Job ID = 5720947 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,975,825 reads read : 13,975,825 reads written : 13,975,825 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: 00:04:03 13975825 reads; of these: 13975825 (100.00%) were unpaired; of these: 1944653 (13.91%) aligned 0 times 8697821 (62.23%) aligned exactly 1 time 3333351 (23.85%) aligned >1 times 86.09% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 1911924 / 12031172 = 0.1589 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 03:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.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 03:35:50: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:35:50: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:35:56: 1000000 INFO @ Thu, 16 Apr 2020 03:36:02: 2000000 INFO @ Thu, 16 Apr 2020 03:36:07: 3000000 INFO @ Thu, 16 Apr 2020 03:36:13: 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 03:36:19: 5000000 INFO @ Thu, 16 Apr 2020 03:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.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 03:36:20: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:36:20: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:36:25: 6000000 INFO @ Thu, 16 Apr 2020 03:36:26: 1000000 INFO @ Thu, 16 Apr 2020 03:36:32: 7000000 INFO @ Thu, 16 Apr 2020 03:36:33: 2000000 INFO @ Thu, 16 Apr 2020 03:36:38: 8000000 INFO @ Thu, 16 Apr 2020 03:36:40: 3000000 INFO @ Thu, 16 Apr 2020 03:36:45: 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 03:36:46: 4000000 INFO @ Thu, 16 Apr 2020 03:36:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.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 03:36:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:36:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:36:52: 10000000 INFO @ Thu, 16 Apr 2020 03:36:53: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:36:53: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:36:53: #1 total tags in treatment: 10119248 INFO @ Thu, 16 Apr 2020 03:36:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:36:53: #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 03:36:53: #1 tags after filtering in treatment: 10119248 INFO @ Thu, 16 Apr 2020 03:36:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:36:53: #1 finished! INFO @ Thu, 16 Apr 2020 03:36:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:36:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:36:53: 5000000 INFO @ Thu, 16 Apr 2020 03:36:53: #2 number of paired peaks: 357 WARNING @ Thu, 16 Apr 2020 03:36:53: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Thu, 16 Apr 2020 03:36:53: start model_add_line... INFO @ Thu, 16 Apr 2020 03:36:54: start X-correlation... INFO @ Thu, 16 Apr 2020 03:36:54: end of X-cor INFO @ Thu, 16 Apr 2020 03:36:54: #2 finished! INFO @ Thu, 16 Apr 2020 03:36:54: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 03:36:54: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 03:36:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.05_model.r INFO @ Thu, 16 Apr 2020 03:36:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:36:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:36:56: 1000000 INFO @ Thu, 16 Apr 2020 03:37:00: 6000000 INFO @ Thu, 16 Apr 2020 03:37:03: 2000000 INFO @ Thu, 16 Apr 2020 03:37:07: 7000000 INFO @ Thu, 16 Apr 2020 03:37:10: 3000000 INFO @ Thu, 16 Apr 2020 03:37:13: 8000000 INFO @ Thu, 16 Apr 2020 03:37:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:37:16: 4000000 INFO @ Thu, 16 Apr 2020 03:37:20: 9000000 INFO @ Thu, 16 Apr 2020 03:37:23: 5000000 INFO @ Thu, 16 Apr 2020 03:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.05_summits.bed INFO @ Thu, 16 Apr 2020 03:37:25: Done! INFO @ Thu, 16 Apr 2020 03:37:27: 10000000 INFO @ Thu, 16 Apr 2020 03:37:28: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:37:28: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:37:28: #1 total tags in treatment: 10119248 INFO @ Thu, 16 Apr 2020 03:37:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:37:28: #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 03:37:28: #1 tags after filtering in treatment: 10119248 INFO @ Thu, 16 Apr 2020 03:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:37:28: #1 finished! INFO @ Thu, 16 Apr 2020 03:37:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:37:29: #2 number of paired peaks: 357 WARNING @ Thu, 16 Apr 2020 03:37:29: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Thu, 16 Apr 2020 03:37:29: start model_add_line... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3176 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:37:29: start X-correlation... INFO @ Thu, 16 Apr 2020 03:37:29: end of X-cor INFO @ Thu, 16 Apr 2020 03:37:29: #2 finished! INFO @ Thu, 16 Apr 2020 03:37:29: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 03:37:29: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 03:37:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.10_model.r INFO @ Thu, 16 Apr 2020 03:37:29: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:37:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:37:30: 6000000 INFO @ Thu, 16 Apr 2020 03:37:36: 7000000 INFO @ Thu, 16 Apr 2020 03:37:42: 8000000 INFO @ Thu, 16 Apr 2020 03:37:48: 9000000 INFO @ Thu, 16 Apr 2020 03:37:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:37:54: 10000000 INFO @ Thu, 16 Apr 2020 03:37:55: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:37:55: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:37:55: #1 total tags in treatment: 10119248 INFO @ Thu, 16 Apr 2020 03:37:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:37:55: #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 03:37:55: #1 tags after filtering in treatment: 10119248 INFO @ Thu, 16 Apr 2020 03:37:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:37:55: #1 finished! INFO @ Thu, 16 Apr 2020 03:37:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:37:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:37:55: #2 number of paired peaks: 357 WARNING @ Thu, 16 Apr 2020 03:37:55: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Thu, 16 Apr 2020 03:37:55: start model_add_line... INFO @ Thu, 16 Apr 2020 03:37:55: start X-correlation... INFO @ Thu, 16 Apr 2020 03:37:56: end of X-cor INFO @ Thu, 16 Apr 2020 03:37:56: #2 finished! INFO @ Thu, 16 Apr 2020 03:37:56: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 03:37:56: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 03:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.20_model.r INFO @ Thu, 16 Apr 2020 03:37:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:38:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:38:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:38:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.10_summits.bed INFO @ Thu, 16 Apr 2020 03:38:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2090 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:38:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:38:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:38:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:38:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386744/SRX6386744.20_summits.bed INFO @ Thu, 16 Apr 2020 03:38:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1231 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。