[2024-01-25 18:57:05,660] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:05,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:05,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f293b2a-33d9-4ace-b9ae-bece26da53d8/dqc_reference
[2024-01-25 18:57:06,754] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:06,755] [INFO] Task started: Prodigal
[2024-01-25 18:57:06,755] [INFO] Running command: gunzip -c /var/lib/cwl/stgab21b31a-d97a-4a42-8123-3749acad048b/GCF_024756255.1_ASM2475625v1_genomic.fna.gz | prodigal -d GCF_024756255.1_ASM2475625v1_genomic.fna/cds.fna -a GCF_024756255.1_ASM2475625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:21,758] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:21,758] [INFO] Task started: HMMsearch
[2024-01-25 18:57:21,758] [INFO] Running command: hmmsearch --tblout GCF_024756255.1_ASM2475625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f293b2a-33d9-4ace-b9ae-bece26da53d8/dqc_reference/reference_markers.hmm GCF_024756255.1_ASM2475625v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:22,049] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:22,050] [INFO] Found 6/6 markers.
[2024-01-25 18:57:22,091] [INFO] Query marker FASTA was written to GCF_024756255.1_ASM2475625v1_genomic.fna/markers.fasta
[2024-01-25 18:57:22,091] [INFO] Task started: Blastn
[2024-01-25 18:57:22,091] [INFO] Running command: blastn -query GCF_024756255.1_ASM2475625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f293b2a-33d9-4ace-b9ae-bece26da53d8/dqc_reference/reference_markers.fasta -out GCF_024756255.1_ASM2475625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:23,101] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:23,104] [INFO] Selected 12 target genomes.
[2024-01-25 18:57:23,104] [INFO] Target genome list was writen to GCF_024756255.1_ASM2475625v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:23,111] [INFO] Task started: fastANI
[2024-01-25 18:57:23,111] [INFO] Running command: fastANI --query /var/lib/cwl/stgab21b31a-d97a-4a42-8123-3749acad048b/GCF_024756255.1_ASM2475625v1_genomic.fna.gz --refList GCF_024756255.1_ASM2475625v1_genomic.fna/target_genomes.txt --output GCF_024756255.1_ASM2475625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:40,123] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:40,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f293b2a-33d9-4ace-b9ae-bece26da53d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:40,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f293b2a-33d9-4ace-b9ae-bece26da53d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:40,132] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:57:40,132] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:57:40,132] [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 agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	100.0	1710	1711	95	inconclusive
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	95.2778	1577	1711	95	inconclusive
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	85.4631	1223	1711	95	below_threshold
Massilia horti	strain=ONC3	GCA_004614195.1	2562153	2562153	type	True	83.4153	1046	1711	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	83.1213	1061	1711	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	82.7676	1054	1711	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	82.7265	1088	1711	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	82.7234	1076	1711	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	82.4241	1026	1711	95	below_threshold
Massilia timonae	strain=CCUG 45783	GCA_000315425.1	47229	47229	type	True	82.4211	1023	1711	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.9933	828	1711	95	below_threshold
Massilia putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	81.9109	1050	1711	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:40,134] [INFO] DFAST Taxonomy check result was written to GCF_024756255.1_ASM2475625v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:40,134] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:40,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:40,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f293b2a-33d9-4ace-b9ae-bece26da53d8/dqc_reference/checkm_data
[2024-01-25 18:57:40,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:40,183] [INFO] Task started: CheckM
[2024-01-25 18:57:40,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024756255.1_ASM2475625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024756255.1_ASM2475625v1_genomic.fna/checkm_input GCF_024756255.1_ASM2475625v1_genomic.fna/checkm_result
[2024-01-25 18:58:30,359] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:30,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:30,379] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:30,379] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:30,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024756255.1_ASM2475625v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:30,380] [INFO] Task started: Blastn
[2024-01-25 18:58:30,380] [INFO] Running command: blastn -query GCF_024756255.1_ASM2475625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f293b2a-33d9-4ace-b9ae-bece26da53d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_024756255.1_ASM2475625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:32,453] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:32,457] [INFO] Selected 21 target genomes.
[2024-01-25 18:58:32,457] [INFO] Target genome list was writen to GCF_024756255.1_ASM2475625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:32,472] [INFO] Task started: fastANI
[2024-01-25 18:58:32,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgab21b31a-d97a-4a42-8123-3749acad048b/GCF_024756255.1_ASM2475625v1_genomic.fna.gz --refList GCF_024756255.1_ASM2475625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024756255.1_ASM2475625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:58,599] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:58,611] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:58:58,612] [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
GCA_003484545.1	s__Massilia sp003484545	83.4622	667	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520365.1	s__Massilia sp003520365	83.4187	662	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614195.1	s__Massilia horti	83.4002	1046	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354135.1	s__Massilia sp002354135	83.1998	829	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018119395.1	s__Massilia sp018119395	83.1729	1041	1711	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	83.1504	1023	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382345.1	s__Massilia niastensis	83.1086	1063	1711	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	82.9916	1047	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412595.2	s__Massilia sp001412595	82.8908	1126	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000427785.1	s__Massilia alkalitolerans	82.8216	1048	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.93	95.88	0.90	0.87	5	-
GCF_012849555.1	s__Massilia sp012849555	82.7398	1086	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745265.1	s__Massilia sp000745265	82.6741	1053	1711	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	82.5374	1014	1711	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	82.4468	1019	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	97.91	95.09	0.93	0.87	8	-
GCF_004798585.1	s__Massilia sp004798585	82.1275	1027	1711	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	82.0409	823	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759615.1	s__Massilia sp000759615	81.938	1060	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941825.1	s__Massilia putida	81.8843	1052	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426525.1	s__Massilia sp001426525	81.8624	1086	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.62	99.38	0.97	0.95	3	-
GCF_900101265.1	s__Massilia sp900101265	81.8542	1064	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614185.1	s__Massilia arenosa	81.4797	860	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:58,613] [INFO] GTDB search result was written to GCF_024756255.1_ASM2475625v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:58,614] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:58,617] [INFO] DFAST_QC result json was written to GCF_024756255.1_ASM2475625v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:58,617] [INFO] DFAST_QC completed!
[2024-01-25 18:58:58,617] [INFO] Total running time: 0h1m53s