Job ID = 10165953 SRX = SRX8832087 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:24 10611046 reads; of these: 10611046 (100.00%) were unpaired; of these: 752643 (7.09%) aligned 0 times 8361589 (78.80%) aligned exactly 1 time 1496814 (14.11%) aligned >1 times 92.91% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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 8 files... [bam_rmdupse_core] 4476127 / 9858403 = 0.4540 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.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 @ Thu, 08 Oct 2020 20:21:18: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:21:18: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:21:23: 1000000 INFO @ Thu, 08 Oct 2020 20:21:29: 2000000 INFO @ Thu, 08 Oct 2020 20:21:34: 3000000 INFO @ Thu, 08 Oct 2020 20:21:39: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:21:45: 5000000 INFO @ Thu, 08 Oct 2020 20:21:47: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:21:47: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:21:47: #1 total tags in treatment: 5382276 INFO @ Thu, 08 Oct 2020 20:21:47: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:21:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:21:47: #1 tags after filtering in treatment: 5382276 INFO @ Thu, 08 Oct 2020 20:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:21:47: #1 finished! INFO @ Thu, 08 Oct 2020 20:21:47: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:21:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:21:47: #2 number of paired peaks: 4003 INFO @ Thu, 08 Oct 2020 20:21:47: start model_add_line... INFO @ Thu, 08 Oct 2020 20:21:47: start X-correlation... INFO @ Thu, 08 Oct 2020 20:21:47: end of X-cor INFO @ Thu, 08 Oct 2020 20:21:47: #2 finished! INFO @ Thu, 08 Oct 2020 20:21:47: #2 predicted fragment length is 149 bps INFO @ Thu, 08 Oct 2020 20:21:47: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 08 Oct 2020 20:21:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.05_model.r INFO @ Thu, 08 Oct 2020 20:21:47: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:21:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:21:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.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 @ Thu, 08 Oct 2020 20:21:48: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:21:48: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:21:53: 1000000 INFO @ Thu, 08 Oct 2020 20:21:59: 2000000 INFO @ Thu, 08 Oct 2020 20:22:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:22:04: 3000000 INFO @ Thu, 08 Oct 2020 20:22:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:22:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:22:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.05_summits.bed INFO @ Thu, 08 Oct 2020 20:22:09: Done! INFO @ Thu, 08 Oct 2020 20:22:10: 4000000 BedGraph に変換中... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7061 records, 4 fields): 9 millis WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:22:15: 5000000 INFO @ Thu, 08 Oct 2020 20:22:17: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:22:17: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:22:17: #1 total tags in treatment: 5382276 INFO @ Thu, 08 Oct 2020 20:22:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:22:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:22:17: #1 tags after filtering in treatment: 5382276 INFO @ Thu, 08 Oct 2020 20:22:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:22:17: #1 finished! INFO @ Thu, 08 Oct 2020 20:22:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:22:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:22:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.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 @ Thu, 08 Oct 2020 20:22:18: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:22:18: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:22:18: #2 number of paired peaks: 4003 INFO @ Thu, 08 Oct 2020 20:22:18: start model_add_line... INFO @ Thu, 08 Oct 2020 20:22:18: start X-correlation... INFO @ Thu, 08 Oct 2020 20:22:18: end of X-cor INFO @ Thu, 08 Oct 2020 20:22:18: #2 finished! INFO @ Thu, 08 Oct 2020 20:22:18: #2 predicted fragment length is 149 bps INFO @ Thu, 08 Oct 2020 20:22:18: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 08 Oct 2020 20:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.10_model.r INFO @ Thu, 08 Oct 2020 20:22:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:22:23: 1000000 INFO @ Thu, 08 Oct 2020 20:22:29: 2000000 INFO @ Thu, 08 Oct 2020 20:22:33: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:22:34: 3000000 INFO @ Thu, 08 Oct 2020 20:22:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:22:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:22:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.10_summits.bed INFO @ Thu, 08 Oct 2020 20:22:39: Done! INFO @ Thu, 08 Oct 2020 20:22:40: 4000000 BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5787 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:22:45: 5000000 INFO @ Thu, 08 Oct 2020 20:22:47: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:22:47: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:22:47: #1 total tags in treatment: 5382276 INFO @ Thu, 08 Oct 2020 20:22:47: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:22:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:22:47: #1 tags after filtering in treatment: 5382276 INFO @ Thu, 08 Oct 2020 20:22:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:22:47: #1 finished! INFO @ Thu, 08 Oct 2020 20:22:47: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:22:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:22:48: #2 number of paired peaks: 4003 INFO @ Thu, 08 Oct 2020 20:22:48: start model_add_line... INFO @ Thu, 08 Oct 2020 20:22:48: start X-correlation... INFO @ Thu, 08 Oct 2020 20:22:48: end of X-cor INFO @ Thu, 08 Oct 2020 20:22:48: #2 finished! INFO @ Thu, 08 Oct 2020 20:22:48: #2 predicted fragment length is 149 bps INFO @ Thu, 08 Oct 2020 20:22:48: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 08 Oct 2020 20:22:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.20_model.r INFO @ Thu, 08 Oct 2020 20:22:48: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:22:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:23:04: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:23:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:23:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:23:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832087/SRX8832087.20_summits.bed INFO @ Thu, 08 Oct 2020 20:23:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4509 records, 4 fields): 6 millis CompletedMACS2peakCalling