[2024-01-24 14:30:16,972] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:16,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:16,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fdf410b-7d8e-4497-9c22-15ab3cbacc94/dqc_reference
[2024-01-24 14:30:18,326] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,332] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,333] [INFO] Running command: gunzip -c /var/lib/cwl/stgacb5b573-6848-4d91-a74a-43763b08930c/GCF_012927275.1_ASM1292727v1_genomic.fna.gz | prodigal -d GCF_012927275.1_ASM1292727v1_genomic.fna/cds.fna -a GCF_012927275.1_ASM1292727v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:32,450] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:32,450] [INFO] Task started: HMMsearch
[2024-01-24 14:30:32,451] [INFO] Running command: hmmsearch --tblout GCF_012927275.1_ASM1292727v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fdf410b-7d8e-4497-9c22-15ab3cbacc94/dqc_reference/reference_markers.hmm GCF_012927275.1_ASM1292727v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:32,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:32,773] [INFO] Found 6/6 markers.
[2024-01-24 14:30:32,876] [INFO] Query marker FASTA was written to GCF_012927275.1_ASM1292727v1_genomic.fna/markers.fasta
[2024-01-24 14:30:32,877] [INFO] Task started: Blastn
[2024-01-24 14:30:32,877] [INFO] Running command: blastn -query GCF_012927275.1_ASM1292727v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fdf410b-7d8e-4497-9c22-15ab3cbacc94/dqc_reference/reference_markers.fasta -out GCF_012927275.1_ASM1292727v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:33,893] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:33,896] [INFO] Selected 12 target genomes.
[2024-01-24 14:30:33,897] [INFO] Target genome list was writen to GCF_012927275.1_ASM1292727v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:33,913] [INFO] Task started: fastANI
[2024-01-24 14:30:33,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb5b573-6848-4d91-a74a-43763b08930c/GCF_012927275.1_ASM1292727v1_genomic.fna.gz --refList GCF_012927275.1_ASM1292727v1_genomic.fna/target_genomes.txt --output GCF_012927275.1_ASM1292727v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:49,858] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:49,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fdf410b-7d8e-4497-9c22-15ab3cbacc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:49,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fdf410b-7d8e-4497-9c22-15ab3cbacc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:49,870] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:30:49,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:49,870] [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 polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	100.0	1493	1495	95	conclusive
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	87.9314	1191	1495	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	85.9069	1004	1495	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	82.9309	967	1495	95	below_threshold
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	82.8201	955	1495	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	82.528	969	1495	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	82.3673	955	1495	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	82.3068	938	1495	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	82.2545	952	1495	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	81.9631	870	1495	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	81.7969	850	1495	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	81.697	877	1495	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:49,872] [INFO] DFAST Taxonomy check result was written to GCF_012927275.1_ASM1292727v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:49,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:49,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:49,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fdf410b-7d8e-4497-9c22-15ab3cbacc94/dqc_reference/checkm_data
[2024-01-24 14:30:49,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:49,921] [INFO] Task started: CheckM
[2024-01-24 14:30:49,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012927275.1_ASM1292727v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012927275.1_ASM1292727v1_genomic.fna/checkm_input GCF_012927275.1_ASM1292727v1_genomic.fna/checkm_result
[2024-01-24 14:31:33,920] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:33,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:33,955] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:33,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:33,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012927275.1_ASM1292727v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:33,957] [INFO] Task started: Blastn
[2024-01-24 14:31:33,957] [INFO] Running command: blastn -query GCF_012927275.1_ASM1292727v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fdf410b-7d8e-4497-9c22-15ab3cbacc94/dqc_reference/reference_markers_gtdb.fasta -out GCF_012927275.1_ASM1292727v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:35,951] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:35,954] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:35,954] [INFO] Target genome list was writen to GCF_012927275.1_ASM1292727v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:35,983] [INFO] Task started: fastANI
[2024-01-24 14:31:35,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb5b573-6848-4d91-a74a-43763b08930c/GCF_012927275.1_ASM1292727v1_genomic.fna.gz --refList GCF_012927275.1_ASM1292727v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012927275.1_ASM1292727v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:59,101] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:59,125] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:59,125] [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_012927275.1	s__Massilia sp012927275	100.0	1493	1495	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_003590855.1	s__Massilia sp003590855	85.8939	1006	1495	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	82.893	972	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760655.1	s__Massilia eurypsychrophila	82.8133	956	1495	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	82.5082	971	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682175.1	s__Massilia frigida	82.3557	957	1495	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	82.3292	984	1495	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	82.309	937	1495	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	82.2631	950	1495	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	82.194	976	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_018119395.1	s__Massilia sp018119395	82.107	918	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCA_002428015.1	s__Massilia sp002428015	82.0411	868	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760665.1	s__Massilia psychrophila	81.9793	851	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003011895.2	s__Massilia glaciei	81.9636	840	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018119405.1	s__Massilia sp018119405	81.9095	906	1495	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	81.5838	849	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129765.1	s__Massilia sp900129765	80.8823	803	1495	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 14:31:59,127] [INFO] GTDB search result was written to GCF_012927275.1_ASM1292727v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:59,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:59,132] [INFO] DFAST_QC result json was written to GCF_012927275.1_ASM1292727v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:59,132] [INFO] DFAST_QC completed!
[2024-01-24 14:31:59,132] [INFO] Total running time: 0h1m42s