[2024-01-25 17:40:35,500] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:35,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:35,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg834adeeb-f96d-42f6-a564-508acbfc7f3b/dqc_reference
[2024-01-25 17:40:36,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:36,650] [INFO] Task started: Prodigal
[2024-01-25 17:40:36,651] [INFO] Running command: gunzip -c /var/lib/cwl/stg53ef2820-0476-4e58-b9b9-81eede538c63/GCF_030161015.1_ASM3016101v1_genomic.fna.gz | prodigal -d GCF_030161015.1_ASM3016101v1_genomic.fna/cds.fna -a GCF_030161015.1_ASM3016101v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:52,884] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:52,885] [INFO] Task started: HMMsearch
[2024-01-25 17:40:52,885] [INFO] Running command: hmmsearch --tblout GCF_030161015.1_ASM3016101v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg834adeeb-f96d-42f6-a564-508acbfc7f3b/dqc_reference/reference_markers.hmm GCF_030161015.1_ASM3016101v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:53,203] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:53,204] [INFO] Found 6/6 markers.
[2024-01-25 17:40:53,257] [INFO] Query marker FASTA was written to GCF_030161015.1_ASM3016101v1_genomic.fna/markers.fasta
[2024-01-25 17:40:53,257] [INFO] Task started: Blastn
[2024-01-25 17:40:53,257] [INFO] Running command: blastn -query GCF_030161015.1_ASM3016101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834adeeb-f96d-42f6-a564-508acbfc7f3b/dqc_reference/reference_markers.fasta -out GCF_030161015.1_ASM3016101v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:54,280] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:54,283] [INFO] Selected 10 target genomes.
[2024-01-25 17:40:54,283] [INFO] Target genome list was writen to GCF_030161015.1_ASM3016101v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:54,291] [INFO] Task started: fastANI
[2024-01-25 17:40:54,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ef2820-0476-4e58-b9b9-81eede538c63/GCF_030161015.1_ASM3016101v1_genomic.fna.gz --refList GCF_030161015.1_ASM3016101v1_genomic.fna/target_genomes.txt --output GCF_030161015.1_ASM3016101v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:11,865] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:11,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg834adeeb-f96d-42f6-a564-508acbfc7f3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:11,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg834adeeb-f96d-42f6-a564-508acbfc7f3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:11,873] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:41:11,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:11,873] [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
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	99.9878	2224	2272	95	conclusive
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	99.9428	2270	2272	95	conclusive
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	88.5584	1583	2272	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	88.5535	1532	2272	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	87.8906	1457	2272	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	87.8099	1485	2272	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	87.2111	1498	2272	95	below_threshold
Methylobacterium phyllostachyos	strain=BL47	GCA_900103445.1	582672	582672	type	True	86.8686	1459	2272	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	85.8475	1365	2272	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	82.6319	1059	2272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:11,875] [INFO] DFAST Taxonomy check result was written to GCF_030161015.1_ASM3016101v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:11,876] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:11,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:11,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg834adeeb-f96d-42f6-a564-508acbfc7f3b/dqc_reference/checkm_data
[2024-01-25 17:41:11,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:11,944] [INFO] Task started: CheckM
[2024-01-25 17:41:11,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161015.1_ASM3016101v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161015.1_ASM3016101v1_genomic.fna/checkm_input GCF_030161015.1_ASM3016101v1_genomic.fna/checkm_result
[2024-01-25 17:42:04,059] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:04,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:04,085] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:04,086] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:04,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161015.1_ASM3016101v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:04,090] [INFO] Task started: Blastn
[2024-01-25 17:42:04,090] [INFO] Running command: blastn -query GCF_030161015.1_ASM3016101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834adeeb-f96d-42f6-a564-508acbfc7f3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161015.1_ASM3016101v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:06,299] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:06,304] [INFO] Selected 10 target genomes.
[2024-01-25 17:42:06,304] [INFO] Target genome list was writen to GCF_030161015.1_ASM3016101v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:06,314] [INFO] Task started: fastANI
[2024-01-25 17:42:06,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ef2820-0476-4e58-b9b9-81eede538c63/GCF_030161015.1_ASM3016101v1_genomic.fna.gz --refList GCF_030161015.1_ASM3016101v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161015.1_ASM3016101v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:24,632] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:24,640] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:24,640] [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_014873335.1	s__Methylobacterium sp014873335	96.299	1779	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017833295.1	s__Methylobacterium sp017833295	92.6491	1705	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003096615.1	s__Methylobacterium organophilum	89.0164	1640	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
GCF_900112625.1	s__Methylobacterium sp900112625	88.5395	1489	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_014138435.1	s__Methylobacterium fujisawaense	88.2399	1471	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	-
GCF_009806555.1	s__Methylobacterium sp009806555	88.1474	1511	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103195.1	s__Methylobacterium sp900103195	88.0017	1509	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_000364445.2	s__Methylobacterium mesophilicum	87.6378	1526	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103445.1	s__Methylobacterium phyllostachyos	86.8227	1467	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001455965.1	s__Methylobacterium sp001455965	85.3046	1354	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:24,644] [INFO] GTDB search result was written to GCF_030161015.1_ASM3016101v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:24,644] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:24,647] [INFO] DFAST_QC result json was written to GCF_030161015.1_ASM3016101v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:24,647] [INFO] DFAST_QC completed!
[2024-01-25 17:42:24,647] [INFO] Total running time: 0h1m49s