GithubHelp home page GithubHelp logo

Error when running JUM step A about jum HOT 21 OPEN

hvicars avatar hvicars commented on September 15, 2024
Error when running JUM step A

from jum.

Comments (21)

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

from jum.

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

from jum.

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

from jum.

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

from jum.

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

Hi,

I re-indexed my genome and re-ran JUM_A after STAR mapping and received the same result. I then typed "ls -l -t -r" in the folder where I redid JUM_A, and this was my result:

total 57129220
-rw-rw----+ 1 hvicars scg_lab_mtfuller 16782164691 Apr 3 12:24 noHSAligned.out.sam
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2066100 Apr 3 12:24 noHSSJ.out.tab
-rw-rw----+ 1 hvicars scg_lab_mtfuller 13542666415 Apr 4 12:21 16hrAligned.out.sam
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1939643 Apr 4 12:22 16hrSJ.out.tab
-rw-rw----+ 1 hvicars scg_lab_mtfuller 3589751512 Apr 4 13:29 noHSAligned.out_sorted.bam
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2941872065 Apr 4 13:56 16hrAligned.out_sorted.bam
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1135 Apr 8 10:08 slurm-42826020.out
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1021 Apr 8 10:10 JUM_stepA_nohs_v_16hr.sh
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1939643 Apr 8 10:12 16hrSJ.out.tab_strand_symbol_scaled
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1266241 Apr 8 10:12 16hr_SJ_coor.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2703283 Apr 8 10:12 UNION_junc_coor_with_junction_ID.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1613719 Apr 8 10:12 UNION_junc_coor.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2066100 Apr 8 10:12 noHSSJ.out.tab_strand_symbol_scaled
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1347469 Apr 8 10:12 noHS_SJ_coor.txt
drwxrws---+ 2 hvicars scg_lab_mtfuller 4096 Apr 8 10:12 con1_1
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1150960 Apr 8 10:12 UNION_junc_coor_with_junction_ID_more_than_10_read_in_at_least_1_samples.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1264687 Apr 8 10:12 UNION_junc_coor_with_junction_ID_more_than_10_read_in_at_least_1_samples_formatted_with_junction_length.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1150960 Apr 8 10:12 UNION_junc_coor_with_junction_ID_more_than_10_read_in_at_least_1_samples_formatted.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2607999 Apr 8 10:12 noHS_junction_counts.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1064334 Apr 8 10:12 condition2_junc_coor_with_junction_ID_more_than_10_read_in_at_least_1_samples_formatted.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1125266 Apr 8 10:12 condition1_junc_coor_with_junction_ID_more_than_10_read_in_at_least_1_samples_formatted.txt
drwxrws---+ 2 hvicars scg_lab_mtfuller 4096 Apr 8 10:12 con2_1
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2449291 Apr 8 10:12 16hr_junction_counts.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 463661 Apr 8 10:12 UNION_junc_coor_with_junction_ID_more_than_10_read_in_at_least_1_samples_formatted_junction_list.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 19964 Apr 8 10:12 more_than_10_union_junc_coor_5_prime_ss_list_with_alternative_3_ss.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 19807 Apr 8 10:12 more_than_10_union_junc_coor_3_prime_ss_list_with_alternative_5_ss.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 389328 Apr 8 10:12 more_than_10_profiled_total_AS_event_junction.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 167491 Apr 8 10:12 more_than_10_profiled_total_AS_event_junction_second_processing_for_JUM_reference_building.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1533426 Apr 8 10:12 more_than_10_profiled_total_AS_event_junction_JUM_annotation.gff
-rw-rw----+ 1 hvicars scg_lab_mtfuller 415284 Apr 8 10:12 more_than_10_profiled_total_AS_event_junction_first_processing_for_JUM_reference_building.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 190299 Apr 8 10:12 more_than_10_profiled_5_ss_and_corresponding_alternative_3_ss_junction_list.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 199029 Apr 8 10:12 more_than_10_profiled_3_ss_and_corresponding_alternative_5_ss_junction_list.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 293881 Apr 8 10:12 noHS_fn_count.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 292773 Apr 8 10:12 16hr_fn_count.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2574382249 Apr 8 10:14 16hr_temp1
-rw-rw----+ 1 hvicars scg_lab_mtfuller 59731 Apr 8 10:14 16hr_sam_header
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2574441980 Apr 8 10:14 16hr_Aligned.out.spanning_junction_reads.sam
-rw-rw----+ 1 hvicars scg_lab_mtfuller 3273212119 Apr 8 10:15 noHS_temp1
-rw-rw----+ 1 hvicars scg_lab_mtfuller 59739 Apr 8 10:15 noHS_sam_header
-rw-rw----+ 1 hvicars scg_lab_mtfuller 3273271858 Apr 8 10:15 noHS_Aligned.out.spanning_junction_reads.sam
-rw-rw----+ 1 hvicars scg_lab_mtfuller 866329467 Apr 8 10:18 16hr_Aligned.out.spanning_junction_reads.bam
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1111440379 Apr 8 10:19 noHS_Aligned.out.spanning_junction_reads.bam
-rw-rw----+ 1 hvicars scg_lab_mtfuller 854182853 Apr 8 10:20 16hr_Aligned.out.spanning_junction_reads.bed
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1982414 Apr 8 10:21 profiled_16hr_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 0 Apr 8 10:21 16hr_trash_out
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1639300 Apr 8 10:21 16hr_junction_counts_more_than_10_in_all_samples_with_both_overhangs.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1346305 Apr 8 10:21 16hr_junction_counts_more_than_10_in_all_samples.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1087446746 Apr 8 10:21 noHS_Aligned.out.spanning_junction_reads.bed
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2036740 Apr 8 10:22 profiled_noHS_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 0 Apr 8 10:22 noHS_trash_out
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1351492 Apr 8 10:22 noHS_junction_counts_more_than_10_in_all_samples.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1451950 Apr 8 10:22 UNION_junc_coor_with_junction_ID_more_than_10_read_in_at_least_1_samples_formatted_with_junction_length_and_overhang_union_from_all_samples.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1324423 Apr 8 10:22 output_short_intron.gff
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2142825 Apr 8 10:22 output_long_intron.gff
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1648222 Apr 8 10:22 noHS_junction_counts_more_than_10_in_all_samples_with_both_overhangs.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 0 Apr 8 10:22 output_short_intron2.gff
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1324423 Apr 8 10:22 output_short_intron1.gff
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2142825 Apr 8 10:22 output_long_intron_sorted.gff
-rw-rw----+ 1 hvicars scg_lab_mtfuller 0 Apr 8 10:22 output_short_intron2_sorted.gff
-rw-rw----+ 1 hvicars scg_lab_mtfuller 0 Apr 8 10:22 output_short_intron_2_adjusted_range_sorted.bed
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1324423 Apr 8 10:22 output_short_intron1_sorted.gff
-rw-rw----+ 1 hvicars scg_lab_mtfuller 678802 Apr 8 10:22 output_short_intron_1_adjusted_range_sorted.bed
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1124213 Apr 8 10:22 output_long_intron_adjusted_range_sorted.bed
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2964878810 Apr 8 10:24 16hrAligned.out.bed
-rw-rw----+ 1 hvicars scg_lab_mtfuller 2964878810 Apr 8 10:34 16hrAligned.out.sorted.bed
-rw-rw----+ 1 hvicars scg_lab_mtfuller 47240647 Apr 8 10:35 16hrAligned.out_intersect_long_intron.txt
-rw-rw----+ 1 hvicars scg_lab_mtfuller 1581 Apr 8 10:35 slurm-42826023.out
-rw-rw----+ 1 hvicars scg_lab_mtfuller 577060 Apr 8 10:35 16hrAligned.out_intersect_short_intron1.txt

Please let me know if this helps at all or if there's anything more I can do to narrow down this issue. Would it be better if I used an older version of JUM?

Thanks!
Hannah

from jum.

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

Okay, I ran the two commands in the directory where I ran JUM_A. The outputs were:

noHSAligned.out.sorted.bed
noHSAligned.out.bed

What would you like me to do next?

from jum.

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024
  1. Output from JUM_A.sh:
    2024-04-15 14:30:15 (625 KB/s) - written to stdout [302419/302419]

App::cpanminus is up to date. (1.7047)
local::lib is up to date. (2.000029)
Array::Utils is up to date. (0.5)
Statistics::Descriptive is up to date. (3.0801)
perl modules successfully loaded
Sample names are:
noHS
16hr
1 input samples to consider under the current condition
1 input samples to consider under the current condition
Preparing for intron retention AS events analyses...
Processing junction overhangs for Sample 16hr... Success.
Processing junction overhangs for Sample noHS... Success.
Line238 Done
ERROR: Sort order was unspecified, and file 16hrAligned.out.sorted.bed is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.

  1. This sorting was successful. No error message popped up.

  2. However, the following files are empty (zero bytes):

output_short_intron2.gff
output_short_intron2_sorted.gff
output_short_intron_2_adjusted_range_sorted.bed

Let me know what else you need from me. Thanks!

from jum.

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

This is the output I got from running those commands:

Tool: bedtools intersect (aka intersectBed)
Version: v2.27.1
Summary: Report overlaps between two feature files.

Usage: bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>

Note: -b may be followed with multiple databases and/or 
wildcard (*) character(s).

Options:
-wa Write the original entry in A for each overlap.

-wb	Write the original entry in B for each overlap.
	- Useful for knowing _what_ A overlaps. Restricted by -f and -r.

-loj	Perform a "left outer join". That is, for each feature in A
	report each overlap with B.  If no overlaps are found, 
	report a NULL feature for B.

-wo	Write the original A and B entries plus the number of base
	pairs of overlap between the two features.
	- Overlaps restricted by -f and -r.
	  Only A features with overlap are reported.

-wao	Write the original A and B entries plus the number of base
	pairs of overlap between the two features.
	- Overlapping features restricted by -f and -r.
	  However, A features w/o overlap are also reported
	  with a NULL B feature and overlap = 0.

-u	Write the original A entry _once_ if _any_ overlaps found in B.
	- In other words, just report the fact >=1 hit was found.
	- Overlaps restricted by -f and -r.

-c	For each entry in A, report the number of overlaps with B.
	- Reports 0 for A entries that have no overlap with B.
	- Overlaps restricted by -f and -r.

-v	Only report those entries in A that have _no overlaps_ with B.
	- Similar to "grep -v" (an homage).

-ubam	Write uncompressed BAM output. Default writes compressed BAM.

-s	Require same strandedness.  That is, only report hits in B
	that overlap A on the _same_ strand.
	- By default, overlaps are reported without respect to strand.

-S	Require different strandedness.  That is, only report hits in B
	that overlap A on the _opposite_ strand.
	- By default, overlaps are reported without respect to strand.

-f	Minimum overlap required as a fraction of A.
	- Default is 1E-9 (i.e., 1bp).
	- FLOAT (e.g. 0.50)

-F	Minimum overlap required as a fraction of B.
	- Default is 1E-9 (i.e., 1bp).
	- FLOAT (e.g. 0.50)

-r	Require that the fraction overlap be reciprocal for A AND B.
	- In other words, if -f is 0.90 and -r is used, this requires
	  that B overlap 90% of A and A _also_ overlaps 90% of B.

-e	Require that the minimum fraction be satisfied for A OR B.
	- In other words, if -e is used with -f 0.90 and -F 0.10 this requires
	  that either 90% of A is covered OR 10% of  B is covered.
	  Without -e, both fractions would have to be satisfied.

-split	Treat "split" BAM or BED12 entries as distinct BED intervals.

-g	Provide a genome file to enforce consistent chromosome sort order
	across input files. Only applies when used with -sorted option.

-nonamecheck	For sorted data, don't throw an error if the file has different naming conventions
		for the same chromosome. ex. "chr1" vs "chr01".

-sorted	Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.

-names	When using multiple databases, provide an alias for each that
	will appear instead of a fileId when also printing the DB record.

-filenames	When using multiple databases, show each complete filename
		instead of a fileId when also printing the DB record.

-sortout	When using multiple databases, sort the output DB hits
		for each record.

-bed	If using BAM input, write output as BED.

-header	Print the header from the A file prior to results.

-nobuf	Disable buffered output. Using this option will cause each line
	of output to be printed as it is generated, rather than saved
	in a buffer. This will make printing large output files 
	noticeably slower, but can be useful in conjunction with
	other software tools and scripts that need to process one
	line of bedtools output at a time.

-iobuf	Specify amount of memory to use for input buffer.
	Takes an integer argument. Optional suffixes K/M/G supported.
	Note: currently has no effect with compressed files.

Notes:
(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist,
and excluded if an overlap cannot be found. If multiple overlaps exist, they are not
reported, as we are only testing for one or more overlaps.

***** ERROR: -b option given, but no database file specified. *****
/var/spool/slurm/slurmd/job42896608/slurm_script: line 12: output_short_intron1_sorted.gff: command not found

Tool: bedtools intersect (aka intersectBed)
Version: v2.27.1
Summary: Report overlaps between two feature files.

Usage: bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>

Note: -b may be followed with multiple databases and/or 
wildcard (*) character(s).

Options:
-wa Write the original entry in A for each overlap.

-wb	Write the original entry in B for each overlap.
	- Useful for knowing _what_ A overlaps. Restricted by -f and -r.

-loj	Perform a "left outer join". That is, for each feature in A
	report each overlap with B.  If no overlaps are found, 
	report a NULL feature for B.

-wo	Write the original A and B entries plus the number of base
	pairs of overlap between the two features.
	- Overlaps restricted by -f and -r.
	  Only A features with overlap are reported.

-wao	Write the original A and B entries plus the number of base
	pairs of overlap between the two features.
	- Overlapping features restricted by -f and -r.
	  However, A features w/o overlap are also reported
	  with a NULL B feature and overlap = 0.

-u	Write the original A entry _once_ if _any_ overlaps found in B.
	- In other words, just report the fact >=1 hit was found.
	- Overlaps restricted by -f and -r.

-c	For each entry in A, report the number of overlaps with B.
	- Reports 0 for A entries that have no overlap with B.
	- Overlaps restricted by -f and -r.

-v	Only report those entries in A that have _no overlaps_ with B.
	- Similar to "grep -v" (an homage).

-ubam	Write uncompressed BAM output. Default writes compressed BAM.

-s	Require same strandedness.  That is, only report hits in B
	that overlap A on the _same_ strand.
	- By default, overlaps are reported without respect to strand.

-S	Require different strandedness.  That is, only report hits in B
	that overlap A on the _opposite_ strand.
	- By default, overlaps are reported without respect to strand.

-f	Minimum overlap required as a fraction of A.
	- Default is 1E-9 (i.e., 1bp).
	- FLOAT (e.g. 0.50)

-F	Minimum overlap required as a fraction of B.
	- Default is 1E-9 (i.e., 1bp).
	- FLOAT (e.g. 0.50)

-r	Require that the fraction overlap be reciprocal for A AND B.
	- In other words, if -f is 0.90 and -r is used, this requires
	  that B overlap 90% of A and A _also_ overlaps 90% of B.

-e	Require that the minimum fraction be satisfied for A OR B.
	- In other words, if -e is used with -f 0.90 and -F 0.10 this requires
	  that either 90% of A is covered OR 10% of  B is covered.
	  Without -e, both fractions would have to be satisfied.

-split	Treat "split" BAM or BED12 entries as distinct BED intervals.

-g	Provide a genome file to enforce consistent chromosome sort order
	across input files. Only applies when used with -sorted option.

-nonamecheck	For sorted data, don't throw an error if the file has different naming conventions
		for the same chromosome. ex. "chr1" vs "chr01".

-sorted	Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.

-names	When using multiple databases, provide an alias for each that
	will appear instead of a fileId when also printing the DB record.

-filenames	When using multiple databases, show each complete filename
		instead of a fileId when also printing the DB record.

-sortout	When using multiple databases, sort the output DB hits
		for each record.

-bed	If using BAM input, write output as BED.

-header	Print the header from the A file prior to results.

-nobuf	Disable buffered output. Using this option will cause each line
	of output to be printed as it is generated, rather than saved
	in a buffer. This will make printing large output files 
	noticeably slower, but can be useful in conjunction with
	other software tools and scripts that need to process one
	line of bedtools output at a time.

-iobuf	Specify amount of memory to use for input buffer.
	Takes an integer argument. Optional suffixes K/M/G supported.
	Note: currently has no effect with compressed files.

Notes:
(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist,
and excluded if an overlap cannot be found. If multiple overlaps exist, they are not
reported, as we are only testing for one or more overlaps.

***** ERROR: -b option given, but no database file specified. *****
/var/spool/slurm/slurmd/job42896608/slurm_script: line 14: output_short_intron2_sorted.gff: command not found
Troubleshooting is now completed!

The following files were created but are empty (zero bytes):
test_bam_short_intron2
test_short_intron1

from jum.

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

I reran the first command by submitting a slurm job sh file:

bedtools intersect -a 16hrAligned.out.sorted.bed -b
output_short_intron1_sorted.gff -sorted -wa -u -f 1 > test_short_intron1

I reran the first command in the directory where I ran JUM_A.sh

This was the result:
Tool: bedtools intersect (aka intersectBed)
Version: v2.27.1
Summary: Report overlaps between two feature files.

Usage: bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>

Note: -b may be followed with multiple databases and/or 
wildcard (*) character(s).

Options:
-wa Write the original entry in A for each overlap.

-wb	Write the original entry in B for each overlap.
	- Useful for knowing _what_ A overlaps. Restricted by -f and -r.

-loj	Perform a "left outer join". That is, for each feature in A
	report each overlap with B.  If no overlaps are found, 
	report a NULL feature for B.

-wo	Write the original A and B entries plus the number of base
	pairs of overlap between the two features.
	- Overlaps restricted by -f and -r.
	  Only A features with overlap are reported.

-wao	Write the original A and B entries plus the number of base
	pairs of overlap between the two features.
	- Overlapping features restricted by -f and -r.
	  However, A features w/o overlap are also reported
	  with a NULL B feature and overlap = 0.

-u	Write the original A entry _once_ if _any_ overlaps found in B.
	- In other words, just report the fact >=1 hit was found.
	- Overlaps restricted by -f and -r.

-c	For each entry in A, report the number of overlaps with B.
	- Reports 0 for A entries that have no overlap with B.
	- Overlaps restricted by -f and -r.

-v	Only report those entries in A that have _no overlaps_ with B.
	- Similar to "grep -v" (an homage).

-ubam	Write uncompressed BAM output. Default writes compressed BAM.

-s	Require same strandedness.  That is, only report hits in B
	that overlap A on the _same_ strand.
	- By default, overlaps are reported without respect to strand.

-S	Require different strandedness.  That is, only report hits in B
	that overlap A on the _opposite_ strand.
	- By default, overlaps are reported without respect to strand.

-f	Minimum overlap required as a fraction of A.
	- Default is 1E-9 (i.e., 1bp).
	- FLOAT (e.g. 0.50)

-F	Minimum overlap required as a fraction of B.
	- Default is 1E-9 (i.e., 1bp).
	- FLOAT (e.g. 0.50)

-r	Require that the fraction overlap be reciprocal for A AND B.
	- In other words, if -f is 0.90 and -r is used, this requires
	  that B overlap 90% of A and A _also_ overlaps 90% of B.

-e	Require that the minimum fraction be satisfied for A OR B.
	- In other words, if -e is used with -f 0.90 and -F 0.10 this requires
	  that either 90% of A is covered OR 10% of  B is covered.
	  Without -e, both fractions would have to be satisfied.

-split	Treat "split" BAM or BED12 entries as distinct BED intervals.

-g	Provide a genome file to enforce consistent chromosome sort order
	across input files. Only applies when used with -sorted option.

-nonamecheck	For sorted data, don't throw an error if the file has different naming conventions
		for the same chromosome. ex. "chr1" vs "chr01".

-sorted	Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.

-names	When using multiple databases, provide an alias for each that
	will appear instead of a fileId when also printing the DB record.

-filenames	When using multiple databases, show each complete filename
		instead of a fileId when also printing the DB record.

-sortout	When using multiple databases, sort the output DB hits
		for each record.

-bed	If using BAM input, write output as BED.

-header	Print the header from the A file prior to results.

-nobuf	Disable buffered output. Using this option will cause each line
	of output to be printed as it is generated, rather than saved
	in a buffer. This will make printing large output files 
	noticeably slower, but can be useful in conjunction with
	other software tools and scripts that need to process one
	line of bedtools output at a time.

-iobuf	Specify amount of memory to use for input buffer.
	Takes an integer argument. Optional suffixes K/M/G supported.
	Note: currently has no effect with compressed files.

Notes:
(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist,
and excluded if an overlap cannot be found. If multiple overlaps exist, they are not
reported, as we are only testing for one or more overlaps.

***** ERROR: -b option given, but no database file specified. *****
/var/spool/slurm/slurmd/job42905970/slurm_script: line 12: output_short_intron1_sorted.gff: command not found

The file output_short_intron1_sorted.gff is in my directory and is 1.3 MB, but the test_short_intron1 file that was created is empty (zero bytes).

from jum.

qqwang-berkeley avatar qqwang-berkeley commented on September 15, 2024

from jum.

hvicars avatar hvicars commented on September 15, 2024

Oh, thanks! I corrected that mistake and reran it. I received this error:

ERROR: Sort order was unspecified, and file 16hrAligned.out.sorted.bed is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.

However, the test_short_intron1 file now contains 577 KB.

from jum.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.