f5c
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Bad fast5 warning . How to I fix ? code I run and output attached ( r10 chemistry)
f5c call-methylation -t 8 -r BC9to16.fastq -b BC9to16decomfast5.sorted.bam -g cdiffstr22457.fasta > BC9to16b.tsv [meth_main::INFO] Default methylation tsv output format is changed from f5c v0.7 onwards to match latest nanopolish output. Set --meth-out-version=1 to fall back to the old format. [init_core::INFO] builtin DNA R9 nucleotide model loaded [init_core::INFO] builtin DNA R9 cpg model loaded [handle_bad_fast5::WARNING] Fast5 file [] for read [4aa8eac1-aed1-5d2e-8e28-b75c17d56812] is unreadable and will be skipped [meth_main::1.4180.71] 512 Entries (1.8M bases) loaded [handle_bad_fast5::WARNING] Fast5 file [] for read [27b43cf4-aa90-5353-8b46-877f6ea301c0] is unreadable and will be skipped [handle_bad_fast5::WARNING] Fast5 file [] for read [31f9cd71-73c5-5cbb-8bd6-eeb3e53defce] is unreadable and will be skipped [pthread_processor::2.6374.19] 512 Entries (1.8M bases) processed [meth_main::2.9123.87] 512 Entries (1.6M bases) loaded [slow_fast5_warn::INFO] Fast5 reading took more time than processing. Try increasing --iop. See http://bit.ly/f5cperf [handle_bad_fast5::WARNING] Fast5 file [] for read [e512156e-595e-5433-9930-0a0198572ed3] is unreadable and will be skipped [pthread_processor::3.9545.08] 512 Entries (1.6M bases) processed [handle_bad_fast5::WARNING] Fast5 file [] for read [e497de0a-6ac2-54f2-861a-85f41c2e2a79] is unreadable and will be skipped [meth_main::4.3124.72] 512 Entries (1.6M bases) loaded [handle_bad_fast5::WARNING] Fast5 file [] for read [54ed3e60-cbc9-50bf-98c1-b4a363d7d8fc] is unreadable and will be skipped [pthread_processor::5.3625.45] 512 Entries (1.6M bases) processed [meth_main::5.6805.19] 512 Entries (1.8M bases) loaded [handle_bad_fast5::WARNING] Fast5 file [] for read [859e33f6-8798-5546-a477-fcb7c4d4107f] is unreadable and will be skipped [handle_bad_fast5::WARNING] Fast5 file [] for read [926f934f-7008-54c2-a08c-92e89903fe9c] is unreadable and will be skipped [handle_bad_fast5::WARNING] Fast5 file [] for read [1ce6a3bf-8c3f-5175-950b-1a3b5268ec42] is unreadable and will be skipped [handle_bad_fast5::WARNING] Fast5 file [] for read [71775be5-93ac-5ae1-b1f8-9ec6a0954b11] is unreadable and will be skipped [handle_bad_fast5::WARNING] Fast5 file [] for read [280d67ea-1915-5f46-b08a-a64e3ce48a1d] is unreadable and will be skipped [pthread_processor::6.8155.74] 512 Entries (1.8M bases) processed [meth_main::7.033*5.59] 512 Entries (1.7M bases) loaded