/var/spool/slurm/d/job2268308/slurm_script: line 22: fg: no job control /var/spool/slurm/d/job2268308/slurm_script: line 33: direct: command not found /var/spool/slurm/d/job2268308/slurm_script: line 36: direct: command not found % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Path to genome folder specified as: /gscratch/srlab/strigg/data/Pgenr/OFS/ Using 28 threads for the top and bottom strand indexing processes each, so using 56 cores in total Aligner to be used: >> Bowtie 2 << (default) Writing bisulfite genomes out into a single MFA (multi FastA) file Bismark Genome Preparation - Step I: Preparing folders Path to Bowtie 2 specified as: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ Bisulfite Genome Indexer version v0.21.0 (last modified: 05 Feb 2019) 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 A directory called /gscratch/srlab/strigg/data/Pgenr/OFS/Bisulfite_Genome/ already exists. Already existing converted sequences and/or already existing Bowtie 2 or HISAT2) indices will be overwritten! Step I - Prepare genome folders - completed Bismark Genome Preparation - Step II: Bisulfite converting reference genome 0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0conversions performed: chromosome C->T G->A Use of uninitialized value $first_line in scalar chomp at /gscratch/srlab/programs/Bismark-0.21.0/bismark_genome_preparation line 305. Use of uninitialized value $fasta_header in substitution (s///) at /gscratch/srlab/programs/Bismark-0.21.0/bismark_genome_preparation line 477. Use of uninitialized value $fasta_header in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark_genome_preparation line 482. The specified chromosome () file doesn't seem to be in FASTA format as required! Path to Bowtie 2 specified as: bowtie2 Failed to execute Bowtie 2 porperly (return code of 'bowtie2 --version' was 32512). Please install Bowtie 2 or HISAT2 first and make sure it is in the PATH, or specify the path to the Bowtie 2 with --path_to_bowtie2 /path/to/bowtie2, or --path_to_hisat2 /path/to/hisat2 /var/spool/slurm/d/job2268308/slurm_script: line 47: --path_to_bowtie: command not found *** Bismark methylation extractor version v0.21.0 *** No SAMtools installation found. Please add SAMtools to the PATH or specify its location with --samtools_path [path] Found no potential alignment reports in the current directory. Please specify a single Bismark alignment report file using the option '--alignment_report FILE' SYNOPSIS: This script uses a Bismark alignment report to generate a graphical HTML report page. Optionally, further reports of the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well. If several Bismark reports are found in the same folder, a separate report will be generated for each of these, whereby the output filename will be derived from the Bismark alignment report file. bismark2report attempts to find optional reports automatically based on the file basename. USAGE: bismark2report [options] -o/--output Name of the output file (optional). If not specified explicitly, the output filename will be derived from the Bismark alignment report file. Specifying an output filename only works if the HTML report is to be generated for a single Bismark alignment report (and potentially additional reports). --dir Output directory. Output is written to the current directory if not specified explicitly. --alignment_report FILE If not specified explicitly, bismark2report attempts to find Bismark report file(s) in the current directory and produces a separate HTML report for each mapping report file. Based on the basename of the Bismark mapping report, bismark2report will also attempt to find the other Bismark reports (see below) for inclusion into the HTML report. Specifying a Bismark alignment report file is mandatory. --dedup_report FILE If not specified explicitly, bismark2report attempts to find a deduplication report file with the same basename as the Bismark mapping report (generated by deduplicate_bismark) in the current working directory. Including a deduplication report is optional, and using the FILE 'none' will skip this step entirely. --splitting_report FILE If not specified explicitly, bismark2report attempts to find a splitting report file with the same basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current working directory. Including a splitting report is optional, and using the FILE 'none' will skip this step entirely. --mbias_report FILE If not specified explicitly, bismark2report attempts to find a single M-bias report file with the same basename as the Bismark mapping report (generated by the Bismark methylation extractor) in the current working directory. Including an M-Bias report is optional, and using the FILE 'none' will skip this step entirely. --nucleotide_report FILE If not specified explicitly, bismark2report attempts to find a single nucleotide coverage report file with the same basename as the Bismark mapping report (generated by Bismark with the option '--nucleotide_coverage') in the current working directory. Including a nucleotide coverage statistics report is optional, and using the FILE 'none' will skip this report entirely. Script last modified: 07 August 2018 0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0No Bismark/Bowtie2 single-end BAM files detected No Bismark/Bowtie2 paired-end BAM files detected No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Error: No Bismark BAM files found to generate a Bismark project summary. Please respecify... USAGE: bismark2summary (*.bam), or bismark2summary --help for more information at /gscratch/srlab/programs/Bismark-0.21.0/bismark2summary line 201.