Pipeline aborting at ntLink stage

[asan-emirsaleh]

Hello!
Thank you for developing promising assembler and advancing open-source software.
Please look at the issue I was recently encountered at the final steps of the Goldrush pipeline:

Running ntLink gap-filling...

Parameters:
	--path w16_x10_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.z1000.trimmed_scafs.path
	--mappings w16_x10_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.z1000.verbose_mapping.tsv
	--trims w16_x10_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.z1000.trimmed_scafs.tsv
	-s w16_x10_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa
	--reads ['lr_comb_conservative.fq']

	-z 1000
	-k 20
	-w 10
	-t 4
	--large_k 40
	-x 0
	--min_gap 1
	-o w16_x10_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.scaffolds.gap_fill.fa

2025-03-25 13:25:22.079772 Reading ntLink read mappings..
2025-03-25 13:25:37.627074 Reading scaffolds..
2025-03-25 13:25:38.262430 Reading trim coordinates..
2025-03-25 13:25:38.325940 Choosing best read..
Traceback (most recent call last):
  File "/home/emirsaleh/miniconda3/envs/goldrush2-env/bin/share/ntlink-1.3.11-1/bin/ntlink_patch_gaps.py", line 840, in <module>
    main()
  File "/home/emirsaleh/miniconda3/envs/goldrush2-env/bin/share/ntlink-1.3.11-1/bin/ntlink_patch_gaps.py", line 806, in main
    choose_best_read_per_pair(pairs, mappings, sequences, args)
  File "/home/emirsaleh/miniconda3/envs/goldrush2-env/bin/share/ntlink-1.3.11-1/bin/ntlink_patch_gaps.py", line 252, in choose_best_read_per_pair
    reads = [(read_id, mappings[read_id][source.strip("+-")].anchors,
  File "/home/emirsaleh/miniconda3/envs/goldrush2-env/bin/share/ntlink-1.3.11-1/bin/ntlink_patch_gaps.py", line 252, in <listcomp>
    reads = [(read_id, mappings[read_id][source.strip("+-")].anchors,
KeyError: '32bd3da0-17e2-44b0-bf58-5c3fa686d15c_trimmed_trimmed-1::32bd3da0-17e2-44b0-bf58-5c3fa686d15c_trimmed_trimmed:0-5161'
make[2]: *** [/home/emirsaleh/miniconda3/envs/goldrush2-env/bin/share/ntlink-1.3.11-1/ntLink:267: w16_x10_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.scaffolds.gap_fill.fa] Error 1
make[2]: Leaving directory '/<path>/25_ass_goldrush'
make[1]: *** [/home/emirsaleh/miniconda3/envs/goldrush2-env/bin/share/ntlink-1.3.11-1/ntLink_rounds:104: w16_x10_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.gap_fill.fa] Error 2
make[1]: Leaving directory '/<path>/25_ass_goldrush'
make: *** [/home/emirsaleh/miniconda3/envs/goldrush2-env/bin/goldrush.make:259: w16_x10_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.gap_fill.5rounds.fa] Error 2

Could you please suggest a solution? Are there a simple fix? Is this a data issue?

Best regards
Asan

[jwcodee]

Hi Asan,

The error seems to be coming from the gap filling stage of ntLink where it tries to gap fill with the best read that it can find. I'm not exactly sure how this error triggered. Can you rerun GoldRush using the same command and see if this error is transient? Goldrush is powered by a makefile so it will only restart from gap filling stage so it should be relatively quick.

[github-actions]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in GoldRush!

[asan-emirsaleh]

Multiple rerun did not succeed.

[lcoombe]

Hi @asan-emirsaleh,

To confirm - have you run our demo to ensure that your installation is working correctly? Or have you had a previous successful run with other data?
If so, could you share your full log so I could take a look? Also, could you share a top of the files w16_x10_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.z1000.verbose_mapping.tsv and lr_comb_conservative.fq if you still have them?