Question about'/aligned/inter.txt'

[linyong shen]

The comparison rate in the generated inter.txt file is abnormal, greater than 100%。

$ cat inter.txt 

Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 144 threads; openjdk version "11.0.9.1-internal" 2020-11-04; /home/SLY68/biosoft/scripts/juicer.sh -d /storage/SLY68/hic/juicer/lean1 -D /home/SLY68/biosoft -y /storage/SLY68/hic/juicer/lean1/restriction_sites/gallus_MboI.txt -z /storage/SLY68/hic/juicer/lean1/references/Gallus_gallus.GRCg6a.dna.toplevel.fa -p /storage/SLY68/hic/juicer/lean1/restriction_sites/gallus.sizes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    

Sequenced Read Pairs:  4,996,588

 Normal Paired: 203,970,661 (4082.20%)

 Chimeric Paired: 26,754,866 (535.46%)

 Chimeric Ambiguous: 0 (0.00%)

 Unmapped: 499,765,617 (10002.14%)

 Ligation Motif Present: 735,487,732 (14719.80%)

Alignable (Normal+Chimeric Paired): 230,725,527 (4617.66%)

Unique Reads: 431,101,368 (8,627.92%)

PCR Duplicates: 269,161,830 (5,386.91%)

Optical Duplicates: 3,473,080 (69.51%)

Library Complexity Estimate: 658,372,110

Intra-fragment Reads: 0 (0.00% / 0.00%)

Below MAPQ Threshold: 34,334,439 (687.16% / 7.96%)

Hi-C Contacts: 396,766,929 (7940.76% / 92.04%)

 Ligation Motif Present: 0  (0.00% / 0.00%)

 3' Bias (Long Range): 50% - 50%

 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%

Inter-chromosomal: 64,174,147  (1284.36% / 14.89%)

Intra-chromosomal: 332,592,782  (6656.40% / 77.15%)

Short Range (<20Kb): 218,546,568  (4373.92% / 50.69%)

Long Range (>20Kb): 114,034,099  (2282.24% / 26.45%)

[Neva Durand]

Something wrong with your *norm*res.txt files (you probably also have an error in your debug/final* files). Look in splits at linecount and *norm*res.txt

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Neva Cherniavsky Durand, Ph.D. | she, her, hers

Assistant Professor |  Molecular and Human Genetics

Aiden Lab | Baylor College of Medicine

www.aidenlab.org

[linyong shen]

Thank you very much for receiving your reply. As you said, my linecount file is empty. The content in the *norm*res.txt file: 

 cat /*/splits/*.fastq .gz_norm.txt.res.txt 

 745746192 5502143 499248621 206929935 34065493

I don't know how I should deal with this kind of problem，and the following is the log file of my running juicer pipeline：

      1 (-: Looking for fastq files...fastq files exist

      2 (-: Aligning files matching /storage/SLY68/hic/juicer/lean1/fastq/*_R*.fastq*

      3  to genome hg19 with site file /storage/SLY68/hic/juicer/lean1/restriction_sites/gallus_MboI.txt

      4 (-: Created /storage/SLY68/hic/juicer/lean1/splits and /storage/SLY68/hic/juicer/lean1/aligned.

      5 /home/SLY68/biosoft/scripts/common/countligations.sh: command substitution: line 33: syntax error near unexpected token `('

      6 /home/SLY68/biosoft/scripts/common/countligations.sh: command substitution: line 33: `paste <(gunzip -c $name1$ext) <(gunzip -c $name2$ext) | awk '!((NR+2)%4)' | g

      7 bwa mem -SP5M -t 144 /storage/SLY68/hic/juicer/lean1/references/Gallus_gallus.GRCg6a.dna.toplevel.fa /storage/SLY68/hic/juicer/lean1/splits/AF124701_R1.fastq.gz /s

      8 [M::bwa_idx_load_from_disk] read 0 ALT contigs

      9 [M::process] read 10431158 sequences (1440000055 bp)...

     10 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (19087, 3330422, 14076, 17770)

....

   3943 100% 

   3944 89 domains written to file: /storage/SLY68/hic/juicer/lean1/aligned/inter_30_contact_domains/5000_blocks.bedpe

   3945 Arrowhead complete

   3946 

   3947 HiCCUPS:

   3948 

   3949 GPUs are not installed so HiCCUPs cannot be run

   3950 

   3951 (-: Postprocessing successfully completed, maps too sparse to annotate or GPUs unavailable (-:

   3952 ***! Error! The statistics do not add up. Alignment likely failed to complete on one or more files. Run relaunch_prep.sh

   3953 Stats don't add up.  Check /storage/SLY68/hic/juicer/lean1/aligned for results

[Neva Durand]

The problem is right at the beginning in your countligations script, it looks like your bash is older / doesn't support this syntax. In any event, you can run this as a series of commands (counting the lines) to be sure your numbers add up. You can also add a "0" as the first field in the res.txt file and rerun awk -f stats_sub.awk to get correct percentages / numbers for the top portion of the inter.txt file. 

Overall it looks to me like it ran fine, so you can just do the above to correct your stats file but your hic file is fine.

/home/SLY68/biosoft/scripts/common/countligations.sh: command substitution: line 33: syntax error near unexpected token `('

/home/SLY68/biosoft/scripts/common/countligations.sh: command substitution: line 33: `paste <(gunzip -c $name1$ext) <(gunzip -c $name2$ext) | awk '!((NR+2)%4)' | grep -cE $ligation)'

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/572dc7c5-3962-4d2f-8b32-c9e58dc1d7a5n%40googlegroups.com.

[linyong shen]

Thank you very much, I have found the perfect solution, using "bash juicer" instead of "sh juicer.sh" to execute the script can run the stats file normally.