NanoporeBC_UMI_finder-1.0: Parsing failed
erosix opened this issue · 2 comments
erosix commented
Reads not found when running: AddBamReadSequenceTag
INFO 2022-04-25 12:13:49 AddBamReadSequenceTag Error: read e1468700-dfc1-426a-9fb7-3dea69323661_REV_pT_Ad5p_TSO3p not found !!!
INFO 2022-04-25 12:13:49 AddBamReadSequenceTag Error: read 86a91211-2e39-44f1-b315-763e79ed9eea_REV_pT_Ad5p_TSO3p not found !!!
INFO 2022-04-25 12:13:49 AddBamReadSequenceTag Error: read ca837cc6-7ddf-4418-b26c-01aae3633ecf_FWD_pA_Ad3p_TSO5p not found !!!
INFO 2022-04-25 12:13:49 AddBamReadSequenceTag Error: read b6ff8701-ce71-4ed9-95f3-5e9f6171911a_FWD_pA_Ad3p not found !!!
INFO 2022-04-25 12:13:49 AddBamReadSequenceTag Error: read 6a5891ad-7d1a-4b3a-a47f-fbbd7a2e7192_REV_pT_Ad5p_TSO3p not found !!!
INFO 2022-04-25 12:13:49 AddBamReadSequenceTag Error: read f5d5d8ad-79d7-4c99-8c6b-3cca96f8ea29_FWD_pA_Ad3p not found !!!
INFO 2022-04-25 12:13:49 AddBamReadSequenceTag Error: read 1b4921aa-ccd2-44a1-98c0-16f2a60d91fc_REV_pT_Ad5p_TSO3p not found !!!
INFO 2022-04-25 12:13:49 AddBamReadSequenceTag Error: read b61c30ed-d395-4d09-96c5-bd6ced0f447c_FWD_pA_Ad3p not found !!!
Then when running NanoporeBC_UMI_finder-1.0 on my own data, I get the current message:
========== P A R S I N G S T A T S ==========
Parsing failed for 566598 Sam records
------------ S T A T S F 0 R R E A D S --------------------------
Number of reads 0
Which are the possible reasons of failed read recognition and parsing of the SAM records?
ucagenomix commented
NanoporeBC_UMI_finder-1.0 needs the read sequence to process correctly and it seems that AddBamReadSequenceTag is giving some errors. Could you check that the reads are present in the fastq file you are providing to AddBamReadSequenceTag. In v2 you need to provide a FASTQIR where is located the fastq files that contain the reads.
erosix commented
Error was due to fastq files in input to AddBamReadSequenceTag being in compressed fastq.gz format.