Can't open union.bed file }g~�sample1_sample2.unionbedcv

[pguarnizob]

Hello,

I've tried to run the run_difcover.sh on the test_data directory but finished with an error message:
Can't open union.bed file }g~�sample1_sample2.unionbedcv
I wish someone could help me with that.

Thanks in advance,
Paul

[timnat]

Hi Paul, Could you provide 1) exact command line that you used 2) and text of the file run_difcover.sh

…

On Thu, Mar 5, 2026 at 8:19 PM Paul ***@***.***> wrote: *pguarnizob* created an issue (timnat/DifCover#5) <#5> Hello, I've tried to run the *run_difcover.sh* on the test_data directory but finished with an error message: Can't open union.bed file }g~�sample1_sample2.unionbedcv I wish someone could help me with that. Thanks in advance, Paul — Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEGJB6ZCH2U2EQ5H6CWLZ5T4PIRRPAVCNFSM6AAAAACWI56MO2VHI2DSMVQWIX3LMV43ASLTON2WKOZUGAZTCNJZHE3TMOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[pguarnizob]

Of course,

1. ./run_difcover.sh in the 'test_data' directory

#!/bin/bash

#DifCover version 3 (changed interface compare to version 2)

FOLDER_PATH=../dif_cover_scripts

BAM1='sample1.bam'
BAM2='sample2.bam'
a=10 #minimum coverage for sample1
A=219 #maximum coverage for sample1
b=10 #minimum coverage for sample2
B=240 #maximum coverage for sample2
v=1000 #target number of valid bases in the window
l=500 #minimum size of window to output (window includes valid and non valid bases)
AC=1.095 #adjustment coefficient - usually computed as ratio (modal coverage of sample2)/(modal coverage of sample1)
bin=1 #for an auxiliary analytical stage (5); generates enrichment scores histogram with scores in bins with floating precision 1. For more detailed histogram use 10, 100
p=2 #threshold for enrichment scores to report in a separate file (for p=2 will report regions with coverage in sample1 being roughly 4 times larger than coverage in sample2)

run stage (1)

echo "# Stage 1"
$FOLDER_PATH/from_bams_to_unionbed.sh $BAM1 $BAM2
if [ ! -s "sample1_sample2.unionbedcv" ]; then
echo "File sample1_sample2.unionbedcv is empty, exit now";
exit;
fi

run stage (2)

echo "# Stage 2"
$FOLDER_PATH/from_unionbed_to_ratio_per_window_CC0 -a $a -A $A -b $b -B $B -v $v -l $l sample1_sample2.unionbedcv
if [ ! -s "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"_l"$l ]; then
echo "File "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"_l"$l is empty, exit now";
exit;
fi
echo " ";

run stage (3)

echo "# Stage 3"
$FOLDER_PATH/from_ratio_per_window__to__DNAcopy_output.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"_l"$l $AC
if [ ! -s "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"l"$l".log2adj"$AC".DNAcopyout" ]; then
echo "File "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"l"$l".log2adj"$AC".DNAcopyout" is empty, exit now";
exit;
fi

run stage (4)

echo "# Stage 4"
$FOLDER_PATH/from_DNAcopyout_to_p_fragments.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"l"$l".log2adj"$AC".DNAcopyout" $p

run stage (5)

echo "# Stage 5"
$FOLDER_PATH/get_DNAcopyout_with_length_of_intervals.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"l"$l".log2adj"$AC".DNAcopyout" ref.length.Vk1s_sorted

echo "Generate rough histogram with given precision order"
$FOLDER_PATH/generate_DNAcopyout_len_histogram.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"l"$l".log2adj"$AC".DNAcopyout.len" $bin

echo "Generate histogram with bins centered at value X reporting scores from [X-0.25 to X+0.25)"
$FOLDER_PATH/generate_DNAcopyout_len_vs_scores_histogram_bin0.5.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"l"$l".log2adj"$AC".DNAcopyout.len"

echo " ";

I attach the error message from the terminal

Hope this can help. Please let me know if you need more information.
Thank you,
Paul

[timnat]

Could you check if file sample1_sample2.unionbedcv was generated after the conclusion of the first stage? If, yes, try running $FOLDER_PATH/from_unionbed_to_ratio_per_window_CC0 -a $a -A $A -b $b -B $B -v $v -l $l sample1_sample2.unionbedcv providing a full pass to the file sample1_sample2.unionbedcv $FOLDER_PATH/from_unionbed_to_ratio_per_window_CC0 -a $a -A $A -b $b -B $B -v $v -l $l /FULL/PATH/sample1_sample2.unionbedcv

…

On Sat, Mar 7, 2026 at 11:50 AM Paul ***@***.***> wrote: *pguarnizob* left a comment (timnat/DifCover#5) <#5 (comment)> Of course, 1. ./run_difcover.sh in the 'test_data' directory 2. #!/bin/bash #DifCover version 3 (changed interface compare to version 2) FOLDER_PATH=../dif_cover_scripts BAM1='sample1.bam' BAM2='sample2.bam' a=10 #minimum coverage for sample1 A=219 #maximum coverage for sample1 b=10 #minimum coverage for sample2 B=240 #maximum coverage for sample2 v=1000 #target number of valid bases in the window l=500 #minimum size of window to output (window includes valid and non valid bases) AC=1.095 #adjustment coefficient - usually computed as ratio (modal coverage of sample2)/(modal coverage of sample1) bin=1 #for an auxiliary analytical stage (5); generates enrichment scores histogram with scores in bins with floating precision 1. For more detailed histogram use 10, 100 p=2 #threshold for enrichment scores to report in a separate file (for p=2 will report regions with coverage in sample1 being roughly 4 times larger than coverage in sample2) run stage (1) echo "# Stage 1" $FOLDER_PATH/from_bams_to_unionbed.sh $BAM1 $BAM2 if [ ! -s "sample1_sample2.unionbedcv" ]; then echo "File sample1_sample2.unionbedcv is empty, exit now"; exit; fi run stage (2) echo "# Stage 2" $FOLDER_PATH/from_unionbed_to_ratio_per_window_CC0 -a $a -A $A -b $b -B $B -v $v -l $l sample1_sample2.unionbedcv if [ ! -s "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"_l"$l ]; then echo "File "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"_l"$l is empty, exit now"; exit; fi echo " "; run stage (3) echo "# Stage 3" $FOLDER_PATH/from_ratio_per_window__to__DNAcopy_output.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v"_l"$l $AC if [ ! -s "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v" *l"$l".log2adj*"$AC".DNAcopyout" ]; then echo "File "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v" *l"$l".log2adj*"$AC".DNAcopyout" is empty, exit now"; exit; fi run stage (4) echo "# Stage 4" $FOLDER_PATH/from_DNAcopyout_to_p_fragments.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v" *l"$l".log2adj*"$AC".DNAcopyout" $p run stage (5) echo "# Stage 5" $FOLDER_PATH/get_DNAcopyout_with_length_of_intervals.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v" *l"$l".log2adj*"$AC".DNAcopyout" ref.length.Vk1s_sorted echo "Generate rough histogram with given precision order" $FOLDER_PATH/generate_DNAcopyout_len_histogram.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v" *l"$l".log2adj*"$AC".DNAcopyout.len" $bin echo "Generate histogram with bins centered at value X reporting scores from [X-0.25 to X+0.25)" $FOLDER_PATH/generate_DNAcopyout_len_vs_scores_histogram_bin0.5.sh "sample1_sample2.ratio_per_w_CC0_a"$a"_A"$A"_b"$b"_B"$B"_v"$v" *l"$l".log2adj*"$AC".DNAcopyout.len" echo " "; I attach the error message from the terminal Screenshot.from.2026-03-07.11-48-43.png (view on web) <https://github.com/user-attachments/assets/2b6b56e1-ac25-46d0-9fda-44d194f87d04> Hope this can help. Please let me know if you need more information. Thank you, Paul — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEGJB65UVWJPCYJX7XAY6RT4PRHODAVCNFSM6AAAAACWI56MO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DAMJWHEYTEMZSGA> . You are receiving this because you commented.Message ID: ***@***.***>

[pguarnizob]

I've tried it. Same error message: "Can't open union.bed file"
I also show size and permissions of all these files

[timnat]

It seems to me that there is a problem with how the file name is read. Could you try to do the following In script dif_cover_scripts <https://github.com/timnat/DifCover/tree/DifCover_v3/dif_cover_scripts>/ from_unionbed_to_ratio_per_window_CC0.cpp uncomment line 58 strncat(fname,argv[optind],strlen(argv[optind])); //printf ("fname=%s\n",fname); Then recompile file and try running again. Also run one time without parameters, and send me an output.

…

On Sun, Mar 8, 2026 at 4:31 PM Paul ***@***.***> wrote: *pguarnizob* left a comment (timnat/DifCover#5) <#5 (comment)> I've tried it. Same error message: "Can't open union.bed file" I also show size and permissions of all these files image.png (view on web) <https://github.com/user-attachments/assets/bdc06b58-32ed-4afa-99be-a047b9e8e5fc> — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEGJB63JS6I2KKDGIAL3DO34PXKALAVCNFSM6AAAAACWI56MO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DAMJZHE2TINJZGU> . You are receiving this because you commented.Message ID: ***@***.***>

[pguarnizob]

I did a "make" with the new .cpp file (uncommented line 58) but same result, it seems something wrong with the file name.

strncat(fname,argv[optind],strlen(argv[optind])); printf ("fname=%s\n",fname);

This time, I tried in a directory without special characters to not interfere with the path, trying also with full path names.

[timnat]

Let's try one more thing. Replace line 23 char fname[1000], fff[1000]; with char fname[1000]="", fff[1000]=""; and recompile again

…

On Sun, Mar 8, 2026 at 5:10 PM Paul ***@***.***> wrote: *pguarnizob* left a comment (timnat/DifCover#5) <#5 (comment)> I did a "make" with the new .cpp file (uncommented line 58) but same result, it seems something wrong with the file name. strncat(fname,argv[optind],strlen(argv[optind])); printf ("fname=%s\n",fname); This time, I tried in a directory without special characters to not interfere with the path, trying also with full path names. image.png (view on web) <https://github.com/user-attachments/assets/ce55f1fe-0882-40a1-af72-fd53dd557c55> — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEGJB63U2NR5DJ373DPPHAT4PXOVRAVCNFSM6AAAAACWI56MO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DAMRQGAYTQNZRGQ> . You are receiving this because you commented.Message ID: ***@***.***>