I am doing blastp from locally in linux. But some times blast run and some times error raise
Error: NCBI C++ Exception:
T0 "/build/ncbi-blast+-GcQwD4/ncbi-blast+-2.6.0/c++/src/objtools/readers/fasta.cpp", line 2428: Error: CFastaReader: Near line 1, there's a line that doesn't look like plausible data, but it's not marked as defline or comment. (m_Pos = 1)
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I am using Blastp in ubuntu inside window10 (WSL).Code runned by Python
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subject = SPECIES+subject # ** later remove this cmd = ["blastp", "-query", "./query/query_"+str(parallel_num), "-subject", subject, "-matrix", blastp_matrix, "-outfmt", "10 qseqid sseqid score length"] run_blastp = subprocess.run(cmd, capture_output=True, text=True, check=False)
for some kinds of genome it work and for some kinds of genome it didnot
From the error it seems that there is a sequence in your data which is not correct. Please check that.
Also check this thread
https://www.researchgate.net/post/I_got_an_error_message_ID68_Error_while_trying_to_run_blast_with_multiple_sequences_What_does_it_mean_and_what_do_I_do_to_get_results
There are some characters in your sequence that do not look like nucleotides: Run this command: grep -o [^AGTCagtcNn] name-of-sequence-file | sort | uniq. This will give you a list of possible culprits. My guess would be - (gap characters), Xs (used for masking), or empty lines.
Hi,
There is/are invalid/incorrect characters in your input file.
Make your input uniform using commands provided by Mark Farman
One more thing, you cannot open and save your sequence files in common text editors such as Word, Textedit, etc. they will insert hidden characters that will also cause the problem you describe. You can check for these hidden characters using the command cat -v filename.
Thank You all, I solved this with reinstalling NCBI.
All information are very helpful.
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