Job ID = 5720745 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,862,148 reads read : 13,724,296 reads written : 6,862,148 reads 0-length : 6,862,148 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: 00:03:15 6862148 reads; of these: 6862148 (100.00%) were unpaired; of these: 590618 (8.61%) aligned 0 times 4261455 (62.10%) aligned exactly 1 time 2010075 (29.29%) aligned >1 times 91.39% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 622721 / 6271530 = 0.0993 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 01:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.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 01:14:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:14:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:14:58: 1000000 INFO @ Thu, 16 Apr 2020 01:15:05: 2000000 INFO @ Thu, 16 Apr 2020 01:15:11: 3000000 INFO @ Thu, 16 Apr 2020 01:15:17: 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 01:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.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 01:15:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:15:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:15:24: 5000000 INFO @ Thu, 16 Apr 2020 01:15:27: 1000000 INFO @ Thu, 16 Apr 2020 01:15:28: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:15:28: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:15:28: #1 total tags in treatment: 5648809 INFO @ Thu, 16 Apr 2020 01:15:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:15:28: #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 01:15:28: #1 tags after filtering in treatment: 5648809 INFO @ Thu, 16 Apr 2020 01:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:15:28: #1 finished! INFO @ Thu, 16 Apr 2020 01:15:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:15:28: #2 number of paired peaks: 922 WARNING @ Thu, 16 Apr 2020 01:15:28: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Thu, 16 Apr 2020 01:15:28: start model_add_line... INFO @ Thu, 16 Apr 2020 01:15:28: start X-correlation... INFO @ Thu, 16 Apr 2020 01:15:28: end of X-cor INFO @ Thu, 16 Apr 2020 01:15:28: #2 finished! INFO @ Thu, 16 Apr 2020 01:15:28: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 01:15:28: #2 alternative fragment length(s) may be 84,549 bps INFO @ Thu, 16 Apr 2020 01:15:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.05_model.r WARNING @ Thu, 16 Apr 2020 01:15:28: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:15:28: #2 You may need to consider one of the other alternative d(s): 84,549 WARNING @ Thu, 16 Apr 2020 01:15:28: #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 01:15:28: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:15:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:15:33: 2000000 INFO @ Thu, 16 Apr 2020 01:15:38: 3000000 INFO @ Thu, 16 Apr 2020 01:15:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:15:44: 4000000 INFO @ Thu, 16 Apr 2020 01:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.05_summits.bed INFO @ Thu, 16 Apr 2020 01:15:47: Done! 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 01:15:49: 5000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2114 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:15:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.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 01:15:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:15:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:15:53: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:15:53: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:15:53: #1 total tags in treatment: 5648809 INFO @ Thu, 16 Apr 2020 01:15:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:15:53: #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 01:15:53: #1 tags after filtering in treatment: 5648809 INFO @ Thu, 16 Apr 2020 01:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:15:53: #1 finished! INFO @ Thu, 16 Apr 2020 01:15:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:15:53: #2 number of paired peaks: 922 WARNING @ Thu, 16 Apr 2020 01:15:53: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Thu, 16 Apr 2020 01:15:53: start model_add_line... INFO @ Thu, 16 Apr 2020 01:15:53: start X-correlation... INFO @ Thu, 16 Apr 2020 01:15:53: end of X-cor INFO @ Thu, 16 Apr 2020 01:15:53: #2 finished! INFO @ Thu, 16 Apr 2020 01:15:53: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 01:15:53: #2 alternative fragment length(s) may be 84,549 bps INFO @ Thu, 16 Apr 2020 01:15:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.10_model.r WARNING @ Thu, 16 Apr 2020 01:15:53: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:15:53: #2 You may need to consider one of the other alternative d(s): 84,549 WARNING @ Thu, 16 Apr 2020 01:15:53: #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 01:15:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:15:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:15:57: 1000000 INFO @ Thu, 16 Apr 2020 01:16:03: 2000000 INFO @ Thu, 16 Apr 2020 01:16:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:16:08: 3000000 INFO @ Thu, 16 Apr 2020 01:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:16:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.10_summits.bed INFO @ Thu, 16 Apr 2020 01:16:11: Done! INFO @ Thu, 16 Apr 2020 01:16:13: 4000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1084 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:16:19: 5000000 INFO @ Thu, 16 Apr 2020 01:16:22: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:16:22: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:16:22: #1 total tags in treatment: 5648809 INFO @ Thu, 16 Apr 2020 01:16:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:16:22: #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 01:16:22: #1 tags after filtering in treatment: 5648809 INFO @ Thu, 16 Apr 2020 01:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:16:22: #1 finished! INFO @ Thu, 16 Apr 2020 01:16:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:16:23: #2 number of paired peaks: 922 WARNING @ Thu, 16 Apr 2020 01:16:23: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Thu, 16 Apr 2020 01:16:23: start model_add_line... INFO @ Thu, 16 Apr 2020 01:16:23: start X-correlation... INFO @ Thu, 16 Apr 2020 01:16:23: end of X-cor INFO @ Thu, 16 Apr 2020 01:16:23: #2 finished! INFO @ Thu, 16 Apr 2020 01:16:23: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 01:16:23: #2 alternative fragment length(s) may be 84,549 bps INFO @ Thu, 16 Apr 2020 01:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.20_model.r WARNING @ Thu, 16 Apr 2020 01:16:23: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:16:23: #2 You may need to consider one of the other alternative d(s): 84,549 WARNING @ Thu, 16 Apr 2020 01:16:23: #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 01:16:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:16:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226984/SRX5226984.20_summits.bed INFO @ Thu, 16 Apr 2020 01:16:41: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (518 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。