Job ID = 5720370 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,686,944 reads read : 3,686,944 reads written : 3,686,944 spots read : 3,653,503 reads read : 3,653,503 reads written : 3,653,503 spots read : 3,706,979 reads read : 3,706,979 reads written : 3,706,979 spots read : 3,632,397 reads read : 3,632,397 reads written : 3,632,397 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: 00:00:01 Multiseed full-index search: 00:04:03 14679823 reads; of these: 14679823 (100.00%) were unpaired; of these: 2201342 (15.00%) aligned 0 times 9417230 (64.15%) aligned exactly 1 time 3061251 (20.85%) aligned >1 times 85.00% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7422970 / 12478481 = 0.5949 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, 16 Apr 2020 00:17:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 00:17:10: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:17:10: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:17:15: 1000000 INFO @ Thu, 16 Apr 2020 00:17:21: 2000000 INFO @ Thu, 16 Apr 2020 00:17:26: 3000000 INFO @ Thu, 16 Apr 2020 00:17:31: 4000000 INFO @ Thu, 16 Apr 2020 00:17:37: 5000000 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, 16 Apr 2020 00:17:37: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:17:37: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:17:37: #1 total tags in treatment: 5055511 INFO @ Thu, 16 Apr 2020 00:17:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:17:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:17:37: #1 tags after filtering in treatment: 5055511 INFO @ Thu, 16 Apr 2020 00:17:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:17:37: #1 finished! INFO @ Thu, 16 Apr 2020 00:17:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:17:38: #2 number of paired peaks: 4762 INFO @ Thu, 16 Apr 2020 00:17:38: start model_add_line... INFO @ Thu, 16 Apr 2020 00:17:38: start X-correlation... INFO @ Thu, 16 Apr 2020 00:17:38: end of X-cor INFO @ Thu, 16 Apr 2020 00:17:38: #2 finished! INFO @ Thu, 16 Apr 2020 00:17:38: #2 predicted fragment length is 238 bps INFO @ Thu, 16 Apr 2020 00:17:38: #2 alternative fragment length(s) may be 238 bps INFO @ Thu, 16 Apr 2020 00:17:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.05_model.r INFO @ Thu, 16 Apr 2020 00:17:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:17:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:17:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 00:17:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:17:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:17:45: 1000000 INFO @ Thu, 16 Apr 2020 00:17:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:17:51: 2000000 INFO @ Thu, 16 Apr 2020 00:17:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:17:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:17:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.05_summits.bed INFO @ Thu, 16 Apr 2020 00:17:56: Done! INFO @ Thu, 16 Apr 2020 00:17:56: 3000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7554 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:18:01: 4000000 INFO @ Thu, 16 Apr 2020 00:18:06: 5000000 INFO @ Thu, 16 Apr 2020 00:18:07: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:18:07: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:18:07: #1 total tags in treatment: 5055511 INFO @ Thu, 16 Apr 2020 00:18:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:18:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Thu, 16 Apr 2020 00:18:07: #1 tags after filtering in treatment: 5055511 INFO @ Thu, 16 Apr 2020 00:18:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:18:07: #1 finished! INFO @ Thu, 16 Apr 2020 00:18:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:18:07: #2 looking for paired plus/minus strand peaks... 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, 16 Apr 2020 00:18:07: #2 number of paired peaks: 4762 INFO @ Thu, 16 Apr 2020 00:18:07: start model_add_line... INFO @ Thu, 16 Apr 2020 00:18:07: start X-correlation... INFO @ Thu, 16 Apr 2020 00:18:07: end of X-cor INFO @ Thu, 16 Apr 2020 00:18:07: #2 finished! INFO @ Thu, 16 Apr 2020 00:18:07: #2 predicted fragment length is 238 bps INFO @ Thu, 16 Apr 2020 00:18:07: #2 alternative fragment length(s) may be 238 bps INFO @ Thu, 16 Apr 2020 00:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.10_model.r INFO @ Thu, 16 Apr 2020 00:18:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:18:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 00:18:10: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:18:10: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:18:15: 1000000 INFO @ Thu, 16 Apr 2020 00:18:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:18:21: 2000000 INFO @ Thu, 16 Apr 2020 00:18:26: 3000000 INFO @ Thu, 16 Apr 2020 00:18:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.10_summits.bed INFO @ Thu, 16 Apr 2020 00:18:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5528 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:18:31: 4000000 INFO @ Thu, 16 Apr 2020 00:18:37: 5000000 INFO @ Thu, 16 Apr 2020 00:18:37: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:18:37: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:18:37: #1 total tags in treatment: 5055511 INFO @ Thu, 16 Apr 2020 00:18:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:18:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:18:37: #1 tags after filtering in treatment: 5055511 INFO @ Thu, 16 Apr 2020 00:18:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:18:37: #1 finished! INFO @ Thu, 16 Apr 2020 00:18:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:18:38: #2 number of paired peaks: 4762 INFO @ Thu, 16 Apr 2020 00:18:38: start model_add_line... INFO @ Thu, 16 Apr 2020 00:18:38: start X-correlation... INFO @ Thu, 16 Apr 2020 00:18:38: end of X-cor INFO @ Thu, 16 Apr 2020 00:18:38: #2 finished! INFO @ Thu, 16 Apr 2020 00:18:38: #2 predicted fragment length is 238 bps INFO @ Thu, 16 Apr 2020 00:18:38: #2 alternative fragment length(s) may be 238 bps INFO @ Thu, 16 Apr 2020 00:18:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.20_model.r INFO @ Thu, 16 Apr 2020 00:18:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:18:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:18:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:18:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:18:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:18:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3548053/ERX3548053.20_summits.bed INFO @ Thu, 16 Apr 2020 00:18:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3465 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。