[2024-01-25 18:06:20,775] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:20,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:20,777] [INFO] DQC Reference Directory: /var/lib/cwl/stgf390a711-307f-4045-a7ed-83c7a9f6c24d/dqc_reference
[2024-01-25 18:06:21,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:21,953] [INFO] Task started: Prodigal
[2024-01-25 18:06:21,954] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7dd617b-b81a-4185-b622-8786705ca8b0/GCF_030409395.1_ASM3040939v1_genomic.fna.gz | prodigal -d GCF_030409395.1_ASM3040939v1_genomic.fna/cds.fna -a GCF_030409395.1_ASM3040939v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:36,881] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:36,882] [INFO] Task started: HMMsearch
[2024-01-25 18:06:36,882] [INFO] Running command: hmmsearch --tblout GCF_030409395.1_ASM3040939v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf390a711-307f-4045-a7ed-83c7a9f6c24d/dqc_reference/reference_markers.hmm GCF_030409395.1_ASM3040939v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:37,171] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:37,173] [INFO] Found 6/6 markers.
[2024-01-25 18:06:37,223] [INFO] Query marker FASTA was written to GCF_030409395.1_ASM3040939v1_genomic.fna/markers.fasta
[2024-01-25 18:06:37,223] [INFO] Task started: Blastn
[2024-01-25 18:06:37,224] [INFO] Running command: blastn -query GCF_030409395.1_ASM3040939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf390a711-307f-4045-a7ed-83c7a9f6c24d/dqc_reference/reference_markers.fasta -out GCF_030409395.1_ASM3040939v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:38,109] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:38,111] [INFO] Selected 16 target genomes.
[2024-01-25 18:06:38,112] [INFO] Target genome list was writen to GCF_030409395.1_ASM3040939v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:38,121] [INFO] Task started: fastANI
[2024-01-25 18:06:38,121] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7dd617b-b81a-4185-b622-8786705ca8b0/GCF_030409395.1_ASM3040939v1_genomic.fna.gz --refList GCF_030409395.1_ASM3040939v1_genomic.fna/target_genomes.txt --output GCF_030409395.1_ASM3040939v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:01,385] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:01,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf390a711-307f-4045-a7ed-83c7a9f6c24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:01,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf390a711-307f-4045-a7ed-83c7a9f6c24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:01,395] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:01,396] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:01,396] [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 longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	99.9685	2082	2113	95	conclusive
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	87.7814	1494	2113	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	87.7491	1471	2113	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	87.4101	1461	2113	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	87.2653	1411	2113	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	87.2291	1413	2113	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	87.2057	1512	2113	95	below_threshold
Methylobacterium phyllostachyos	strain=BL47	GCA_900103445.1	582672	582672	type	True	86.2942	1362	2113	95	below_threshold
Methylobacterium brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	85.5986	1383	2113	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	85.502	1351	2113	95	below_threshold
Methylobacterium pseudosasicola	strain=BL36	GCA_900114535.1	582667	582667	type	True	85.3705	1377	2113	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	82.3562	1020	2113	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	77.6318	431	2113	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	77.5814	412	2113	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	76.908	299	2113	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	74.856	317	2113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:01,397] [INFO] DFAST Taxonomy check result was written to GCF_030409395.1_ASM3040939v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:01,398] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:01,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:01,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf390a711-307f-4045-a7ed-83c7a9f6c24d/dqc_reference/checkm_data
[2024-01-25 18:07:01,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:01,462] [INFO] Task started: CheckM
[2024-01-25 18:07:01,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409395.1_ASM3040939v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409395.1_ASM3040939v1_genomic.fna/checkm_input GCF_030409395.1_ASM3040939v1_genomic.fna/checkm_result
[2024-01-25 18:07:50,319] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:50,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:50,337] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:50,337] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:50,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409395.1_ASM3040939v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:50,340] [INFO] Task started: Blastn
[2024-01-25 18:07:50,340] [INFO] Running command: blastn -query GCF_030409395.1_ASM3040939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf390a711-307f-4045-a7ed-83c7a9f6c24d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409395.1_ASM3040939v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:52,127] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:52,130] [INFO] Selected 18 target genomes.
[2024-01-25 18:07:52,130] [INFO] Target genome list was writen to GCF_030409395.1_ASM3040939v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:52,146] [INFO] Task started: fastANI
[2024-01-25 18:07:52,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7dd617b-b81a-4185-b622-8786705ca8b0/GCF_030409395.1_ASM3040939v1_genomic.fna.gz --refList GCF_030409395.1_ASM3040939v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409395.1_ASM3040939v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:17,955] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:17,965] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:08:17,965] [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_000364445.2	s__Methylobacterium mesophilicum	87.9674	1529	2113	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	87.7032	1500	2113	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	87.6941	1457	2113	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	87.3137	1408	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	-
GCF_900103195.1	s__Methylobacterium sp900103195	87.3106	1454	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_014873335.1	s__Methylobacterium sp014873335	87.2397	1446	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017833295.1	s__Methylobacterium sp017833295	87.0353	1476	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009806555.1	s__Methylobacterium sp009806555	86.8095	1371	2113	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	86.3099	1359	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697185.1	s__Methylobacterium brachiatum	85.6635	1369	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.08	95.77	0.85	0.80	4	-
GCF_900114535.1	s__Methylobacterium pseudosasicola	85.3609	1379	2113	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	84.9831	1328	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141855.1	s__Methylobacterium dankookense	82.2688	1087	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040045.1	s__Methylobacterium sp008040045	81.9066	1046	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.25	98.17	0.85	0.85	3	-
GCF_003173715.1	s__Methylobacterium durans	81.2247	976	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869215.1	s__Z2-YC6860 sp016869215	76.9466	297	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:08:17,967] [INFO] GTDB search result was written to GCF_030409395.1_ASM3040939v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:17,968] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:17,971] [INFO] DFAST_QC result json was written to GCF_030409395.1_ASM3040939v1_genomic.fna/dqc_result.json
[2024-01-25 18:08:17,971] [INFO] DFAST_QC completed!
[2024-01-25 18:08:17,971] [INFO] Total running time: 0h1m57s