[2024-01-25 18:15:50,741] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:50,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:50,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4ae25f3-6d35-4f7c-abb6-f718c0974145/dqc_reference
[2024-01-25 18:15:51,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:51,918] [INFO] Task started: Prodigal
[2024-01-25 18:15:51,918] [INFO] Running command: gunzip -c /var/lib/cwl/stgf077d52a-0127-4176-ba88-dcfe8d4e0024/GCF_000382345.1_ASM38234v1_genomic.fna.gz | prodigal -d GCF_000382345.1_ASM38234v1_genomic.fna/cds.fna -a GCF_000382345.1_ASM38234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:08,792] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:08,792] [INFO] Task started: HMMsearch
[2024-01-25 18:16:08,792] [INFO] Running command: hmmsearch --tblout GCF_000382345.1_ASM38234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4ae25f3-6d35-4f7c-abb6-f718c0974145/dqc_reference/reference_markers.hmm GCF_000382345.1_ASM38234v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:09,062] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:09,064] [INFO] Found 6/6 markers.
[2024-01-25 18:16:09,114] [INFO] Query marker FASTA was written to GCF_000382345.1_ASM38234v1_genomic.fna/markers.fasta
[2024-01-25 18:16:09,114] [INFO] Task started: Blastn
[2024-01-25 18:16:09,114] [INFO] Running command: blastn -query GCF_000382345.1_ASM38234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ae25f3-6d35-4f7c-abb6-f718c0974145/dqc_reference/reference_markers.fasta -out GCF_000382345.1_ASM38234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:10,145] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:10,147] [INFO] Selected 11 target genomes.
[2024-01-25 18:16:10,148] [INFO] Target genome list was writen to GCF_000382345.1_ASM38234v1_genomic.fna/target_genomes.txt
[2024-01-25 18:16:10,157] [INFO] Task started: fastANI
[2024-01-25 18:16:10,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgf077d52a-0127-4176-ba88-dcfe8d4e0024/GCF_000382345.1_ASM38234v1_genomic.fna.gz --refList GCF_000382345.1_ASM38234v1_genomic.fna/target_genomes.txt --output GCF_000382345.1_ASM38234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:27,548] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:27,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4ae25f3-6d35-4f7c-abb6-f718c0974145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:27,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4ae25f3-6d35-4f7c-abb6-f718c0974145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:27,557] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:27,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:27,558] [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 niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	100.0	2116	2125	95	conclusive
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	85.7054	1292	2125	95	below_threshold
Massilia timonae	strain=CCUG 45783	GCA_000315425.1	47229	47229	type	True	85.5934	1290	2125	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	85.3653	1269	2125	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	85.2318	1274	2125	95	below_threshold
Massilia arenae	strain=GEM5	GCA_008014745.1	2603288	2603288	type	True	85.0929	1292	2125	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	83.7377	1196	2125	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	83.5937	1181	2125	95	below_threshold
Massilia aurea	strain=JCM 13879	GCA_024753205.1	373040	373040	type	True	83.1083	1116	2125	95	below_threshold
Massilia horti	strain=ONC3	GCA_004614195.1	2562153	2562153	type	True	82.8867	989	2125	95	below_threshold
Massilia putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	82.2236	1204	2125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:27,559] [INFO] DFAST Taxonomy check result was written to GCF_000382345.1_ASM38234v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:27,560] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:27,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:27,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4ae25f3-6d35-4f7c-abb6-f718c0974145/dqc_reference/checkm_data
[2024-01-25 18:16:27,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:27,620] [INFO] Task started: CheckM
[2024-01-25 18:16:27,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000382345.1_ASM38234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000382345.1_ASM38234v1_genomic.fna/checkm_input GCF_000382345.1_ASM38234v1_genomic.fna/checkm_result
[2024-01-25 18:17:17,257] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:17,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:17,276] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:17,276] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:17,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000382345.1_ASM38234v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:17,277] [INFO] Task started: Blastn
[2024-01-25 18:17:17,277] [INFO] Running command: blastn -query GCF_000382345.1_ASM38234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ae25f3-6d35-4f7c-abb6-f718c0974145/dqc_reference/reference_markers_gtdb.fasta -out GCF_000382345.1_ASM38234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:19,458] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:19,461] [INFO] Selected 12 target genomes.
[2024-01-25 18:17:19,461] [INFO] Target genome list was writen to GCF_000382345.1_ASM38234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:19,492] [INFO] Task started: fastANI
[2024-01-25 18:17:19,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgf077d52a-0127-4176-ba88-dcfe8d4e0024/GCF_000382345.1_ASM38234v1_genomic.fna.gz --refList GCF_000382345.1_ASM38234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000382345.1_ASM38234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:37,425] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:37,433] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:37,433] [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_000382345.1	s__Massilia niastensis	100.0	2116	2125	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_018119395.1	s__Massilia sp018119395	87.2825	1315	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_018119405.1	s__Massilia sp018119405	87.2781	1298	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007115.1	s__Massilia sp002007115	86.7364	1358	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427785.1	s__Massilia alkalitolerans	85.7063	1291	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.93	95.88	0.90	0.87	5	-
GCF_902506415.1	s__Massilia sp902506415	85.5159	1291	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740675.1	s__Massilia sp000740675	85.4317	1201	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017582745.1	s__Massilia oculi	85.3224	1308	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.07	95.07	0.86	0.86	2	-
GCA_003520365.1	s__Massilia sp003520365	85.1592	712	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339265.1	s__Massilia sp002339265	84.9416	1071	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849555.1	s__Massilia sp012849555	83.5773	1183	2125	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	83.2292	1127	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.89	99.89	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:37,436] [INFO] GTDB search result was written to GCF_000382345.1_ASM38234v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:37,436] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:37,439] [INFO] DFAST_QC result json was written to GCF_000382345.1_ASM38234v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:37,440] [INFO] DFAST_QC completed!
[2024-01-25 18:17:37,440] [INFO] Total running time: 0h1m47s