Error when running get_abundance_post_collapse.py about cdna_cupcake

[Magdoll]

Hi @rnett42 ,

This just means it is expecting the FL reads to have one of the following formats and it doesn't see them. It should either be:

<movie>/<zmw>/<start>_<end>_CCS

or

<movie>/<zmw>/ccs

Take a look at the read IDs in cluster_report.csv and tell me what you see.

--Liz

[rnett42]

Here are the first several lines of the cluster_report.csv file:

cluster_id,read_id,read_type
cb10903_c6,m54181_180816_205716/66650816/2268_72_CCS,FL
cb11609_c66,m54181_180811_131943/31326766/24_2619_CCS,FL
cb10545_c5,m54181_180816_205716/23921070/25_1430_CCS,FL
cb12600_c2,m54181_180817_172336/44630666/2140_72_CCS,FL
cb10265_c4,m54181_180817_172336/47513679/1886_68_CCS,FL
cb10265_c4,m54181_180817_172336/48038495/1991_74_CCS,FL
cb10265_c4,m54181_180817_172336/62062786/2026_213_CCS,FL
cb10265_c4,m54181_180808_113023/55706169/1525_63_CCS,NonFL
cb10265_c7,m54181_180808_113023/30998607/24_1961_CCS,FL
cb10265_c7,m54181_180816_205716/35193672/2056_109_CCS,FL
cb10265_c7,m54181_180808_113023/55706169/1525_63_CCS,NonFL
cb10265_c7,m54181_180816_205716/47972524/2019_84_CCS,NonFL
cb10265_c7,m54181_180811_131943/63046101/0_1898_CCS,NonFL
cb10265_c7,m54181_180808_113023/52167517/699_0_CCS,NonFL
cb10265_c7,m54181_180816_205716/50135474/1188_68_CCS,NonFL
cb10265_c6,m54181_180808_113023/36897616/25_1531_CCS,FL
cb10265_c6,m54181_180817_172336/58851400/24_1521_CCS,FL
cb10265_c6,m54181_180811_131943/21103556/23_1443_CCS,FL
cb10265_c6,m54181_180811_131943/66716148/1610_79_CCS,FL

[Magdoll]

Hmm, that looks pretty good to me. Do you mind emailing me the following files for me to do a quick test?

• cluster_report.csv
• all files starting with hq_isoforms.fasta.no5merge.collapsed.

to [email protected].

Thx!

[rnett42]

Downloading the cluster_report.csv file via command line (instead of through the SMRT link GUI) resolved this issue. Thanks!

[Magdoll]

Good to hear!