#!/bin/bash

cd /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution
tmpDir=$(mkdir -p "/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/tmp.11d2d012" && echo "/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/tmp.11d2d012")

export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution

)
out72f6f9f6="${tmpDir}/out.$$" err72f6f9f6="${tmpDir}/err.$$"
mkfifo "$out72f6f9f6" "$err72f6f9f6"
trap 'rm "$out72f6f9f6" "$err72f6f9f6"' EXIT
touch '/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution/stdout' '/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution/stderr'
tee '/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution/stdout' < "$out72f6f9f6" &
tee '/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution/stderr' < "$err72f6f9f6" >&2 &
(
cd /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution


set -vex

input_assembly_merged_fasta="/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-polish_merge/execution/assembly.merged.fasta" \
input_p_ctg_fasta="/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/inputs/250313208/p_ctg.fasta" \
input_a_ctg_fasta="/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/inputs/250313208/a_ctg.fasta" \
params_log_level="INFO" \
params_tmp_dir="/tmp" \
params_polish_run=1 \
output_p_ctg_fasta="p_ctg.fasta" \
output_a_ctg_fasta="a_ctg.fasta" \
    ipa2-task separate_p_from_a
echo `pwd`/p_ctg.fasta > p_ctg_fasta_fn
echo `pwd`/a_ctg.fasta > a_ctg_fasta_fn
)  > "$out72f6f9f6" 2> "$err72f6f9f6"
echo $? > /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution/rc.tmp
(
# add a .file in every empty directory to facilitate directory delocalization on the cloud
cd /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution
find . -type d -exec sh -c '[ -z "$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \;
)
(
cd /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution
sync


)
mv /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution/rc.tmp /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution/rc