Job ID = 16432624 SRX = SRX9091665 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 159 READS because READLEN < 1 Read 50505688 spots for SRR12608194/SRR12608194.sra Written 50505688 spots for SRR12608194/SRR12608194.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436120 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 40 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 43707042 / 44584913 = 0.9803 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 11:08:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:08:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:08:55: 1000000 INFO @ Tue, 02 Aug 2022 11:09:03: 2000000 INFO @ Tue, 02 Aug 2022 11:09:08: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:09:08: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:09:08: #1 total tags in treatment: 864863 INFO @ Tue, 02 Aug 2022 11:09:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:09:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:09:08: #1 tags after filtering in treatment: 531722 INFO @ Tue, 02 Aug 2022 11:09:08: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 02 Aug 2022 11:09:08: #1 finished! INFO @ Tue, 02 Aug 2022 11:09:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:09:08: #2 number of paired peaks: 1288 INFO @ Tue, 02 Aug 2022 11:09:08: start model_add_line... INFO @ Tue, 02 Aug 2022 11:09:08: start X-correlation... INFO @ Tue, 02 Aug 2022 11:09:08: end of X-cor INFO @ Tue, 02 Aug 2022 11:09:08: #2 finished! INFO @ Tue, 02 Aug 2022 11:09:08: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 11:09:08: #2 alternative fragment length(s) may be 128,144 bps INFO @ Tue, 02 Aug 2022 11:09:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.05_model.r WARNING @ Tue, 02 Aug 2022 11:09:08: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:09:08: #2 You may need to consider one of the other alternative d(s): 128,144 WARNING @ Tue, 02 Aug 2022 11:09:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:09:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:09:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:09:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.05_summits.bed INFO @ Tue, 02 Aug 2022 11:09:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 41 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 11:09:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:09:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:09:24: 1000000 INFO @ Tue, 02 Aug 2022 11:09:32: 2000000 INFO @ Tue, 02 Aug 2022 11:09:37: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:09:37: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:09:37: #1 total tags in treatment: 864863 INFO @ Tue, 02 Aug 2022 11:09:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:09:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:09:37: #1 tags after filtering in treatment: 531722 INFO @ Tue, 02 Aug 2022 11:09:37: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 02 Aug 2022 11:09:37: #1 finished! INFO @ Tue, 02 Aug 2022 11:09:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:09:37: #2 number of paired peaks: 1288 INFO @ Tue, 02 Aug 2022 11:09:37: start model_add_line... INFO @ Tue, 02 Aug 2022 11:09:37: start X-correlation... INFO @ Tue, 02 Aug 2022 11:09:37: end of X-cor INFO @ Tue, 02 Aug 2022 11:09:37: #2 finished! INFO @ Tue, 02 Aug 2022 11:09:37: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 11:09:37: #2 alternative fragment length(s) may be 128,144 bps INFO @ Tue, 02 Aug 2022 11:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.10_model.r WARNING @ Tue, 02 Aug 2022 11:09:37: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:09:37: #2 You may need to consider one of the other alternative d(s): 128,144 WARNING @ Tue, 02 Aug 2022 11:09:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:09:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:09:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:09:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:09:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.10_summits.bed INFO @ Tue, 02 Aug 2022 11:09:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (425 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:09:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 11:09:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:09:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:09:54: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:10:02: 2000000 INFO @ Tue, 02 Aug 2022 11:10:07: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:10:07: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:10:07: #1 total tags in treatment: 864863 INFO @ Tue, 02 Aug 2022 11:10:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:10:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:10:07: #1 tags after filtering in treatment: 531722 INFO @ Tue, 02 Aug 2022 11:10:07: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 02 Aug 2022 11:10:07: #1 finished! INFO @ Tue, 02 Aug 2022 11:10:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:10:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:10:07: #2 number of paired peaks: 1288 INFO @ Tue, 02 Aug 2022 11:10:07: start model_add_line... INFO @ Tue, 02 Aug 2022 11:10:07: start X-correlation... INFO @ Tue, 02 Aug 2022 11:10:07: end of X-cor INFO @ Tue, 02 Aug 2022 11:10:07: #2 finished! INFO @ Tue, 02 Aug 2022 11:10:07: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 11:10:07: #2 alternative fragment length(s) may be 128,144 bps INFO @ Tue, 02 Aug 2022 11:10:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.20_model.r WARNING @ Tue, 02 Aug 2022 11:10:07: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:10:07: #2 You may need to consider one of the other alternative d(s): 128,144 WARNING @ Tue, 02 Aug 2022 11:10:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:10:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:10:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:10:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9091665/SRX9091665.20_summits.bed INFO @ Tue, 02 Aug 2022 11:10:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 24 millis CompletedMACS2peakCalling