Job ID = 5720444 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,742,813 reads read : 24,742,813 reads written : 24,742,813 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289689.sra.cache’: 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: 00:07:41 24742813 reads; of these: 24742813 (100.00%) were unpaired; of these: 1830042 (7.40%) aligned 0 times 18174339 (73.45%) aligned exactly 1 time 4738432 (19.15%) aligned >1 times 92.60% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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_sort_core] merging from 12 files... [bam_rmdupse_core] 8047369 / 22912771 = 0.3512 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 00:41:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.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 00:41:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:41:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:41:54: 1000000 INFO @ Thu, 16 Apr 2020 00:42:00: 2000000 INFO @ Thu, 16 Apr 2020 00:42:06: 3000000 INFO @ Thu, 16 Apr 2020 00:42:12: 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 00:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.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 00:42:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:42:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:42:18: 5000000 INFO @ Thu, 16 Apr 2020 00:42:24: 1000000 INFO @ Thu, 16 Apr 2020 00:42:25: 6000000 INFO @ Thu, 16 Apr 2020 00:42:30: 2000000 INFO @ Thu, 16 Apr 2020 00:42:31: 7000000 INFO @ Thu, 16 Apr 2020 00:42:36: 3000000 INFO @ Thu, 16 Apr 2020 00:42:37: 8000000 INFO @ Thu, 16 Apr 2020 00:42:42: 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 00:42:44: 9000000 INFO @ Thu, 16 Apr 2020 00:42:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.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 00:42:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:42:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:42:49: 5000000 INFO @ Thu, 16 Apr 2020 00:42:50: 10000000 INFO @ Thu, 16 Apr 2020 00:42:53: 1000000 INFO @ Thu, 16 Apr 2020 00:42:55: 6000000 INFO @ Thu, 16 Apr 2020 00:42:57: 11000000 INFO @ Thu, 16 Apr 2020 00:43:00: 2000000 INFO @ Thu, 16 Apr 2020 00:43:01: 7000000 INFO @ Thu, 16 Apr 2020 00:43:03: 12000000 INFO @ Thu, 16 Apr 2020 00:43:06: 3000000 INFO @ Thu, 16 Apr 2020 00:43:08: 8000000 INFO @ Thu, 16 Apr 2020 00:43:10: 13000000 INFO @ Thu, 16 Apr 2020 00:43:13: 4000000 INFO @ Thu, 16 Apr 2020 00:43:14: 9000000 INFO @ Thu, 16 Apr 2020 00:43:16: 14000000 INFO @ Thu, 16 Apr 2020 00:43:19: 5000000 INFO @ Thu, 16 Apr 2020 00:43:20: 10000000 INFO @ Thu, 16 Apr 2020 00:43:22: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:43:22: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:43:22: #1 total tags in treatment: 14865402 INFO @ Thu, 16 Apr 2020 00:43:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:43:22: #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 00:43:22: #1 tags after filtering in treatment: 14865402 INFO @ Thu, 16 Apr 2020 00:43:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:43:22: #1 finished! INFO @ Thu, 16 Apr 2020 00:43:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:43:23: #2 number of paired peaks: 591 WARNING @ Thu, 16 Apr 2020 00:43:23: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Thu, 16 Apr 2020 00:43:23: start model_add_line... INFO @ Thu, 16 Apr 2020 00:43:23: start X-correlation... INFO @ Thu, 16 Apr 2020 00:43:23: end of X-cor INFO @ Thu, 16 Apr 2020 00:43:23: #2 finished! INFO @ Thu, 16 Apr 2020 00:43:23: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 00:43:23: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 00:43:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.05_model.r INFO @ Thu, 16 Apr 2020 00:43:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:43:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:43:25: 6000000 INFO @ Thu, 16 Apr 2020 00:43:26: 11000000 INFO @ Thu, 16 Apr 2020 00:43:32: 7000000 INFO @ Thu, 16 Apr 2020 00:43:33: 12000000 INFO @ Thu, 16 Apr 2020 00:43:38: 8000000 INFO @ Thu, 16 Apr 2020 00:43:39: 13000000 INFO @ Thu, 16 Apr 2020 00:43:44: 9000000 INFO @ Thu, 16 Apr 2020 00:43:45: 14000000 INFO @ Thu, 16 Apr 2020 00:43:50: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:43:50: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:43:50: #1 total tags in treatment: 14865402 INFO @ Thu, 16 Apr 2020 00:43:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:43:50: #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 00:43:51: #1 tags after filtering in treatment: 14865402 INFO @ Thu, 16 Apr 2020 00:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:43:51: #1 finished! INFO @ Thu, 16 Apr 2020 00:43:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:43:51: 10000000 INFO @ Thu, 16 Apr 2020 00:43:52: #2 number of paired peaks: 591 WARNING @ Thu, 16 Apr 2020 00:43:52: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Thu, 16 Apr 2020 00:43:52: start model_add_line... INFO @ Thu, 16 Apr 2020 00:43:52: start X-correlation... INFO @ Thu, 16 Apr 2020 00:43:52: end of X-cor INFO @ Thu, 16 Apr 2020 00:43:52: #2 finished! INFO @ Thu, 16 Apr 2020 00:43:52: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 00:43:52: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 00:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.10_model.r INFO @ Thu, 16 Apr 2020 00:43:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:43:57: 11000000 INFO @ Thu, 16 Apr 2020 00:44:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:44:02: 12000000 INFO @ Thu, 16 Apr 2020 00:44:08: 13000000 INFO @ Thu, 16 Apr 2020 00:44:14: 14000000 INFO @ Thu, 16 Apr 2020 00:44:19: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:44:19: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:44:19: #1 total tags in treatment: 14865402 INFO @ Thu, 16 Apr 2020 00:44:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:44:19: #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 00:44:19: #1 tags after filtering in treatment: 14865402 INFO @ Thu, 16 Apr 2020 00:44:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:44:19: #1 finished! INFO @ Thu, 16 Apr 2020 00:44:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:44:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:44:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:44:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.05_summits.bed INFO @ Thu, 16 Apr 2020 00:44:20: Done! INFO @ Thu, 16 Apr 2020 00:44:21: #2 number of paired peaks: 591 WARNING @ Thu, 16 Apr 2020 00:44:21: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Thu, 16 Apr 2020 00:44:21: start model_add_line... INFO @ Thu, 16 Apr 2020 00:44:21: start X-correlation... INFO @ Thu, 16 Apr 2020 00:44:21: end of X-cor INFO @ Thu, 16 Apr 2020 00:44:21: #2 finished! INFO @ Thu, 16 Apr 2020 00:44:21: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 00:44:21: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 00:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.20_model.r INFO @ Thu, 16 Apr 2020 00:44:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:44:21: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (17331 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:44:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:44:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.10_summits.bed INFO @ Thu, 16 Apr 2020 00:44:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12543 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:44:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:45:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:45:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:45:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592412/SRX2592412.20_summits.bed INFO @ Thu, 16 Apr 2020 00:45:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7457 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。