Step 7: Error 72

[MCampos92]

Hi! I'm running Ipyrad [v.0.9.81] and I'm having problems with step 7. When I run the software without reference (de novo) it works fine. But now i'm trying to do it using a genome of reference and it works until step 7, that gives me this error.

This is the full stats files: ipyrad -p params-staceiFR.txt -r

Full stats files

step 1: ./IpyradStaceiFR/StaceiFR_s1_demultiplex_stats.txt step 2: ./IpyradStaceiFR/StaceiFR_edits/s2_rawedit_stats.txt step 3: ./IpyradStaceiFR/StaceiFR_clust_0.85/s3_cluster_stats.txt step 4: ./IpyradStaceiFR/StaceiFR_clust_0.85/s4_joint_estimate.txt step 5: ./IpyradStaceiFR/StaceiFR_consens/s5_consens_stats.txt step 6: ./IpyradStaceiFR/StaceiFR_across/StaceiFR_clust_database.fa step 7: None

And when I run step 7: ipyrad -p params-staceiFR.txt -s 7 -d

loading Assembly: StaceiFR from saved path: /RadSeq/IpyradStaceiFR/StaceiFR.json

---

ipyrad [v.0.9.81] Interactive assembly and analysis of RAD-seq data

Parallel connection | UBUNTUSRV: 12 cores

Step 7: Filtering and formatting output files [####################] 100% 0:02:36 | applying filters [####################] 100% 0:04:57 | building arrays

Encountered an Error. Message: KeyError: 72 Parallel connection closed. ---------------------------------------------------------------------------KeyError Traceback (most recent call last) in ~/miniconda3/lib/python3.8/site-packages/ipyrad/assemble/write_outputs.py in fill_snp_array(data, ntaxa, nsnps) 2156 # fill for each taxon 2157 for sidx in range(ntaxa): -> 2158 resos = [DCONS[i] for i in snparr[sidx, :]] 2159 2160 # pseudoref version ~/miniconda3/lib/python3.8/site-packages/ipyrad/assemble/write_outputs.py in (.0) 2156 # fill for each taxon 2157 for sidx in range(ntaxa): -> 2158 resos = [DCONS[i] for i in snparr[sidx, :]] 2159 2160 # pseudoref version KeyError: 72

Could you help me to solve this problem?

Thanks, Miguel

[MCampos92]

Solved. The reference sequences had ambiguities.

[isaacovercast]

Glad you solved it! Thanks for updating the issue. Ambiguities in the reference would definitely do it. Glad you figured it out.