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neufeld / pandaseq

PAired-eND Assembler for DNA sequences
GNU General Public License v3.0
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ERR BADID #83

Open Junaidkori opened 2 years ago

Junaidkori commented 2 years ago

I was trying to merge paired ends with this command pandaseq -B -f 2AS16_R1_prinseq_good_bAoZ.fastq -r 2AS16_R2_prinseq_good_kkfu.fastq -w 2AS16_merged.fasta However I was getting an error of the ID as

"ERR BADID M03839:::23:0:0:0: M03839:23:000000000-G5BY5:1:1101:22509:11054:N:0:29#0/1

CDI-PMCC commented 1 year ago

same problem and i'm using biopython converted fastq file from abi file ，and my problem looks like this: ARG[0] pandaseq ARG[1] -f ARG[2] A1-6-1.fastq ARG[3] -r ARG[4] A1-6-.fastq ARG[5] -B STAT THREADS 24 0x5653afe15870:0 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:0 STAT ELAPSED 0 0x5653afe15870:0 STAT READS 0 0x5653afe15870:0 STAT NOALGN 0 0x5653afe15870:0 STAT LOWQ 0 0x5653afe15870:0 STAT BADR 0 0x5653afe15870:0 STAT SLOW 0 0x5653afe15870:0 STAT OK 0 0x5653afe15870:0 STAT OVERLAPS 0 0x5653afe15870:23 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:23 STAT ELAPSED 0 0x5653afe15870:23 STAT READS 0 0x5653afe15870:23 STAT NOALGN 0 0x5653afe15870:23 STAT LOWQ 0 0x5653afe15870:23 STAT BADR 0 0x5653afe15870:23 STAT SLOW 0 0x5653afe15870:23 STAT OK 0 0x5653afe15870:23 STAT OVERLAPS 0 0x5653afe15870:22 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:22 STAT ELAPSED 0 0x5653afe15870:22 STAT READS 0 0x5653afe15870:22 STAT NOALGN 0 0x5653afe15870:22 STAT LOWQ 0 0x5653afe15870:22 STAT BADR 0 0x5653afe15870:22 STAT SLOW 0 0x5653afe15870:22 STAT OK 0 0x5653afe15870:22 STAT OVERLAPS 0 0x5653afe15870:21 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:21 STAT ELAPSED 0 0x5653afe15870:21 STAT READS 0 0x5653afe15870:21 STAT NOALGN 0 0x5653afe15870:21 STAT LOWQ 0 0x5653afe15870:21 STAT BADR 0 0x5653afe15870:21 STAT SLOW 0 0x5653afe15870:21 STAT OK 0 0x5653afe15870:21 STAT OVERLAPS 0 0x5653afe15870:20 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:20 STAT ELAPSED 0 0x5653afe15870:20 STAT READS 0 0x5653afe15870:20 STAT NOALGN 0 0x5653afe15870:20 STAT LOWQ 0 0x5653afe15870:20 STAT BADR 0 0x5653afe15870:20 STAT SLOW 0 0x5653afe15870:20 STAT OK 0 0x5653afe15870:20 STAT OVERLAPS 0 0x5653afe15870:19 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:19 STAT ELAPSED 0 0x5653afe15870:19 STAT READS 0 0x5653afe15870:19 STAT NOALGN 0 0x5653afe15870:19 STAT LOWQ 0 0x5653afe15870:19 STAT BADR 0 0x5653afe15870:19 STAT SLOW 0 0x5653afe15870:19 STAT OK 0 0x5653afe15870:19 STAT OVERLAPS 0 0x5653afe15870:18 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:18 STAT ELAPSED 0 0x5653afe15870:18 STAT READS 0 0x5653afe15870:18 STAT NOALGN 0 0x5653afe15870:18 STAT LOWQ 0 0x5653afe15870:18 STAT BADR 0 0x5653afe15870:18 STAT SLOW 0 0x5653afe15870:18 STAT OK 0 0x5653afe15870:18 STAT OVERLAPS 0 0x5653afe15870:17 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:17 STAT ELAPSED 0 0x5653afe15870:17 STAT READS 0 0x5653afe15870:17 STAT NOALGN 0 0x5653afe15870:17 STAT LOWQ 0 0x5653afe15870:17 STAT BADR 0 0x5653afe15870:17 STAT SLOW 0 0x5653afe15870:17 STAT OK 0 0x5653afe15870:17 STAT OVERLAPS 0 0x5653afe15870:16 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:16 STAT ELAPSED 0 0x5653afe15870:16 STAT READS 0 0x5653afe15870:16 STAT NOALGN 0 0x5653afe15870:16 STAT LOWQ 0 0x5653afe15870:16 STAT BADR 0 0x5653afe15870:16 STAT SLOW 0 0x5653afe15870:16 STAT OK 0 0x5653afe15870:16 STAT OVERLAPS 0 0x5653afe15870:15 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:15 STAT ELAPSED 0 0x5653afe15870:15 STAT READS 0 0x5653afe15870:15 STAT NOALGN 0 0x5653afe15870:15 STAT LOWQ 0 0x5653afe15870:15 STAT BADR 0 0x5653afe15870:15 STAT SLOW 0 0x5653afe15870:15 STAT OK 0 0x5653afe15870:15 STAT OVERLAPS 0 0x5653afe15870:14 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:14 STAT ELAPSED 0 0x5653afe15870:14 STAT READS 0 0x5653afe15870:14 STAT NOALGN 0 0x5653afe15870:14 STAT LOWQ 0 0x5653afe15870:14 STAT BADR 0 0x5653afe15870:14 STAT SLOW 0 0x5653afe15870:14 STAT OK 0 0x5653afe15870:14 STAT OVERLAPS 0 0x5653afe15870:12 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:12 STAT ELAPSED 0 0x5653afe15870:12 STAT READS 0 0x5653afe15870:12 STAT NOALGN 0 0x5653afe15870:12 STAT LOWQ 0 0x5653afe15870:12 STAT BADR 0 0x5653afe15870:12 STAT SLOW 0 0x5653afe15870:12 STAT OK 0 0x5653afe15870:12 STAT OVERLAPS 0 0x5653afe15870:13 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:13 STAT ELAPSED 0 0x5653afe15870:13 STAT READS 0 0x5653afe15870:13 STAT NOALGN 0 0x5653afe15870:13 STAT LOWQ 0 0x5653afe15870:13 STAT BADR 0 0x5653afe15870:13 STAT SLOW 0 0x5653afe15870:13 STAT OK 0 0x5653afe15870:13 STAT OVERLAPS 0 0x5653afe15870:11 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:11 STAT ELAPSED 0 0x5653afe15870:11 STAT READS 0 0x5653afe15870:11 STAT NOALGN 0 0x5653afe15870:11 STAT LOWQ 0 0x5653afe15870:11 STAT BADR 0 0x5653afe15870:11 STAT SLOW 0 0x5653afe15870:11 STAT OK 0 0x5653afe15870:11 STAT OVERLAPS 0 0x5653afe15870:10 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:10 STAT ELAPSED 0 0x5653afe15870:10 STAT READS 0 0x5653afe15870:10 STAT NOALGN 0 0x5653afe15870:10 STAT LOWQ 0 0x5653afe15870:10 STAT BADR 0 0x5653afe15870:10 STAT SLOW 0 0x5653afe15870:10 STAT OK 0 0x5653afe15870:10 STAT OVERLAPS 0 0x5653afe15870:9 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:9 STAT ELAPSED 0 0x5653afe15870:9 STAT READS 0 0x5653afe15870:9 STAT NOALGN 0 0x5653afe15870:9 STAT LOWQ 0 0x5653afe15870:9 STAT BADR 0 0x5653afe15870:9 STAT SLOW 0 0x5653afe15870:9 STAT OK 0 0x5653afe15870:9 STAT OVERLAPS 0 0x5653afe15870:8 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:8 STAT ELAPSED 0 0x5653afe15870:8 STAT READS 0 0x5653afe15870:8 STAT NOALGN 0 0x5653afe15870:8 STAT LOWQ 0 0x5653afe15870:8 STAT BADR 0 0x5653afe15870:8 STAT SLOW 0 0x5653afe15870:8 STAT OK 0 0x5653afe15870:8 STAT OVERLAPS 0 0x5653afe15870:7 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:7 STAT ELAPSED 0 0x5653afe15870:7 STAT READS 0 0x5653afe15870:7 STAT NOALGN 0 0x5653afe15870:7 STAT LOWQ 0 0x5653afe15870:7 STAT BADR 0 0x5653afe15870:7 STAT SLOW 0 0x5653afe15870:7 STAT OK 0 0x5653afe15870:7 STAT OVERLAPS 0 0x5653afe15870:5 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:5 STAT ELAPSED 0 0x5653afe15870:5 STAT READS 0 0x5653afe15870:5 STAT NOALGN 0 0x5653afe15870:5 STAT LOWQ 0 0x5653afe15870:5 STAT BADR 0 0x5653afe15870:5 STAT SLOW 0 0x5653afe15870:5 STAT OK 0 0x5653afe15870:5 STAT OVERLAPS 0 0x5653afe15870:6 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:6 STAT ELAPSED 0 0x5653afe15870:6 STAT READS 0 0x5653afe15870:6 STAT NOALGN 0 0x5653afe15870:6 STAT LOWQ 0 0x5653afe15870:6 STAT BADR 0 0x5653afe15870:6 STAT SLOW 0 0x5653afe15870:6 STAT OK 0 0x5653afe15870:6 STAT OVERLAPS 0 0x5653afe15870:4 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:4 STAT ELAPSED 0 0x5653afe15870:4 STAT READS 0 0x5653afe15870:4 STAT NOALGN 0 0x5653afe15870:4 STAT LOWQ 0 0x5653afe15870:4 STAT BADR 0 0x5653afe15870:4 STAT SLOW 0 0x5653afe15870:4 STAT OK 0 0x5653afe15870:4 STAT OVERLAPS 0 0x5653afe15870:3 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:3 STAT ELAPSED 0 0x5653afe15870:3 STAT READS 0 0x5653afe15870:3 STAT NOALGN 0 0x5653afe15870:3 STAT LOWQ 0 0x5653afe15870:3 STAT BADR 0 0x5653afe15870:3 STAT SLOW 0 0x5653afe15870:3 STAT OK 0 0x5653afe15870:3 STAT OVERLAPS 0 0x5653afe15870:2 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:2 STAT ELAPSED 0 0x5653afe15870:2 STAT READS 0 0x5653afe15870:2 STAT NOALGN 0 0x5653afe15870:2 STAT LOWQ 0 0x5653afe15870:2 STAT BADR 0 0x5653afe15870:2 STAT SLOW 0 0x5653afe15870:2 STAT OK 0 0x5653afe15870:2 STAT OVERLAPS 0 0x5653afe15870:1 STAT TIME Thu Jul 13 21:10:20 2023 0x5653afe15870:1 STAT ELAPSED 0 0x5653afe15870:1 STAT READS 0 0x5653afe15870:1 STAT NOALGN 0 0x5653afe15870:1 STAT LOWQ 0 0x5653afe15870:1 STAT BADR 0 0x5653afe15870:1 STAT SLOW 0 0x5653afe15870:1 STAT OK 0 0x5653afe15870:1 STAT OVERLAPS 0 ERR BADID :::0:0:0:0:

CDI-PMCC commented 1 year ago

also with checkid i got this： A1-6-1.fastq ^ BAD instrument = "A1-6-1.fastq" run = "" flowcell = "" lane = 0 tile = 0 x = 0 y = 0 tag = "" generator = CASAVA 1.7+

jimrybarski commented 10 months ago

You need your sequence identifiers to be formatted like:

@SIM:1:FCX:1:15:6329:1045 1:N:0:2 - if you leave of the part after the space (the read/filtered status/control number/sample number) it will fail to parse. @CDI-PMCC pandaseq-checkid expects a sequence ID, not a filename.

Looking through the source it does allow a few other sequence ID formats but I'm not familiar with how they all vary.