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Published 20 hours ago • verified publisher icon jtamames

DAS tool issue (SqueezeMeta v1.5)

Open pedres opened this issue 2 years ago • 10 comments

Hi, I have finished a full run of SqueezeMeta pipeline using three binners (-binners metabat2,maxbin,concoct), and when I check the method file I saw that apparently only metabat2 and maxbin2 were used:

Binning was done using Metabat2 (Kang et al 2019, PeerJ 7, e7359) Binning was done using MaxBin2 (Wu et al 2016, Bioinformatics 32(4), 605-7) Combination of binning results was done using DAS Tool (Sieber et al 2018, Nat Microbiol 3(7), 836-43)

After checking the syslog I saw that the pipeline also run concoct. Also, I have revised the script 15 to see how DAS tool "works" and I think that it searchs for binners in the folder binners within the intermediate folder. In my project this folder has folder for the three binners, however the concoct folder only have a coverage_table.tsv file (there are not any fasta file). Maybe there was a problem while running concoct, or the problem was with DAS tool?

Thank you very much for your help,

Manuel

RUNNING concoct Creating /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct directory Working for vermi_MAGs_binners.CT21_C.sam Creating sorted BAM for vermi_MAGs_binners.CT21_C.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.CT21_C.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT21_C.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT21_C.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.EW21_B.sam Creating sorted BAM for vermi_MAGs_binners.EW21_B.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.EW21_B.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW21_B.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW21_B.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.CT63_C.sam Creating sorted BAM for vermi_MAGs_binners.CT63_C.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.CT63_C.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT63_C.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT63_C.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.CT63_A.sam Creating sorted BAM for vermi_MAGs_binners.CT63_A.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.CT63_A.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT63_A.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT63_A.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.EW21_C.sam Creating sorted BAM for vermi_MAGs_binners.EW21_C.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.EW21_C.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW21_C.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW21_C.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.EW63_B.sam Creating sorted BAM for vermi_MAGs_binners.EW63_B.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.EW63_B.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW63_B.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW63_B.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.EW63_C.sam Creating sorted BAM for vermi_MAGs_binners.EW63_C.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.EW63_C.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW63_C.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW63_C.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.EW21_A.sam Creating sorted BAM for vermi_MAGs_binners.EW21_A.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.EW21_A.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW21_A.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW21_A.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.EW63_A.sam Creating sorted BAM for vermi_MAGs_binners.EW63_A.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.EW63_A.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW63_A.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.EW63_A.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.CT63_B.sam Creating sorted BAM for vermi_MAGs_binners.CT63_B.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.CT63_B.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT63_B.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT63_B.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.CT21_A.sam Creating sorted BAM for vermi_MAGs_binners.CT21_A.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.CT21_A.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT21_A.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT21_A.sorted.bam > /dev/null 2>&1 Working for vermi_MAGs_binners.CT21_B.sam Creating sorted BAM for vermi_MAGs_binners.CT21_B.sam: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools sort /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/data/sam/vermi_MAGs_binners.CT21_B.sam -o /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT21_B.sorted.bam -@128 > /dev/null 2>&1 Indexing sorted BAM: LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/lib /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/samtools index /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.CT21_B.sorted.bam > /dev/null 2>&1

Cutting contigs in pieces!: python3 /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/cut_up_fasta.py /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/results/01.vermi_MAGs_binners.fasta -c 10000 -o 0 --merge_last -b /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.contigs.bed > /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.choppedcontigs.fasta Creating abundance table: PATH=/mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin:$PATH python3 /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/concoct_coverage_table.py /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.contigs.bed /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/*.sorted.bam > /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/coverage_table.tsv Running concoct: OMP_THREAD_LIMIT=128 python3 /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/CONCOCT-1.1.0/bin/concoct --composition_file /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.choppedcontigs.fasta --coverage_file /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/coverage_table.tsv --threads 128 -m 2500 -b /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/concoct_int/ > /dev/null 2>&1 Merging clusters: /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/merge_cutup_clustering.py /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/concoct_int/clustering_gt1000.csv > /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/concoct_int/clustering_merged.csv Extracting final bins: python3 /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/CONCOCT-1.1.0/scripts/extract_fasta_bins.py /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/results/01.vermi_MAGs_binners.fasta /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/concoct_int/clustering_merged.csv --output_path /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct > /dev/null 2>&1

pedres avatar Oct 05 '22 06:10 pedres

What happens if you just run

OMP_THREAD_LIMIT=128 python3 /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/CONCOCT-1.1.0/bin/concoct --composition_file /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.choppedcontigs.fasta --coverage_file /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/coverage_table.tsv --threads 128 -m 2500 -b /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/concoct_int/

?

fpusan avatar Oct 05 '22 07:10 fpusan

Hello Which version are you using? Any chance that you are mixing versions (like re-running an older project with a new version of Squeezemeta)?

jtamames avatar Oct 05 '22 07:10 jtamames

What happens if you just run

OMP_THREAD_LIMIT=128 python3 /mnt/netapp2/Store_uni/home/uvi/ba/mav/conda/envs/SqueezeMeta/SqueezeMeta/bin/CONCOCT-1.1.0/bin/concoct --composition_file /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/temp/vermi_MAGs_binners.choppedcontigs.fasta --coverage_file /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/coverage_table.tsv --threads 128 -m 2500 -b /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/concoct_int/

?

It gives: concoct: error: unrecognized arguments -m 2500 If a remove this parameter it gives the following error (see attached picture). The log file said 2022-10-05 14:30:34,142:INFO:root:Results created at /mnt/lustre/scratch/nlsas/home/uvi/ba/mav/vermi_MAGs_binners/intermediate/binners/concoct/concoct_int

Captura de pantalla 2022-10-05 143145

pedres avatar Oct 05 '22 12:10 pedres

Hello Which version are you using? Any chance that you are mixing versions (like re-running an older project with a new version of Squeezemeta)?

I am running version 1.5.1. It was a fresh run with only one restart from step 14.

pedres avatar Oct 05 '22 12:10 pedres

Maybe related with this, after running sqm2tables.py vermi_MAGs_binners vermi_MAGs_binners/results/tables and try to load it on R. It gives me this error:

vermi_MAGs_binners<-loadSQM("vermi_MAGs_binners") Loading orfs table... abundances... sequences taxonomy... Loading contigs table... abundances... sequences... taxonomy... binning info... Aggregation function missing: defaulting to length Error in dim(ordered) <- ns : dims [producto 256284] no coincide con la longitud del objeto [3075385]

pedres avatar Oct 06 '22 06:10 pedres

Not necessarily, this is a different bug that was fixed in v1.6.0. Can you update to v1.6.0 and re-run the project?

fpusan avatar Oct 06 '22 08:10 fpusan

Not necessarily, this is a different bug that was fixed in v1.6.0. Can you update to v1.6.0 and re-run the project?

I will try it later because in the server that error does not appear when using loadSQM. By now I have run sqm2tables.py and then loadSQMlite pointing to tables directory works without problems.

pedres avatar Oct 06 '22 10:10 pedres

Hi, I am running version 1.5.1.

It was a "fresh" run. I had to do only a restart , which started from step 14

Javier Tamames @.***> escribió:

Hello Which version are you using? Any chance that you are mixing versions
(like re-running an older project with a new version of Squeezemeta)?

-- Reply to this email directly or view it on GitHub: https://github.com/jtamames/SqueezeMeta/issues/554#issuecomment-1268075645 You are receiving this because you authored the thread.

Message ID: @.***>

pedres avatar Oct 11 '22 08:10 pedres

I will try it later because in the server that error does not appear when using loadSQM. By now I have run sqm2tables.py and then loadSQMlite pointing to tables directory works without problems.

Yeah, the bug we fixed in 1.6.0 seemed to happen randomly. Anyways, even if the project is loading be aware that you likely don't have the bins from CONCOCT (only those from metabat2 and maxbin)

fpusan avatar Oct 11 '22 08:10 fpusan

I will try it later because in the server that error does not appear when using loadSQM. By now I have run sqm2tables.py and then loadSQMlite pointing to tables directory works without problems.

Yeah, the bug we fixed in 1.6.0 seemed to happen randomly. Anyways, even if the project is loading be aware that you likely don't have the bins from CONCOCT (only those from metabat2 and maxbin)

I know. I am planning to install last version of SqueezeMeta and rerun the analysis, but I can play and understand how to work with this output in R and anvio. Should I download again databases when updating SqueezeMeta?

Thanks for your help

pedres avatar Oct 11 '22 10:10 pedres

Sorry I let this slip. No, you don't need to download them again, just activate the new environment and then run

configure_nodb.pl /path/to/db
test_install.pl

fpusan avatar Oct 26 '22 11:10 fpusan

Sorry I let this slip. No, you don't need to download them again, just activate the new environment and then run

configure_nodb.pl /path/to/db
test_install.pl

No problem, I did it in that way

Regards,

Manuel

pedres avatar Oct 26 '22 11:10 pedres

Re: [jtamames/SqueezeMeta] DAS tool issue (SqueezeMeta v1.5) (Issue #554)

Con fecha miércoles, 26 de octubre de 2022, 13:03:29, escribió:

Sorry I let this slip. No, you don't need to download them again, just activate the new environment and then run configure_nodb.pl /path/to/db test_install.pl — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

No problem. I did it in that way.

Regards,

--

 Manuel Aira  Grupo Ecoloxía Animal  Universidade de Vigo  Spain

pedres avatar Nov 30 '22 09:11 pedres