Need some clarifications about the methylation mapper Bismark

Question

[Antonio R. Franco]

I run Bismark using the --parallel 8 option Instructions claim the following

Once all processes have completed, the individual BAM files, mapping reports, unmapped or ambiguous FastQ files are merged into single files in very much the same way as they would have been generated running Bismark conventionally with only a single instance.

I had accessible in the PATH bismark, bowtie2 and also samtools only in case this latter was required to join the bam files that are obtained with the 8 parallel processes

But I got the following (only showing part of the directory), where you can see two behaviours. First, that bam files are not merged together. Second that the report.txt files remained empty

The actual bash command I run was

bismark --parallel 8 -N 1 -L 20 --non_directional -p 8 /home/arfranco/METILOMA/ASSEMBLY /home/arfranco/METILOMA/Fres2_1_1.fastq.gz

-rw-rw-r-- 1 arfranco arfranco 1071768327 mar 1 12:50 Fres2_1_1.fastq.gz.temp.1 -rw-rw-r-- 1 arfranco arfranco 0 mar 1 12:53 Fres2_1_1.fastq.gz.temp.1_bismark_bt2.bam -rw-rw-r-- 1 arfranco arfranco 0 mar 1 12:53 Fres2_1_1.fastq.gz.temp.1_bismark_bt2_SE_report.txt -rw-rw-r-- 1 arfranco arfranco 1071768327 mar 1 12:52 Fres2_1_1.fastq.gz.temp.1_C_to_T.fastq -rw-rw-r-- 1 arfranco arfranco 1071768327 mar 1 12:52 Fres2_1_1.fastq.gz.temp.1_G_to_A.fastq -rw-rw-r-- 1 arfranco arfranco 1071767989 mar 1 12:50 Fres2_1_1.fastq.gz.temp.2 -rw-rw-r-- 1 arfranco arfranco 0 mar 1 12:53 Fres2_1_1.fastq.gz.temp.2_bismark_bt2.bam -rw-rw-r-- 1 arfranco arfranco 0 mar 1 12:53 Fres2_1_1.fastq.gz.temp.2_bismark_bt2_SE_report.txt -rw-rw-r-- 1 arfranco arfranco 1071767989 mar 1 12:52 Fres2_1_1.fastq.gz.temp.2_C_to_T.fastq -rw-rw-r-- 1 arfranco arfranco 1071767989 mar 1 12:52 Fres2_1_1.fastq.gz.temp.2_G_to_A.fastq -rw-rw-r-- 1 arfranco arfranco 1071768318 mar 1 12:50 Fres2_1_1.fastq.gz.temp.3 -rw-rw-r-- 1 arfranco arfranco 0 mar 1 12:53 Fres2_1_1.fastq.gz.temp.3_bismark_bt2.bam -rw-rw-r-- 1 arfranco arfranco 0 mar 1 12:53 Fres2_1_1.fastq.gz.temp.3_bismark_bt2_SE_report.txt -rw-rw-r-- 1 arfranco arfranco 1071768318 mar 1 12:52 Fres2_1_1.fastq.gz.temp.3_C_to_T.fastq -rw-rw-r-- 1 arfranco arfranco 1071768318 mar 1 12:52 Fres2_1_1.fastq.gz.temp.3_G_to_A.fastq -rw-rw-r-- 1 arfranco arfranco 1071768399 mar 1 12:50 Fres2_1_1.fastq.gz.temp.4 -rw-rw-r-- 1 arfranco arfranco 0 mar 1 12:53 Fres2_1_1.fastq.gz.temp.4_bismark_bt2.bam -rw-rw-r-- 1 arfranco arfranco 0 mar 1 12:53 Fres2_1_1.fastq.gz.temp.4_bismark_bt2_SE_report.txt -rw-rw-r-- 1 arfranco arfranco 1071768399 mar 1 12:52 Fres2_1_1.fastq.gz.temp.4_C_to_T.fastq -rw-rw-r-- 1 arfranco arfranco 1071768399 mar 1 12:52 Fres2_1_1.fastq.gz.temp.4_G_to_A.fastq -rw-rw-r-- 1 arfranco arfranco 1071768476 mar 1 12:50 Fres2_1_1.fastq.gz.temp.5 -rw-rw-r-- 1 arfranco arfranco 0 mar 1 13:08 Fres2_1_1.fastq.gz.temp.5_bismark_bt2.bam -rw-rw-r-- 1 arfranco arfranco 0 mar 1 13:08 Fres2_1_1.fastq.gz.temp.5_bismark_bt2_SE_report.txt -rw-rw-r-- 1 arfranco arfranco 1071768476 mar 1 12:53 Fres2_1_1.fastq.gz.temp.5_C_to_T.fastq -rw-rw-r-- 1 arfranco arfranco 1071768476 mar 1 12:53 Fres2_1_1.fastq.gz.temp.5_G_to_A.fastq

Any hint ?

[GenoMax]

@Felix Kruger participates regularly on SeqAnswers.com (not sure if he is on BioStars). You may want to post this there as well.

BTW: Where is the first claim that you quoted made? In Bismark documentation?

[Antonio R. Franco]

Need only to run bismark - h and you get that information about - - parallel

[Antonio R. Franco]

It seems that it is advisable to use a máximum number of threads of 4, so I am going to change that and let the people know what happens