# Humann\_unpack\_pathways command **URL:** \ **Category:** HUMAnN\ **Created:** [January 26, 2024, 6:21pm UTC](https://forum.biobakery.org/t/humann-unpack-pathways-command/6530 "2024-01-26T18:21:36Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![young\_doktor](https://avatars.discourse-cdn.com/v4/letter/y/dc4da7/32.png) [@young\_doktor](https://forum.biobakery.org/u/young_doktor)\ **Post date:** [January 26, 2024, 6:21pm UTC](https://forum.biobakery.org/t/humann-unpack-pathways-command/6530/1 "2024-01-26T18:21:36Z")
I am using humann version 3.8 I am trying to determine which gene corresponds to each pathway in my pathways.tsv file. I am running the following command: humann\_unpack\_pathways --input-genes Name1.genefamilies.tsv --input-pathways Name1.pathabundance.tsv --output Name1\_Pathway\_genes.tsv It seems to assign the gene correctly, however, numbers for RPK are only showing up for one of my samples, while the remaining samples are blank. ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/7/7d43008bfe3e05ca475434e45a1c7af87dd4d7f3.png) What can I do to fix this? Thank you! ---
**Author:** ![bplet01](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/bplet01/32/2990_2.png) [@bplet01](https://forum.biobakery.org/u/bplet01)\ **Post date:** [September 25, 2024, 2:55pm UTC](https://forum.biobakery.org/t/humann-unpack-pathways-command/6530/2 "2024-09-25T14:55:19Z")
I have this same issue - did you ever resolve? ---
**Author:** ![young\_doktor](https://avatars.discourse-cdn.com/v4/letter/y/dc4da7/32.png) [@young\_doktor](https://forum.biobakery.org/u/young_doktor)\ **Post date:** [September 25, 2024, 6:51pm UTC](https://forum.biobakery.org/t/humann-unpack-pathways-command/6530/3 "2024-09-25T18:51:41Z")
I didn’t, I got distracted by something else. This would be useful though. I wonder if anyone from the Huttenhower lab might know how to trouble shoot this. Eventually I will need to figure it out. @bplet01 ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [October 11, 2024, 7:30pm UTC](https://forum.biobakery.org/t/humann-unpack-pathways-command/6530/4 "2024-10-11T19:30:15Z")
Most HUMAnN helper scripts (including this one) are only intended to work on one sample at a time, since that’s how HUMAnN itself works. You would need to use a loop to run this script on each of your samples individually and then merge the results to get the sort of integrated “unpacked” view I think you are trying for? ---
**Author:** ![estanton](https://avatars.discourse-cdn.com/v4/letter/e/ea5d25/32.png) [@estanton](https://forum.biobakery.org/u/estanton)\ **Post date:** [October 18, 2024, 5:25pm UTC](https://forum.biobakery.org/t/humann-unpack-pathways-command/6530/5 "2024-10-18T17:25:08Z")
Running the following command to merge the unpacked data from multiple samples into a single table causes an error: Command: humann\_join\_tables.py –input humann –output humann\_unpack.tsv –file\_name unpack Error: Traceback (most recent call last): File “/usr/local/bin/humann\_join\_tables”, line 11, in load\_entry\_point(‘humann==3.9’, ‘console\_scripts’, ‘humann\_join\_tables’)() File “/usr/local/lib/python3.6/dist-packages/humann/tools/join\_tables.py”, line 238, in main join\_gene\_tables(gene\_tables,args.output,verbose=args.verbose) File “/usr/local/lib/python3.6/dist-packages/humann/tools/join\_tables.py”, line 98, in join\_gene\_tables sorted\_gene\_list=util.fsort(list(gene\_table\_data)) File “/usr/local/lib/python3.6/dist-packages/humann/tools/util.py”, line 403, in fsort features = sorted( features, key=lambda f: c\_topsort.get( fsplit( f )[0], default ) ) File “/usr/local/lib/python3.6/dist-packages/humann/tools/util.py”, line 403, in features = sorted( features, key=lambda f: c\_topsort.get( fsplit( f )[0], default ) ) File “/usr/local/lib/python3.6/dist-packages/humann/tools/util.py”, line 377, in fsplit sys.exit( “LETHAL ERROR: bad feature name: {}”.format( f ) ) NameError: name ‘f’ is not defined I suspect that the extra delimiter is causing the problem. ---
**Author:** ![SantosRAC](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/santosrac/32/3581_2.png) [@SantosRAC](https://forum.biobakery.org/u/SantosRAC)\ **Post date:** [April 15, 2026, 1:02pm UTC](https://forum.biobakery.org/t/humann-unpack-pathways-command/6530/6 "2026-04-15T13:02:31Z")
I am having the same problem. @estanton were you able to solve this issue?