Job ID = 5720715 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,778,126 reads read : 16,778,126 reads written : 16,778,126 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: 00:03:34 16778126 reads; of these: 16778126 (100.00%) were unpaired; of these: 329793 (1.97%) aligned 0 times 15311049 (91.26%) aligned exactly 1 time 1137284 (6.78%) aligned >1 times 98.03% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 2870187 / 16448333 = 0.1745 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 01:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.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 01:18:07: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:18:07: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:18:13: 1000000 INFO @ Thu, 16 Apr 2020 01:18:18: 2000000 INFO @ Thu, 16 Apr 2020 01:18:24: 3000000 INFO @ Thu, 16 Apr 2020 01:18:30: 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 01:18:35: 5000000 INFO @ Thu, 16 Apr 2020 01:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.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 01:18:37: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:18:37: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:18:42: 6000000 INFO @ Thu, 16 Apr 2020 01:18:43: 1000000 INFO @ Thu, 16 Apr 2020 01:18:48: 7000000 INFO @ Thu, 16 Apr 2020 01:18:50: 2000000 INFO @ Thu, 16 Apr 2020 01:18:55: 8000000 INFO @ Thu, 16 Apr 2020 01:18:56: 3000000 INFO @ Thu, 16 Apr 2020 01:19:01: 9000000 INFO @ Thu, 16 Apr 2020 01:19:03: 4000000 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 01:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.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 01:19:07: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:19:07: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:19:08: 10000000 INFO @ Thu, 16 Apr 2020 01:19:09: 5000000 INFO @ Thu, 16 Apr 2020 01:19:14: 1000000 INFO @ Thu, 16 Apr 2020 01:19:14: 11000000 INFO @ Thu, 16 Apr 2020 01:19:16: 6000000 INFO @ Thu, 16 Apr 2020 01:19:20: 2000000 INFO @ Thu, 16 Apr 2020 01:19:21: 12000000 INFO @ Thu, 16 Apr 2020 01:19:23: 7000000 INFO @ Thu, 16 Apr 2020 01:19:26: 3000000 INFO @ Thu, 16 Apr 2020 01:19:27: 13000000 INFO @ Thu, 16 Apr 2020 01:19:29: 8000000 INFO @ Thu, 16 Apr 2020 01:19:31: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:19:31: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:19:31: #1 total tags in treatment: 13578146 INFO @ Thu, 16 Apr 2020 01:19:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:19:31: #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 01:19:31: #1 tags after filtering in treatment: 13578146 INFO @ Thu, 16 Apr 2020 01:19:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:19:31: #1 finished! INFO @ Thu, 16 Apr 2020 01:19:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:19:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:19:33: 4000000 INFO @ Thu, 16 Apr 2020 01:19:33: #2 number of paired peaks: 11036 INFO @ Thu, 16 Apr 2020 01:19:33: start model_add_line... INFO @ Thu, 16 Apr 2020 01:19:33: start X-correlation... INFO @ Thu, 16 Apr 2020 01:19:33: end of X-cor INFO @ Thu, 16 Apr 2020 01:19:33: #2 finished! INFO @ Thu, 16 Apr 2020 01:19:33: #2 predicted fragment length is 148 bps INFO @ Thu, 16 Apr 2020 01:19:33: #2 alternative fragment length(s) may be 3,148 bps INFO @ Thu, 16 Apr 2020 01:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.05_model.r INFO @ Thu, 16 Apr 2020 01:19:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:19:35: 9000000 INFO @ Thu, 16 Apr 2020 01:19:39: 5000000 INFO @ Thu, 16 Apr 2020 01:19:42: 10000000 INFO @ Thu, 16 Apr 2020 01:19:46: 6000000 INFO @ Thu, 16 Apr 2020 01:19:48: 11000000 INFO @ Thu, 16 Apr 2020 01:19:53: 7000000 INFO @ Thu, 16 Apr 2020 01:19:55: 12000000 INFO @ Thu, 16 Apr 2020 01:19:59: 8000000 INFO @ Thu, 16 Apr 2020 01:20:01: 13000000 INFO @ Thu, 16 Apr 2020 01:20:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:20:05: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:20:05: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:20:05: #1 total tags in treatment: 13578146 INFO @ Thu, 16 Apr 2020 01:20:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:20:05: #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 01:20:05: #1 tags after filtering in treatment: 13578146 INFO @ Thu, 16 Apr 2020 01:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:20:05: #1 finished! INFO @ Thu, 16 Apr 2020 01:20:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:20:06: 9000000 INFO @ Thu, 16 Apr 2020 01:20:07: #2 number of paired peaks: 11036 INFO @ Thu, 16 Apr 2020 01:20:07: start model_add_line... INFO @ Thu, 16 Apr 2020 01:20:07: start X-correlation... INFO @ Thu, 16 Apr 2020 01:20:07: end of X-cor INFO @ Thu, 16 Apr 2020 01:20:07: #2 finished! INFO @ Thu, 16 Apr 2020 01:20:07: #2 predicted fragment length is 148 bps INFO @ Thu, 16 Apr 2020 01:20:07: #2 alternative fragment length(s) may be 3,148 bps INFO @ Thu, 16 Apr 2020 01:20:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.10_model.r INFO @ Thu, 16 Apr 2020 01:20:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:20:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:20:12: 10000000 INFO @ Thu, 16 Apr 2020 01:20:17: 11000000 INFO @ Thu, 16 Apr 2020 01:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.05_summits.bed INFO @ Thu, 16 Apr 2020 01:20:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9196 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:20:23: 12000000 INFO @ Thu, 16 Apr 2020 01:20:29: 13000000 INFO @ Thu, 16 Apr 2020 01:20:32: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:20:32: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:20:32: #1 total tags in treatment: 13578146 INFO @ Thu, 16 Apr 2020 01:20:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:20:32: #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 01:20:33: #1 tags after filtering in treatment: 13578146 INFO @ Thu, 16 Apr 2020 01:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:20:33: #1 finished! INFO @ Thu, 16 Apr 2020 01:20:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:20:34: #2 number of paired peaks: 11036 INFO @ Thu, 16 Apr 2020 01:20:34: start model_add_line... INFO @ Thu, 16 Apr 2020 01:20:34: start X-correlation... INFO @ Thu, 16 Apr 2020 01:20:34: end of X-cor INFO @ Thu, 16 Apr 2020 01:20:34: #2 finished! INFO @ Thu, 16 Apr 2020 01:20:34: #2 predicted fragment length is 148 bps INFO @ Thu, 16 Apr 2020 01:20:34: #2 alternative fragment length(s) may be 3,148 bps INFO @ Thu, 16 Apr 2020 01:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.20_model.r INFO @ Thu, 16 Apr 2020 01:20:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:20:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.10_summits.bed INFO @ Thu, 16 Apr 2020 01:20:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5966 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:21:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:21:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158179/SRX4158179.20_summits.bed INFO @ Thu, 16 Apr 2020 01:21:21: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2280 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。