[2024-01-24 15:26:04,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,583] [INFO] DQC Reference Directory: /var/lib/cwl/stge31ab2ed-f902-4b76-ae01-866f2185e3d7/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,023] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,023] [INFO] Running command: gunzip -c /var/lib/cwl/stgd53826e8-1d61-41a0-96ba-783e3a1b7c7d/GCF_030161815.1_ASM3016181v1_genomic.fna.gz | prodigal -d GCF_030161815.1_ASM3016181v1_genomic.fna/cds.fna -a GCF_030161815.1_ASM3016181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:24,774] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:24,775] [INFO] Task started: HMMsearch
[2024-01-24 15:26:24,775] [INFO] Running command: hmmsearch --tblout GCF_030161815.1_ASM3016181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge31ab2ed-f902-4b76-ae01-866f2185e3d7/dqc_reference/reference_markers.hmm GCF_030161815.1_ASM3016181v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:25,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:25,112] [INFO] Found 6/6 markers.
[2024-01-24 15:26:25,166] [INFO] Query marker FASTA was written to GCF_030161815.1_ASM3016181v1_genomic.fna/markers.fasta
[2024-01-24 15:26:25,167] [INFO] Task started: Blastn
[2024-01-24 15:26:25,167] [INFO] Running command: blastn -query GCF_030161815.1_ASM3016181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge31ab2ed-f902-4b76-ae01-866f2185e3d7/dqc_reference/reference_markers.fasta -out GCF_030161815.1_ASM3016181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:26,184] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:26,189] [INFO] Selected 14 target genomes.
[2024-01-24 15:26:26,189] [INFO] Target genome list was writen to GCF_030161815.1_ASM3016181v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:26,196] [INFO] Task started: fastANI
[2024-01-24 15:26:26,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgd53826e8-1d61-41a0-96ba-783e3a1b7c7d/GCF_030161815.1_ASM3016181v1_genomic.fna.gz --refList GCF_030161815.1_ASM3016181v1_genomic.fna/target_genomes.txt --output GCF_030161815.1_ASM3016181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:43,869] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:43,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge31ab2ed-f902-4b76-ae01-866f2185e3d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:43,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge31ab2ed-f902-4b76-ae01-866f2185e3d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:43,888] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:43,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:43,889] [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
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	99.908	1977	2120	95	conclusive
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	90.5182	1092	2120	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	90.1949	1511	2120	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	89.0094	1466	2120	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	86.8888	1159	2120	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	85.4731	1226	2120	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	85.27	1241	2120	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	84.8029	1214	2120	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	82.7409	1014	2120	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.2408	782	2120	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.3626	292	2120	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	77.0531	285	2120	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	76.9849	220	2120	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	76.2801	165	2120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:43,890] [INFO] DFAST Taxonomy check result was written to GCF_030161815.1_ASM3016181v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:43,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:43,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:43,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge31ab2ed-f902-4b76-ae01-866f2185e3d7/dqc_reference/checkm_data
[2024-01-24 15:26:43,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:43,953] [INFO] Task started: CheckM
[2024-01-24 15:26:43,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161815.1_ASM3016181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161815.1_ASM3016181v1_genomic.fna/checkm_input GCF_030161815.1_ASM3016181v1_genomic.fna/checkm_result
[2024-01-24 15:27:37,506] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:37,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:37,547] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:37,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:37,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161815.1_ASM3016181v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:37,548] [INFO] Task started: Blastn
[2024-01-24 15:27:37,548] [INFO] Running command: blastn -query GCF_030161815.1_ASM3016181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge31ab2ed-f902-4b76-ae01-866f2185e3d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161815.1_ASM3016181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:39,368] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:39,372] [INFO] Selected 14 target genomes.
[2024-01-24 15:27:39,372] [INFO] Target genome list was writen to GCF_030161815.1_ASM3016181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:39,392] [INFO] Task started: fastANI
[2024-01-24 15:27:39,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgd53826e8-1d61-41a0-96ba-783e3a1b7c7d/GCF_030161815.1_ASM3016181v1_genomic.fna.gz --refList GCF_030161815.1_ASM3016181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161815.1_ASM3016181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:57,471] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:57,487] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:57,488] [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_003111705.1	s__Methylobacterium sp003111705	96.9493	1689	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.28	97.28	0.88	0.88	3	conclusive
GCF_002355515.1	s__Methylobacterium populi_A	90.2252	1522	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199985.1	s__Methylobacterium rhodesianum	90.2021	1510	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.84	98.11	0.88	0.84	5	-
GCF_014191355.1	s__Methylobacterium sp014191355	89.6884	1436	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014138645.1	s__Methylobacterium thiocyanatum	89.5856	1481	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.87	97.76	0.88	0.86	7	-
GCF_001423405.1	s__Methylobacterium sp001423405	89.1129	1412	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542815.1	s__Methylobacterium sp001542815	89.0694	1394	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.78	0.92	0.92	2	-
GCF_900234795.1	s__Methylobacterium extorquens	89.0149	1467	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	-
GCF_003201865.1	s__Methylobacterium sp003201865	87.6372	1348	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014845115.1	s__Methylobacterium zatmanii	86.8783	1160	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	77.0437	286	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506555.1	s__Parasphingorhabdus sp902506555	76.2625	56	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927115.1	s__Sphingomonas sp012927115	75.9128	177	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001047015.1	s__Sphingopyxis sp001047015	75.7415	129	2120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:57,490] [INFO] GTDB search result was written to GCF_030161815.1_ASM3016181v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:57,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:57,495] [INFO] DFAST_QC result json was written to GCF_030161815.1_ASM3016181v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:57,495] [INFO] DFAST_QC completed!
[2024-01-24 15:27:57,495] [INFO] Total running time: 0h1m53s