 13:18:51,026] [INFO] Task started: Blastn
[2024-01-24 13:18:51,026] [INFO] Running command: blastn -query GCF_003011895.2_ASM301189v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg00271a62-be9a-4df0-be24-15dd3490060c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003011895.2_ASM301189v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:53,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:53,233] [INFO] Selected 15 target genomes.
[2024-01-24 13:18:53,233] [INFO] Target genome list was writen to GCF_003011895.2_ASM301189v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:53,248] [INFO] Task started: fastANI
[2024-01-24 13:18:53,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f2ffac7-e3ca-4dc3-ac88-18f785140971/GCF_003011895.2_ASM301189v2_genomic.fna.gz --refList GCF_003011895.2_ASM301189v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003011895.2_ASM301189v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:15,360] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:15,373] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:15,373] [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_003011895.2	s__Massilia glaciei	100.0	1931	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002760655.1	s__Massilia eurypsychrophila	82.5154	974	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428015.1	s__Massilia sp002428015	82.5033	934	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003953935.1	s__Massilia atriviolacea	82.2663	1039	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	82.207	489	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760665.1	s__Massilia psychrophila	82.0265	846	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900114705.1	s__Rugamonas rubra	81.9629	1005	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	-
GCF_011682145.1	s__Massilia mucilaginosa	81.8791	1045	1945	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	81.8651	1040	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_011682175.1	s__Massilia frigida	81.8512	1013	1945	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	81.8445	1032	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590855.1	s__Massilia sp003590855	81.7162	837	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315425.1	s__Massilia timonae	80.7731	892	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	97.91	95.09	0.93	0.87	8	-
GCF_013003915.1	s__Massilia aromaticivorans	80.6957	848	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014171595.1	s__Massilia sp014171595	80.5645	840	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.89	99.89	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:15,375] [INFO] GTDB search result was written to GCF_003011895.2_ASM301189v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:15,376] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:15,382] [INFO] DFAST_QC result json was written to GCF_003011895.2_ASM301189v2_genomic.fna/dqc_result.json
[2024-01-24 13:19:15,382] [INFO] DFAST_QC completed!
[2024-01-24 13:19:15,383] [INFO] Total running time: 0h2m10s