[2024-01-24 13:40:46,173] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,175] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,175] [INFO] DQC Reference Directory: /var/lib/cwl/stgbad5ce40-790e-4546-bd79-17b0f2be1f73/dqc_reference
[2024-01-24 13:40:47,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,494] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg69bda10d-faf3-4b5a-ac89-e95c0158bb5a/GCF_030160915.1_ASM3016091v1_genomic.fna.gz | prodigal -d GCF_030160915.1_ASM3016091v1_genomic.fna/cds.fna -a GCF_030160915.1_ASM3016091v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:02,126] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:02,126] [INFO] Task started: HMMsearch
[2024-01-24 13:41:02,126] [INFO] Running command: hmmsearch --tblout GCF_030160915.1_ASM3016091v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbad5ce40-790e-4546-bd79-17b0f2be1f73/dqc_reference/reference_markers.hmm GCF_030160915.1_ASM3016091v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:02,424] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:02,426] [INFO] Found 6/6 markers.
[2024-01-24 13:41:02,475] [INFO] Query marker FASTA was written to GCF_030160915.1_ASM3016091v1_genomic.fna/markers.fasta
[2024-01-24 13:41:02,476] [INFO] Task started: Blastn
[2024-01-24 13:41:02,476] [INFO] Running command: blastn -query GCF_030160915.1_ASM3016091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbad5ce40-790e-4546-bd79-17b0f2be1f73/dqc_reference/reference_markers.fasta -out GCF_030160915.1_ASM3016091v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:03,470] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:03,474] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:03,475] [INFO] Target genome list was writen to GCF_030160915.1_ASM3016091v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:03,480] [INFO] Task started: fastANI
[2024-01-24 13:41:03,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg69bda10d-faf3-4b5a-ac89-e95c0158bb5a/GCF_030160915.1_ASM3016091v1_genomic.fna.gz --refList GCF_030160915.1_ASM3016091v1_genomic.fna/target_genomes.txt --output GCF_030160915.1_ASM3016091v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:16,820] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:16,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbad5ce40-790e-4546-bd79-17b0f2be1f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:16,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbad5ce40-790e-4546-bd79-17b0f2be1f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:16,831] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:16,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:16,831] [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 brachythecii	strain=DSM 24105	GCA_014196345.1	1176177	1176177	type	True	99.998	1744	1756	95	conclusive
Methylobacterium gnaphalii	strain=NBRC 107716	GCA_007992215.1	1010610	1010610	type	True	86.8571	1134	1756	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	86.7184	1109	1756	95	below_threshold
Methylobacterium haplocladii	strain=DSM 24195	GCA_022179265.1	1176176	1176176	type	True	84.5402	1018	1756	95	below_threshold
Methylobacterium haplocladii	strain=NBRC 107714	GCA_007992175.1	1176176	1176176	type	True	84.4891	1054	1756	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	81.8468	744	1756	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	81.4517	906	1756	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	81.3337	768	1756	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	80.9814	880	1756	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	79.7989	773	1756	95	below_threshold
Methylobacterium frigidaeris	strain=IER25-16	GCA_002759055.1	2038277	2038277	type	True	79.6479	535	1756	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.3233	263	1756	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:16,833] [INFO] DFAST Taxonomy check result was written to GCF_030160915.1_ASM3016091v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:16,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:16,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:16,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbad5ce40-790e-4546-bd79-17b0f2be1f73/dqc_reference/checkm_data
[2024-01-24 13:41:16,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:16,890] [INFO] Task started: CheckM
[2024-01-24 13:41:16,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160915.1_ASM3016091v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160915.1_ASM3016091v1_genomic.fna/checkm_input GCF_030160915.1_ASM3016091v1_genomic.fna/checkm_result
[2024-01-24 13:42:01,560] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:01,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.24%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:01,586] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:01,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:01,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160915.1_ASM3016091v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:01,587] [INFO] Task started: Blastn
[2024-01-24 13:42:01,587] [INFO] Running command: blastn -query GCF_030160915.1_ASM3016091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbad5ce40-790e-4546-bd79-17b0f2be1f73/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160915.1_ASM3016091v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:03,299] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:03,302] [INFO] Selected 11 target genomes.
[2024-01-24 13:42:03,302] [INFO] Target genome list was writen to GCF_030160915.1_ASM3016091v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:03,423] [INFO] Task started: fastANI
[2024-01-24 13:42:03,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg69bda10d-faf3-4b5a-ac89-e95c0158bb5a/GCF_030160915.1_ASM3016091v1_genomic.fna.gz --refList GCF_030160915.1_ASM3016091v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160915.1_ASM3016091v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:16,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:16,122] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:16,122] [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_014196345.1	s__Methylobacterium brachythecii	99.998	1744	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007992215.1	s__Methylobacterium gnaphalii	86.8558	1134	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992175.1	s__Methylobacterium haplocladii	84.5148	1050	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040035.1	s__Methylobacterium sp008040035	84.5135	1048	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199935.1	s__Methylobacterium rhodinum	81.5664	942	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	81.3799	865	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCA_002778835.1	s__Methylobacterium sp002778835	81.2491	794	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.93	99.92	0.96	0.96	4	-
GCF_008806345.1	s__Methylobacterium sp008806345	81.1171	886	1756	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	80.4692	812	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422815.1	s__Methylobacterium sp001422815	80.2235	779	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.57	97.58	0.90	0.88	3	-
GCF_008630155.1	s__Rhodovastum atsumiense	76.2848	255	1756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:16,124] [INFO] GTDB search result was written to GCF_030160915.1_ASM3016091v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:16,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:16,132] [INFO] DFAST_QC result json was written to GCF_030160915.1_ASM3016091v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:16,132] [INFO] DFAST_QC completed!
[2024-01-24 13:42:16,132] [INFO] Total running time: 0h1m30s