[2024-01-25 19:56:50,745] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:50,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:50,753] [INFO] DQC Reference Directory: /var/lib/cwl/stgf71acb3b-1cad-489e-8f45-aa2e469d363c/dqc_reference
[2024-01-25 19:56:51,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:51,878] [INFO] Task started: Prodigal
[2024-01-25 19:56:51,878] [INFO] Running command: gunzip -c /var/lib/cwl/stge5e59925-769e-4485-9f66-67b97b260c34/GCF_014635065.1_ASM1463506v1_genomic.fna.gz | prodigal -d GCF_014635065.1_ASM1463506v1_genomic.fna/cds.fna -a GCF_014635065.1_ASM1463506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:01,053] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:01,053] [INFO] Task started: HMMsearch
[2024-01-25 19:57:01,053] [INFO] Running command: hmmsearch --tblout GCF_014635065.1_ASM1463506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf71acb3b-1cad-489e-8f45-aa2e469d363c/dqc_reference/reference_markers.hmm GCF_014635065.1_ASM1463506v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:01,265] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:01,266] [INFO] Found 6/6 markers.
[2024-01-25 19:57:01,292] [INFO] Query marker FASTA was written to GCF_014635065.1_ASM1463506v1_genomic.fna/markers.fasta
[2024-01-25 19:57:01,292] [INFO] Task started: Blastn
[2024-01-25 19:57:01,292] [INFO] Running command: blastn -query GCF_014635065.1_ASM1463506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf71acb3b-1cad-489e-8f45-aa2e469d363c/dqc_reference/reference_markers.fasta -out GCF_014635065.1_ASM1463506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:02,279] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:02,285] [INFO] Selected 23 target genomes.
[2024-01-25 19:57:02,285] [INFO] Target genome list was writen to GCF_014635065.1_ASM1463506v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:02,296] [INFO] Task started: fastANI
[2024-01-25 19:57:02,297] [INFO] Running command: fastANI --query /var/lib/cwl/stge5e59925-769e-4485-9f66-67b97b260c34/GCF_014635065.1_ASM1463506v1_genomic.fna.gz --refList GCF_014635065.1_ASM1463506v1_genomic.fna/target_genomes.txt --output GCF_014635065.1_ASM1463506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:24,445] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:24,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf71acb3b-1cad-489e-8f45-aa2e469d363c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:24,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf71acb3b-1cad-489e-8f45-aa2e469d363c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:24,459] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:24,459] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:24,459] [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
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	100.0	1066	1067	95	conclusive
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	82.3227	655	1067	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	80.7448	503	1067	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	80.67	489	1067	95	below_threshold
Oxalicibacterium faecigallinarum	strain=CCM 2767	GCA_014635705.1	573741	573741	type	True	80.3377	577	1067	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	80.2129	401	1067	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	80.0816	443	1067	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	80.0682	432	1067	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	80.038	433	1067	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	80.0271	450	1067	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	79.9965	485	1067	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	79.9902	443	1067	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	79.8755	443	1067	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	79.849	451	1067	95	below_threshold
Herbaspirillum frisingense	strain=GSF30	GCA_000300975.2	92645	92645	type	True	79.826	434	1067	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	79.6955	452	1067	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	79.6532	423	1067	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	79.6437	405	1067	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	79.545	448	1067	95	below_threshold
Massilia horti	strain=ONC3	GCA_004614195.1	2562153	2562153	type	True	79.5027	399	1067	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	79.4651	410	1067	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	79.3924	423	1067	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	79.308	438	1067	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:24,461] [INFO] DFAST Taxonomy check result was written to GCF_014635065.1_ASM1463506v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:24,461] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:24,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:24,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf71acb3b-1cad-489e-8f45-aa2e469d363c/dqc_reference/checkm_data
[2024-01-25 19:57:24,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:24,497] [INFO] Task started: CheckM
[2024-01-25 19:57:24,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635065.1_ASM1463506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635065.1_ASM1463506v1_genomic.fna/checkm_input GCF_014635065.1_ASM1463506v1_genomic.fna/checkm_result
[2024-01-25 19:57:56,120] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:56,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:56,135] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:56,136] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:56,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635065.1_ASM1463506v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:56,136] [INFO] Task started: Blastn
[2024-01-25 19:57:56,136] [INFO] Running command: blastn -query GCF_014635065.1_ASM1463506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf71acb3b-1cad-489e-8f45-aa2e469d363c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635065.1_ASM1463506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:58,221] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:58,224] [INFO] Selected 22 target genomes.
[2024-01-25 19:57:58,224] [INFO] Target genome list was writen to GCF_014635065.1_ASM1463506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:58,243] [INFO] Task started: fastANI
[2024-01-25 19:57:58,244] [INFO] Running command: fastANI --query /var/lib/cwl/stge5e59925-769e-4485-9f66-67b97b260c34/GCF_014635065.1_ASM1463506v1_genomic.fna.gz --refList GCF_014635065.1_ASM1463506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635065.1_ASM1463506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:18,399] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:18,412] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:18,412] [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_014635065.1	s__Oxalicibacterium flavum	100.0	1066	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014635845.1	s__Oxalicibacterium solurbis	82.3051	657	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715495.1	s__Herbaspirillum sp006715495	80.7617	470	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	99.71	99.15	0.99	0.96	4	-
GCA_017744395.1	s__Herbaspirillum sp017744395	80.7495	480	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213415.1	s__Herbaspirillum robiniae	80.7331	504	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	80.4279	459	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635705.1	s__Oxalicibacterium faecigallinarum	80.3377	577	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000256565.1	s__Herbaspirillum lusitanum	80.1421	406	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	80.0913	308	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590835.1	s__Paucimonas sp003590835	80.0905	422	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010974945.1	s__Noviherbaspirillum galbum	80.0242	451	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	80.0093	397	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	79.9748	474	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382345.1	s__Massilia niastensis	79.9733	445	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000261365.1	s__Herbaspirillum sp000261365	79.8933	423	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.65	98.65	0.93	0.93	2	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	79.8611	450	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018119395.1	s__Massilia sp018119395	79.7129	443	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_003590855.1	s__Massilia sp003590855	79.6636	406	1067	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	79.5515	447	1067	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	79.4654	402	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584185.1	s__Collimonas pratensis	79.4587	412	1067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_011682145.1	s__Massilia mucilaginosa	79.2762	441	1067	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 19:58:18,413] [INFO] GTDB search result was written to GCF_014635065.1_ASM1463506v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:18,414] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:18,417] [INFO] DFAST_QC result json was written to GCF_014635065.1_ASM1463506v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:18,418] [INFO] DFAST_QC completed!
[2024-01-25 19:58:18,418] [INFO] Total running time: 0h1m28s