Hi Rittik,
You should use the pynast_aligned_seqs/rep_set_aligned.fasta file that's in the output directory created by pick_open_reference_otus.py. For -a, use the same PyNAST template alignment that was used for aligning the sequences. You can find what template alignment was used by looking for "pynast_template_alignment_fp" in the log file in your pick_open_ref output directory. That field should be located near the beginning of the file and will contain an absolute path to the template alignment. Note that the template alignment may be different depending on what version of QIIME you're using (it used to be core_set_aligned.fasta.imputed, now it is 85_otus.pynast.fasta). As long as you use the template alignment indicated in your log file you should be fine.
For example, on my laptop with MacQIIME 1.9.1:
identify_chimeric_seqs.py -m ChimeraSlayer -i pick_open_ref_output/pynast_aligned_seqs/rep_set_aligned.fasta -a /macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta -o chimeric_seqs.txt
Next, filter the alignment to remove chimeric sequences:
filter_fasta.py -f pick_open_ref_output/pynast_aligned_seqs/rep_set_aligned.fasta -o non_chimeric_rep_set_aligned.fasta -s chimeric_seqs.txt -n
Apply lanemask filtering to the non-chimeric alignment:
filter_alignment.py -o non_chimeric_filtered_alignment -i non_chimeric_rep_set_aligned.fasta
Build your phylogenetic tree:
make_phylogeny.py -i non_chimeric_filtered_alignment/non_chimeric_rep_set_aligned_pfiltered.fasta -o non_chimeric_rep_set.tre
Filter chimeric sequences from your OTU table:
filter_otus_from_otu_table.py -i pick_open_ref_output/otu_table_mc2_w_tax_no_pynast_failures.biom -o non_chimeric_otu_table.biom -e chimeric_seqs.txt
Let us know how it goes!
Jai