juicer2 mega map mega.sh mega_from_bams.sh error

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Vanessa Roy

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Dec 7, 2023, 6:09:18 PM12/7/23

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Hi everyone,

I would be very grateful for your help on this: I am using juicer2 and trying to get a megamap using mega.sh and mega_from_bams.sh, but it does not seem to work for me. I keep getting the following error messages, and I don't know how to resolve them. Could you please point me in the direction so I can try to find out what I am doing wrong?

Here is (part) of the error message I get:

Using /storage/apps/juicer2/CPU/restriction_sites/danio_rerio_GRCz11_MboI.txt as site file

java.lang.NumberFormatException: For input string: "96% - 4%"

at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.base/java.lang.Long.parseLong(Long.java:692)

at java.base/java.lang.Long.parseLong(Long.java:817)

at sfh.merger.StatsMerger.processLine(StatsMerger.java:41)

at sfh.merger.StatsMerger.parse(StatsMerger.java:16)

at sfh.StatsUtils.merge(StatsUtils.java:10)

at sfh.MergeStats.main(MergeStats.java:50)

java.lang.NumberFormatException: For input string: "96% - 4%"

at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.base/java.lang.Long.parseLong(Long.java:692)

at java.base/java.lang.Long.parseLong(Long.java:817)

at sfh.merger.StatsMerger.processLine(StatsMerger.java:41)

at sfh.merger.StatsMerger.parse(StatsMerger.java:16)

at sfh.StatsUtils.merge(StatsUtils.java:10)

at sfh.MergeStats.main(MergeStats.java:50)

java.lang.NumberFormatException: For input string: "96% - 4%"

at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.base/java.lang.Long.parseLong(Long.java:692)

at java.base/java.lang.Long.parseLong(Long.java:817)

at sfh.merger.StatsMerger.processLine(StatsMerger.java:41)

at sfh.merger.StatsMerger.parse(StatsMerger.java:16)

at sfh.StatsUtils.merge(StatsUtils.java:10)

at sfh.MergeStats.main(MergeStats.java:50)

Usage: java -jar stats-from-hic.jar <inter_stem> <in.hic> [... in2.hic in3.hic]

(-: Finished creating top stats files.

sort: read failed: -: Bad file descriptor

(-: Finished sorting all files into a single merge.

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

Using 24 CPU thread(s) for primary task

Using 10 CPU thread(s) for secondary task

Unable to find All-All or All-All

Unable to find 1-KN149697.1 or KN149697.1-1

Unable to find 1-KN149698.1 or KN149698.1-1

Unable to find 1-KN149758.1 or KN149758.1-1

Unable to find 1-KN149766.1 or KN149766.1-1

Unable to find 1-KN149801.1 or KN149801.1-1

Unable to find 1-KN149810.1 or KN149810.1-1

Unable to find 1-KN149811.1 or KN149811.1-1

Unable to find 1-KN149837.1 or KN149837.1-1

Unable to find 1-KN149857.1 or KN149857.1-1

Unable to find 1-KN149951.1 or KN149951.1-1

Unable to find 1-KN150020.1 or KN150020.1-1

Unable to find 1-KN150065.1 or KN150065.1-1

Unable to find 1-KN150155.1 or KN150155.1-1

Unable to find 1-KN150231.1 or KN150231.1-1

Unable to find 1-KN150287.1 or KN150287.1-1

Unable to find 1-KN150418.1 or KN150418.1-1

Unable to find 1-KN150525.1 or KN150525.1-1

Unable to find 1-KN150528.1 or KN150528.1-1

Unable to find 1-KN150556.1 or KN150556.1-1

Unable to find 1-KZ115948.1 or KZ115948.1-1

Unable to find 1-KZ115951.1 or KZ115951.1-1

Unable to find 1-KZ115953.1 or KZ115953.1-1

Unable to find 1-KZ115955.1 or KZ115955.1-1

Unable to find 1-KZ115967.1 or KZ115967.1-1

Unable to find 1-KZ115978.1 or KZ115978.1-1

Unable to find KZ116067.1-MT or MT-KZ116067.1

Not including fragment map

Error while reading graphs file: java.io.FileNotFoundException: /storage/apps/juicer2/CPU/work_vanessaroy/old_mega_newtry/mega/aligned/inter_hists.m (No such file or directory)

Start preprocess

Writing header

Writing body

----------

Using /storage/apps/juicer2/CPU/restriction_sites/danio_rerio_GRCz11_MboI.txt as site file

merge: invalid option -- 'o'

Usage: samtools merge [-nurlf] [-h inh.sam] [-b <bamlist.fofn>] <out.bam> <in1.bam> [<in2.bam> ... <inN.bam>]

Options:

-n Input files are sorted by read name

-t TAG Input files are sorted by TAG value

-r Attach RG tag (inferred from file names)

-u Uncompressed BAM output

-f Overwrite the output BAM if exist

-1 Compress level 1

-l INT Compression level, from 0 to 9 [-1]

-R STR Merge file in the specified region STR [all]

-h FILE Copy the header in FILE to <out.bam> [in1.bam]

-c Combine @RG headers with colliding IDs [alter IDs to be distinct]

-p Combine @PG headers with colliding IDs [alter IDs to be distinct]

-s VALUE Override random seed

-b FILE List of input BAM filenames, one per line [null]

-X Use customized index files

-L FILE Specify a BED file for multiple region filtering [null]

--no-PG do not add a PG line

--input-fmt-option OPT[=VAL]

Specify a single input file format option in the form

of OPTION or OPTION=VALUE

-O, --output-fmt FORMAT[,OPT[=VAL]]...

Specify output format (SAM, BAM, CRAM)

--output-fmt-option OPT[=VAL]

Specify a single output file format option in the form

of OPTION or OPTION=VALUE

--reference FILE

Reference sequence FASTA FILE [null]

-@, --threads INT

Number of additional threads to use [0]

--write-index

Automatically index the output files [off]

--verbosity INT

Set level of verbosity

[E::hts_open_format] Failed to open file "/storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/mega_merged_dedup.bam" : No such file or directory

samtools view: failed to open "/storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/mega_merged_dedup.bam" for reading: No such file or directory

[E::hts_open_format] Failed to open file "/storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/mega_merged_dedup.bam" : No such file or directory

samtools view: failed to open "/storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/mega_merged_dedup.bam" for reading: No such file or directory

[E::hts_open_format] Failed to open file "/storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/mega_merged_dedup.bam" : No such file or directory

samtools view: failed to open "/storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/mega_merged_dedup.bam" for reading: No such file or directory

cat: '/*.res.txt': No such file or directory

awk: /storage/apps/juicer2/CPU/scripts/common/stats_sub.awk:65: fatal: division by zero attempted

(-: Finished creating top stats files.

(-: Finished sorting all files into a single merge.

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

Using 1 CPU thread(s) for primary task

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

Using 1 CPU thread(s) for primary task

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

Using 24 CPU thread(s) for primary task

Using 10 CPU thread(s) for secondary task

Unable to read merged nodups index

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

Using 24 CPU thread(s) for primary task

Error reading dataset/storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/inter.hic (No such file or directory)

java.io.FileNotFoundException: /storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/inter.hic (No such file or directory)

at java.base/java.io.RandomAccessFile.open0(Native Method)

at java.base/java.io.RandomAccessFile.open(RandomAccessFile.java:345)

at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:259)

at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:214)

at htsjdk.samtools.seekablestream.SeekableFileStream.<init>(SeekableFileStream.java:47)

at org.broad.igv.util.stream.IGVSeekableStreamFactory.getStreamFor(IGVSeekableStreamFactory.java:84)

at juicebox.data.DatasetReaderV2.getValidStream(DatasetReaderV2.java:242)

at juicebox.data.DatasetReaderV2.read(DatasetReaderV2.java:89)

at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:137)

at juicebox.tools.clt.old.AddNorm.launch(AddNorm.java:83)

at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:137)

at juicebox.tools.HiCTools.main(HiCTools.java:97)

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

Using 24 CPU thread(s) for primary task

Using 10 CPU thread(s) for secondary task

Unable to read merged nodups index

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

Using 24 CPU thread(s) for primary task

Error reading dataset/storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/inter_30.hic (No such file or directory)

java.io.FileNotFoundException: /storage/apps/juicer2/CPU/work_vanessaroy/mega_danio_rerio_WTAB_muscle_adult/mega/aligned/inter_30.hic (No such file or directory)