Job ID = 5720713 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,995,461 reads read : 6,995,461 reads written : 6,995,461 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:01:41 6995461 reads; of these: 6995461 (100.00%) were unpaired; of these: 296146 (4.23%) aligned 0 times 6209705 (88.77%) aligned exactly 1 time 489610 (7.00%) aligned >1 times 95.77% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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_rmdupse_core] 1142489 / 6699315 = 0.1705 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 01:07:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.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 01:07:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:07:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:07:21: 1000000 INFO @ Thu, 16 Apr 2020 01:07:27: 2000000 INFO @ Thu, 16 Apr 2020 01:07:34: 3000000 INFO @ Thu, 16 Apr 2020 01:07:41: 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, 16 Apr 2020 01:07:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.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 01:07:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:07:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:07:48: 5000000 INFO @ Thu, 16 Apr 2020 01:07:51: 1000000 INFO @ Thu, 16 Apr 2020 01:07:52: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:07:52: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:07:52: #1 total tags in treatment: 5556826 INFO @ Thu, 16 Apr 2020 01:07:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:07:52: #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 01:07:53: #1 tags after filtering in treatment: 5556826 INFO @ Thu, 16 Apr 2020 01:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:07:53: #1 finished! INFO @ Thu, 16 Apr 2020 01:07:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:07:53: #2 number of paired peaks: 8697 INFO @ Thu, 16 Apr 2020 01:07:53: start model_add_line... INFO @ Thu, 16 Apr 2020 01:07:53: start X-correlation... INFO @ Thu, 16 Apr 2020 01:07:53: end of X-cor INFO @ Thu, 16 Apr 2020 01:07:53: #2 finished! INFO @ Thu, 16 Apr 2020 01:07:53: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 01:07:53: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 01:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.05_model.r INFO @ Thu, 16 Apr 2020 01:07:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:07:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:07:57: 2000000 INFO @ Thu, 16 Apr 2020 01:08:03: 3000000 INFO @ Thu, 16 Apr 2020 01:08:09: 4000000 INFO @ Thu, 16 Apr 2020 01:08:09: #3 Call peaks for each chromosome... BedGraph に変換中... 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 01:08:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.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 01:08:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:08:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:08:15: 5000000 INFO @ Thu, 16 Apr 2020 01:08:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:08:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.05_summits.bed INFO @ Thu, 16 Apr 2020 01:08:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6464 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:08:18: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:08:18: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:08:18: #1 total tags in treatment: 5556826 INFO @ Thu, 16 Apr 2020 01:08:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:08:18: #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 01:08:18: #1 tags after filtering in treatment: 5556826 INFO @ Thu, 16 Apr 2020 01:08:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:08:18: #1 finished! INFO @ Thu, 16 Apr 2020 01:08:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:08:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:08:19: #2 number of paired peaks: 8697 INFO @ Thu, 16 Apr 2020 01:08:19: start model_add_line... INFO @ Thu, 16 Apr 2020 01:08:19: start X-correlation... INFO @ Thu, 16 Apr 2020 01:08:19: end of X-cor INFO @ Thu, 16 Apr 2020 01:08:19: #2 finished! INFO @ Thu, 16 Apr 2020 01:08:19: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 01:08:19: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 01:08:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.10_model.r INFO @ Thu, 16 Apr 2020 01:08:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:08:20: 1000000 INFO @ Thu, 16 Apr 2020 01:08:25: 2000000 INFO @ Thu, 16 Apr 2020 01:08:31: 3000000 INFO @ Thu, 16 Apr 2020 01:08:34: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:08:37: 4000000 INFO @ Thu, 16 Apr 2020 01:08:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.10_summits.bed INFO @ Thu, 16 Apr 2020 01:08:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5985 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:08:42: 5000000 INFO @ Thu, 16 Apr 2020 01:08:46: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:08:46: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:08:46: #1 total tags in treatment: 5556826 INFO @ Thu, 16 Apr 2020 01:08:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:08:46: #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 01:08:46: #1 tags after filtering in treatment: 5556826 INFO @ Thu, 16 Apr 2020 01:08:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:08:46: #1 finished! INFO @ Thu, 16 Apr 2020 01:08:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:08:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:08:46: #2 number of paired peaks: 8697 INFO @ Thu, 16 Apr 2020 01:08:46: start model_add_line... INFO @ Thu, 16 Apr 2020 01:08:47: start X-correlation... INFO @ Thu, 16 Apr 2020 01:08:47: end of X-cor INFO @ Thu, 16 Apr 2020 01:08:47: #2 finished! INFO @ Thu, 16 Apr 2020 01:08:47: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 01:08:47: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 01:08:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.20_model.r INFO @ Thu, 16 Apr 2020 01:08:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:08:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:09:02: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158177/SRX4158177.20_summits.bed INFO @ Thu, 16 Apr 2020 01:09:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5112 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。