[2024-01-24 13:41:41,396] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:41,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:41,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg463dff53-a616-4366-90fe-d94d49737208/dqc_reference
[2024-01-24 13:41:42,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,627] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,627] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6018c91-14e4-4286-90c8-5ffb693d2c08/GCF_008014745.1_ASM801474v1_genomic.fna.gz | prodigal -d GCF_008014745.1_ASM801474v1_genomic.fna/cds.fna -a GCF_008014745.1_ASM801474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:42:01,096] [INFO] Task succeeded: Prodigal
[2024-01-24 13:42:01,096] [INFO] Task started: HMMsearch
[2024-01-24 13:42:01,096] [INFO] Running command: hmmsearch --tblout GCF_008014745.1_ASM801474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg463dff53-a616-4366-90fe-d94d49737208/dqc_reference/reference_markers.hmm GCF_008014745.1_ASM801474v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:42:01,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:42:01,454] [INFO] Found 6/6 markers.
[2024-01-24 13:42:01,514] [INFO] Query marker FASTA was written to GCF_008014745.1_ASM801474v1_genomic.fna/markers.fasta
[2024-01-24 13:42:01,515] [INFO] Task started: Blastn
[2024-01-24 13:42:01,515] [INFO] Running command: blastn -query GCF_008014745.1_ASM801474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463dff53-a616-4366-90fe-d94d49737208/dqc_reference/reference_markers.fasta -out GCF_008014745.1_ASM801474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:02,555] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:02,569] [INFO] Selected 11 target genomes.
[2024-01-24 13:42:02,569] [INFO] Target genome list was writen to GCF_008014745.1_ASM801474v1_genomic.fna/target_genomes.txt
[2024-01-24 13:42:02,575] [INFO] Task started: fastANI
[2024-01-24 13:42:02,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6018c91-14e4-4286-90c8-5ffb693d2c08/GCF_008014745.1_ASM801474v1_genomic.fna.gz --refList GCF_008014745.1_ASM801474v1_genomic.fna/target_genomes.txt --output GCF_008014745.1_ASM801474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:19,790] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:19,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg463dff53-a616-4366-90fe-d94d49737208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:19,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg463dff53-a616-4366-90fe-d94d49737208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:19,804] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:19,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:19,804] [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 arenae	strain=GEM5	GCA_008014745.1	2603288	2603288	type	True	100.0	1955	1959	95	conclusive
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	93.2277	1622	1959	95	below_threshold
Massilia timonae	strain=CCUG 45783	GCA_000315425.1	47229	47229	type	True	93.1366	1641	1959	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	85.2133	1271	1959	95	below_threshold
Massilia aurea	strain=JCM 13879	GCA_024753205.1	373040	373040	type	True	85.0464	1311	1959	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	84.3638	1302	1959	95	below_threshold
Massilia yuzhufengensis	strain=CGMCC 1.12041	GCA_900112225.1	1164594	1164594	type	True	84.2005	1242	1959	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	84.1556	1242	1959	95	below_threshold
Massilia aromaticivorans	strain=ML15P13	GCA_013003915.1	2725995	2725995	type	True	83.7345	1198	1959	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	82.6321	1149	1959	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	82.5372	1195	1959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:19,806] [INFO] DFAST Taxonomy check result was written to GCF_008014745.1_ASM801474v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:19,806] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:19,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:19,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg463dff53-a616-4366-90fe-d94d49737208/dqc_reference/checkm_data
[2024-01-24 13:42:19,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:19,872] [INFO] Task started: CheckM
[2024-01-24 13:42:19,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008014745.1_ASM801474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008014745.1_ASM801474v1_genomic.fna/checkm_input GCF_008014745.1_ASM801474v1_genomic.fna/checkm_result
[2024-01-24 13:43:12,376] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:12,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:12,400] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:12,401] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:12,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008014745.1_ASM801474v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:12,402] [INFO] Task started: Blastn
[2024-01-24 13:43:12,402] [INFO] Running command: blastn -query GCF_008014745.1_ASM801474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463dff53-a616-4366-90fe-d94d49737208/dqc_reference/reference_markers_gtdb.fasta -out GCF_008014745.1_ASM801474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:14,326] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:14,331] [INFO] Selected 5 target genomes.
[2024-01-24 13:43:14,331] [INFO] Target genome list was writen to GCF_008014745.1_ASM801474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:14,337] [INFO] Task started: fastANI
[2024-01-24 13:43:14,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6018c91-14e4-4286-90c8-5ffb693d2c08/GCF_008014745.1_ASM801474v1_genomic.fna.gz --refList GCF_008014745.1_ASM801474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008014745.1_ASM801474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:23,267] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:23,273] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:23,273] [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_003719535.1	s__Massilia aurea_A	95.7754	1551	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.87	95.87	0.88	0.88	2	conclusive
GCF_017582745.1	s__Massilia oculi	93.9024	1711	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.07	95.07	0.86	0.86	2	-
GCF_000315425.1	s__Massilia timonae	93.1464	1640	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	97.91	95.09	0.93	0.87	8	-
GCA_002339265.1	s__Massilia sp002339265	91.8972	1409	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222695.1	s__Massilia sp005222695	90.7179	1586	1959	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 13:43:23,274] [INFO] GTDB search result was written to GCF_008014745.1_ASM801474v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:23,275] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:23,278] [INFO] DFAST_QC result json was written to GCF_008014745.1_ASM801474v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:23,278] [INFO] DFAST_QC completed!
[2024-01-24 13:43:23,278] [INFO] Total running time: 0h1m42s