Problem in running cstacks: Error: Failed to initialize the catalog.

[Sanchari Sircar]

Hello,

I am using the Stacks version 2.62. I am running the denovo pipeline by hand. 

I ran unstacks and have the results in the folder /unstacks_trial_v1

Now I am running cstacks:

 cstacks -P ./unstacks_trial_v1 -M single_fastq_pop.txt -n 4 -p 15

My files in unstacks_trial_v1 (first three):

000H535FM_1_Bacchus_0.alleles.tsv

000H535FM_1_Bacchus_0.snps.tsv 

000H535FM_1_Bacchus_0.tags.tsv 

My population map looks like (I have no special way for categorizing the samples, so just the same sample names are repeated in the two columns):

000H535FM_1_Bacchus_0   000H535FM_1_Bacchus_0
000H535FM_1_Bacchus_14    000H535FM_1_Bacchus_14
000H535FM_1_Bacchus_15    000H535FM_1_Bacchus_15
000H535FM_1_Bacchus_16    000H535FM_1_Bacchus_16
000H535FM_1_Bacchus_17    000H535FM_1_Bacchus_17

Any help will be very much appreciated. 

Thanks,

Sanchari

[Sanchari Sircar]

Would like to update the solution, so that others may find it useful,

The fastq header had additional tags from our own inhouse demultiplex script about the primer info and barcodes use. I had to get rid of them as they produce additional columns in unstacks. 

Sanchari