BLAT error

[irvinng98]

Hello,

I'm running into an issue during GA_BWA_merge (that's the last item on bypass_log.txt).

This is the error:

2024-11-20 05:15:32.337389 BLAT_pair_2_9028_2005359.fasta job submitted.  mem: 5 GB
2024-11-20 05:15:32.337760 RUNNING: pair_2_9028_blat_838.fasta
2024-11-20 05:15:32.340219 BLAT_pair_2_9028_838.fasta job submitted.  mem: 10 GB
2024-11-20 05:15:32.340568 RUNNING: pair_2_9028_blat_44013.fasta
2024-11-20 05:15:32.342904 BLAT_pair_2_9028_44013.fasta job submitted.  mem: 15 GB
2024-11-20 05:15:32.343233 RUNNING: pair_2_9028_blat_1678.fasta
2024-11-20 05:15:21.107950 BLAT annotation for pair_2_9028 2005359.fasta
2024-11-20 05:15:32.347735 BLAT_pair_2_9028_1678.fasta job submitted.  mem: 20 GB
2024-11-20 05:15:32.348076 RUNNING: pair_2_9028_blat_104264.fasta
2024-11-20 05:15:32.338130 BLAT annotation for pair_2_9028 838.fasta
2024-11-20 05:15:32.350973 BLAT_pair_2_9028_104264.fasta job submitted.  mem: 25 GB
2024-11-20 05:15:32.351303 RUNNING: pair_2_9028_blat_1485.fasta
2024-11-20 05:15:32.340800 BLAT annotation for pair_2_9028 44013.fasta
2024-11-20 05:15:32.355435 BLAT_pair_2_9028_1485.fasta job submitted.  mem: 30 GB
2024-11-20 05:15:32.355782 RUNNING: pair_2_9028_blat_239934.fasta
2024-11-20 05:15:32.343481 BLAT annotation for pair_2_9028 1678.fasta
2024-11-20 05:15:32.359195 BLAT_pair_2_9028_239934.fasta job submitted.  mem: 35 GB
2024-11-20 05:15:32.359543 RUNNING: pair_2_9028_blat_946234.fasta
2024-11-20 05:15:32.348299 BLAT annotation for pair_2_9028 104264.fasta
2024-11-20 05:15:32.362491 BLAT_pair_2_9028_946234.fasta job submitted.  mem: 40 GB
2024-11-20 05:15:32.363208 RUNNING: singletons_990040_blat_816.fasta
2024-11-20 05:15:32.351533 BLAT annotation for pair_2_9028 1485.fasta
2024-11-20 05:15:32.366735 BLAT_singletons_990040_816.fasta job submitted.  mem: 45 GB
2024-11-20 05:15:32.367063 RUNNING: singletons_990040_blat_836.fasta
2024-11-20 05:15:32.356008 BLAT annotation for pair_2_9028 239934.fasta
2024-11-20 05:15:32.370525 BLAT_singletons_990040_836.fasta job submitted.  mem: 50 GB
2024-11-20 05:15:32.370868 RUNNING: singletons_990040_blat_1918540.fasta
2024-11-20 05:15:32.359762 BLAT annotation for pair_2_9028 946234.fasta
2024-11-20 05:15:32.374202 BLAT_singletons_990040_1918540.fasta job submitted.  mem: 55 GB
2024-11-20 05:15:32.374543 RUNNING: singletons_990040_blat_2767887.fasta
2024-11-20 05:15:32.363463 BLAT annotation for singletons_990040 816.fasta
2024-11-20 05:15:32.376884 BLAT_singletons_990040_2767887.fasta job submitted.  mem: 60 GB
2024-11-20 05:15:32.377222 RUNNING: singletons_990040_blat_2518495.fasta
2024-11-20 05:15:32.367345 BLAT annotation for singletons_990040 836.fasta
2024-11-20 05:15:32.380667 BLAT_singletons_990040_2518495.fasta job submitted.  mem: 65 GB
2024-11-20 05:15:32.380987 RUNNING: singletons_990040_blat_375288.fasta
2024-11-20 05:15:32.371141 BLAT annotation for singletons_990040 1918540.fasta
2024-11-20 05:15:32.384018 BLAT_singletons_990040_375288.fasta job submitted.  mem: 70 GB
2024-11-20 05:15:32.384330 RUNNING: singletons_990040_blat_307628.fasta
2024-11-20 05:15:32.374867 BLAT annotation for singletons_990040 2767887.fasta
2024-11-20 05:15:32.388603 BLAT_singletons_990040_307628.fasta job submitted.  mem: 75 GB
2024-11-20 05:15:32.388952 RUNNING: singletons_990040_blat_191303.fasta
2024-11-20 05:15:32.391548 BLAT_singletons_990040_191303.fasta job submitted.  mem: 80 GB
2024-11-20 05:15:32.391878 RUNNING: singletons_990040_blat_572511.fasta
2024-11-20 05:15:32.381297 BLAT annotation for singletons_990040 375288.fasta
2024-11-20 05:15:32.377519 BLAT annotation for singletons_990040 2518495.fasta
2024-11-20 05:15:32.396013 BLAT_singletons_990040_572511.fasta job submitted.  mem: 85 GB
2024-11-20 05:15:32.396347 RUNNING: singletons_990040_blat_1729679.fasta
2024-11-20 05:15:32.384677 BLAT annotation for singletons_990040 307628.fasta
2024-11-20 05:15:32.398866 BLAT_singletons_990040_1729679.fasta job submitted.  mem: 90 GB
2024-11-20 05:15:32.399215 RUNNING: singletons_990040_blat_2005359.fasta
2024-11-20 05:15:32.389246 BLAT annotation for singletons_990040 191303.fasta
2024-11-20 05:15:32.401636 BLAT_singletons_990040_2005359.fasta job submitted.  mem: 95 GB
2024-11-20 05:15:32.401976 RUNNING: singletons_990040_blat_838.fasta
2024-11-20 05:15:32.392161 BLAT annotation for singletons_990040 572511.fasta
2024-11-20 05:15:32.404978 BLAT_singletons_990040_838.fasta job submitted.  mem: 100 GB
2024-11-20 05:15:32.405312 RUNNING: singletons_990040_blat_44013.fasta
2024-11-20 05:15:32.396635 BLAT annotation for singletons_990040 1729679.fasta
2024-11-20 05:15:32.408345 BLAT_singletons_990040_44013.fasta job submitted.  mem: 105 GB
2024-11-20 05:15:32.408672 RUNNING: singletons_990040_blat_1678.fasta
2024-11-20 05:15:32.399495 BLAT annotation for singletons_990040 2005359.fasta
2024-11-20 05:15:32.411748 BLAT_singletons_990040_1678.fasta job submitted.  mem: 110 GB
2024-11-20 05:15:32.412065 RUNNING: singletons_990040_blat_104264.fasta
2024-11-20 05:15:32.402255 BLAT annotation for singletons_990040 838.fasta
2024-11-20 05:15:32.415611 BLAT_singletons_990040_104264.fasta job submitted.  mem: 115 GB
2024-11-20 05:15:32.415943 RUNNING: singletons_990040_blat_1485.fasta
2024-11-20 05:15:32.405607 BLAT annotation for singletons_990040 44013.fasta
2024-11-20 05:15:32.418544 BLAT_singletons_990040_1485.fasta job submitted.  mem: 120 GB
2024-11-20 05:15:32.418864 RUNNING: singletons_990040_blat_239934.fasta
2024-11-20 05:15:32.408968 BLAT annotation for singletons_990040 1678.fasta
2024-11-20 05:15:32.422364 BLAT_singletons_990040_239934.fasta job submitted.  mem: 125 GB
2024-11-20 05:15:32.422688 RUNNING: singletons_990040_blat_946234.fasta
2024-11-20 05:15:32.412362 BLAT annotation for singletons_990040 104264.fasta
2024-11-20 05:15:32.426188 BLAT_singletons_990040_946234.fasta job submitted.  mem: 130 GB
2024-11-20 05:15:32.426890 RUNNING: singletons_9876_blat_816.fasta
2024-11-20 05:15:32.416283 BLAT annotation for singletons_990040 1485.fasta
2024-11-20 05:15:32.430491 BLAT_singletons_9876_816.fasta job submitted.  mem: 135 GB
2024-11-20 05:15:32.430829 RUNNING: singletons_9876_blat_836.fasta
2024-11-20 05:15:32.419203 BLAT annotation for singletons_990040 239934.fasta
2024-11-20 05:15:32.433765 BLAT_singletons_9876_836.fasta job submitted.  mem: 140 GB
2024-11-20 05:15:32.434099 RUNNING: singletons_9876_blat_1918540.fasta
2024-11-20 05:15:32.422988 BLAT annotation for singletons_990040 946234.fasta
2024-11-20 05:15:32.437772 BLAT_singletons_9876_1918540.fasta job submitted.  mem: 145 GB
2024-11-20 05:15:32.438105 RUNNING: singletons_9876_blat_2767887.fasta
2024-11-20 05:15:32.427129 BLAT annotation for singletons_9876 816.fasta
2024-11-20 05:15:32.441713 BLAT_singletons_9876_2767887.fasta job submitted.  mem: 150 GB
2024-11-20 05:15:32.442044 RUNNING: singletons_9876_blat_2518495.fasta
2024-11-20 05:15:32.431129 BLAT annotation for singletons_9876 836.fasta
2024-11-20 05:15:32.445758 BLAT_singletons_9876_2518495.fasta job submitted.  mem: 155 GB
2024-11-20 05:15:32.446096 RUNNING: singletons_9876_blat_375288.fasta
2024-11-20 05:15:32.434370 BLAT annotation for singletons_9876 1918540.fasta
2024-11-20 05:15:32.438394 BLAT annotation for singletons_9876 2767887.fasta
2024-11-20 05:15:32.442344 BLAT annotation for singletons_9876 2518495.fasta
2024-11-20 05:15:32.446393 BLAT annotation for singletons_9876 375288.fasta
Invalid fasta format: sequence size == 0 for element 1796646__A0A1B1S688__A4V02_00140|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Muribaculaceae.g__Muribaculum.s__
Invalid fasta format: sequence size == 0 for element 1796646__A0A1B1S688__A4V02_00140|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Muribaculaceae.g__Muribaculum.s__

I took a look online and some mentioned this:

Looks like your input file has variants/SNP's listed for specific positions? This file is NOT going to work with blat (which requires a simple fasta format file at a minimum)

I am using the pre-built databases from your website.

Thanks!