Job ID = 5720718 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,828,807 reads read : 13,828,807 reads written : 13,828,807 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: 00:04:43 13828807 reads; of these: 13828807 (100.00%) were unpaired; of these: 409220 (2.96%) aligned 0 times 7833061 (56.64%) aligned exactly 1 time 5586526 (40.40%) aligned >1 times 97.04% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 1433354 / 13419587 = 0.1068 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 01:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.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 01:17:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:17:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:17:33: 1000000 INFO @ Thu, 16 Apr 2020 01:17:39: 2000000 INFO @ Thu, 16 Apr 2020 01:17:45: 3000000 INFO @ Thu, 16 Apr 2020 01:17:51: 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 01:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.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 01:17:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:17:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:17:57: 5000000 INFO @ Thu, 16 Apr 2020 01:18:03: 1000000 INFO @ Thu, 16 Apr 2020 01:18:03: 6000000 INFO @ Thu, 16 Apr 2020 01:18:09: 2000000 INFO @ Thu, 16 Apr 2020 01:18:10: 7000000 INFO @ Thu, 16 Apr 2020 01:18:15: 3000000 INFO @ Thu, 16 Apr 2020 01:18:16: 8000000 INFO @ Thu, 16 Apr 2020 01:18:22: 4000000 INFO @ Thu, 16 Apr 2020 01:18:22: 9000000 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 01:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.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 01:18:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:18:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:18:28: 5000000 INFO @ Thu, 16 Apr 2020 01:18:28: 10000000 INFO @ Thu, 16 Apr 2020 01:18:32: 1000000 INFO @ Thu, 16 Apr 2020 01:18:34: 6000000 INFO @ Thu, 16 Apr 2020 01:18:34: 11000000 INFO @ Thu, 16 Apr 2020 01:18:38: 2000000 INFO @ Thu, 16 Apr 2020 01:18:40: 7000000 INFO @ Thu, 16 Apr 2020 01:18:40: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:18:40: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:18:40: #1 total tags in treatment: 11986233 INFO @ Thu, 16 Apr 2020 01:18:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:18:40: #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 01:18:41: #1 tags after filtering in treatment: 11986233 INFO @ Thu, 16 Apr 2020 01:18:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:18:41: #1 finished! INFO @ Thu, 16 Apr 2020 01:18:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:18:41: #2 number of paired peaks: 465 WARNING @ Thu, 16 Apr 2020 01:18:41: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Thu, 16 Apr 2020 01:18:41: start model_add_line... INFO @ Thu, 16 Apr 2020 01:18:42: start X-correlation... INFO @ Thu, 16 Apr 2020 01:18:42: end of X-cor INFO @ Thu, 16 Apr 2020 01:18:42: #2 finished! INFO @ Thu, 16 Apr 2020 01:18:42: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 01:18:42: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 16 Apr 2020 01:18:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.05_model.r WARNING @ Thu, 16 Apr 2020 01:18:42: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:18:42: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 16 Apr 2020 01:18:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:18:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:18:44: 3000000 INFO @ Thu, 16 Apr 2020 01:18:46: 8000000 INFO @ Thu, 16 Apr 2020 01:18:49: 4000000 INFO @ Thu, 16 Apr 2020 01:18:52: 9000000 INFO @ Thu, 16 Apr 2020 01:18:55: 5000000 INFO @ Thu, 16 Apr 2020 01:18:59: 10000000 INFO @ Thu, 16 Apr 2020 01:19:01: 6000000 INFO @ Thu, 16 Apr 2020 01:19:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:19:05: 11000000 INFO @ Thu, 16 Apr 2020 01:19:06: 7000000 INFO @ Thu, 16 Apr 2020 01:19:11: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:19:11: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:19:11: #1 total tags in treatment: 11986233 INFO @ Thu, 16 Apr 2020 01:19:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:19:11: #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 01:19:11: #1 tags after filtering in treatment: 11986233 INFO @ Thu, 16 Apr 2020 01:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:19:11: #1 finished! INFO @ Thu, 16 Apr 2020 01:19:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:19:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:19:12: 8000000 INFO @ Thu, 16 Apr 2020 01:19:12: #2 number of paired peaks: 465 WARNING @ Thu, 16 Apr 2020 01:19:12: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Thu, 16 Apr 2020 01:19:12: start model_add_line... INFO @ Thu, 16 Apr 2020 01:19:12: start X-correlation... INFO @ Thu, 16 Apr 2020 01:19:12: end of X-cor INFO @ Thu, 16 Apr 2020 01:19:12: #2 finished! INFO @ Thu, 16 Apr 2020 01:19:12: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 01:19:12: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 16 Apr 2020 01:19:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.10_model.r WARNING @ Thu, 16 Apr 2020 01:19:12: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:19:12: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 16 Apr 2020 01:19:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:19:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:19:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:19:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:19:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:19:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.05_summits.bed INFO @ Thu, 16 Apr 2020 01:19:16: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (3172 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:19:17: 9000000 INFO @ Thu, 16 Apr 2020 01:19:22: 10000000 INFO @ Thu, 16 Apr 2020 01:19:27: 11000000 INFO @ Thu, 16 Apr 2020 01:19:33: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:19:33: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:19:33: #1 total tags in treatment: 11986233 INFO @ Thu, 16 Apr 2020 01:19:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:19:33: #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 01:19:33: #1 tags after filtering in treatment: 11986233 INFO @ Thu, 16 Apr 2020 01:19:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:19:33: #1 finished! INFO @ Thu, 16 Apr 2020 01:19:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:19:34: #2 number of paired peaks: 465 WARNING @ Thu, 16 Apr 2020 01:19:34: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Thu, 16 Apr 2020 01:19:34: start model_add_line... INFO @ Thu, 16 Apr 2020 01:19:34: start X-correlation... INFO @ Thu, 16 Apr 2020 01:19:34: end of X-cor INFO @ Thu, 16 Apr 2020 01:19:34: #2 finished! INFO @ Thu, 16 Apr 2020 01:19:34: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 01:19:34: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 16 Apr 2020 01:19:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.20_model.r WARNING @ Thu, 16 Apr 2020 01:19:34: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:19:34: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 16 Apr 2020 01:19:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:19:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:19:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:19:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:19:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:19:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:19:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.10_summits.bed INFO @ Thu, 16 Apr 2020 01:19:47: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1659 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:19:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:20:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:20:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:20:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158182/SRX4158182.20_summits.bed INFO @ Thu, 16 Apr 2020 01:20:08: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (748 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。