Job ID = 5720924 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,504,881 reads read : 31,504,881 reads written : 31,504,881 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: 00:08:00 31504881 reads; of these: 31504881 (100.00%) were unpaired; of these: 8802160 (27.94%) aligned 0 times 16759518 (53.20%) aligned exactly 1 time 5943203 (18.86%) aligned >1 times 72.06% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 7307446 / 22702721 = 0.3219 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 03:43:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.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 03:43:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:43:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:43:33: 1000000 INFO @ Thu, 16 Apr 2020 03:43:38: 2000000 INFO @ Thu, 16 Apr 2020 03:43:44: 3000000 INFO @ Thu, 16 Apr 2020 03:43:50: 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 03:43:56: 5000000 INFO @ Thu, 16 Apr 2020 03:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.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 03:43:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:43:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:44:01: 6000000 INFO @ Thu, 16 Apr 2020 03:44:03: 1000000 INFO @ Thu, 16 Apr 2020 03:44:07: 7000000 INFO @ Thu, 16 Apr 2020 03:44:09: 2000000 INFO @ Thu, 16 Apr 2020 03:44:13: 8000000 INFO @ Thu, 16 Apr 2020 03:44:14: 3000000 INFO @ Thu, 16 Apr 2020 03:44:19: 9000000 INFO @ Thu, 16 Apr 2020 03:44:20: 4000000 INFO @ Thu, 16 Apr 2020 03:44:24: 10000000 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 03:44:26: 5000000 INFO @ Thu, 16 Apr 2020 03:44:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.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 03:44:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:44:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:44:30: 11000000 INFO @ Thu, 16 Apr 2020 03:44:31: 6000000 INFO @ Thu, 16 Apr 2020 03:44:33: 1000000 INFO @ Thu, 16 Apr 2020 03:44:36: 12000000 INFO @ Thu, 16 Apr 2020 03:44:37: 7000000 INFO @ Thu, 16 Apr 2020 03:44:38: 2000000 INFO @ Thu, 16 Apr 2020 03:44:41: 13000000 INFO @ Thu, 16 Apr 2020 03:44:43: 8000000 INFO @ Thu, 16 Apr 2020 03:44:44: 3000000 INFO @ Thu, 16 Apr 2020 03:44:47: 14000000 INFO @ Thu, 16 Apr 2020 03:44:48: 9000000 INFO @ Thu, 16 Apr 2020 03:44:50: 4000000 INFO @ Thu, 16 Apr 2020 03:44:53: 15000000 INFO @ Thu, 16 Apr 2020 03:44:54: 10000000 INFO @ Thu, 16 Apr 2020 03:44:55: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:44:55: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:44:55: #1 total tags in treatment: 15395275 INFO @ Thu, 16 Apr 2020 03:44:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:44:55: #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 03:44:55: #1 tags after filtering in treatment: 15395275 INFO @ Thu, 16 Apr 2020 03:44:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:44:55: #1 finished! INFO @ Thu, 16 Apr 2020 03:44:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:44:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:44:55: 5000000 INFO @ Thu, 16 Apr 2020 03:44:56: #2 number of paired peaks: 356 WARNING @ Thu, 16 Apr 2020 03:44:56: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Thu, 16 Apr 2020 03:44:56: start model_add_line... INFO @ Thu, 16 Apr 2020 03:44:57: start X-correlation... INFO @ Thu, 16 Apr 2020 03:44:57: end of X-cor INFO @ Thu, 16 Apr 2020 03:44:57: #2 finished! INFO @ Thu, 16 Apr 2020 03:44:57: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 03:44:57: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 03:44:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.05_model.r INFO @ Thu, 16 Apr 2020 03:44:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:45:00: 11000000 INFO @ Thu, 16 Apr 2020 03:45:01: 6000000 INFO @ Thu, 16 Apr 2020 03:45:05: 12000000 INFO @ Thu, 16 Apr 2020 03:45:07: 7000000 INFO @ Thu, 16 Apr 2020 03:45:11: 13000000 INFO @ Thu, 16 Apr 2020 03:45:13: 8000000 INFO @ Thu, 16 Apr 2020 03:45:17: 14000000 INFO @ Thu, 16 Apr 2020 03:45:18: 9000000 INFO @ Thu, 16 Apr 2020 03:45:22: 15000000 INFO @ Thu, 16 Apr 2020 03:45:24: 10000000 INFO @ Thu, 16 Apr 2020 03:45:24: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:45:24: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:45:24: #1 total tags in treatment: 15395275 INFO @ Thu, 16 Apr 2020 03:45:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:45:24: #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 03:45:25: #1 tags after filtering in treatment: 15395275 INFO @ Thu, 16 Apr 2020 03:45:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:45:25: #1 finished! INFO @ Thu, 16 Apr 2020 03:45:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:45:26: #2 number of paired peaks: 356 WARNING @ Thu, 16 Apr 2020 03:45:26: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Thu, 16 Apr 2020 03:45:26: start model_add_line... INFO @ Thu, 16 Apr 2020 03:45:26: start X-correlation... INFO @ Thu, 16 Apr 2020 03:45:26: end of X-cor INFO @ Thu, 16 Apr 2020 03:45:26: #2 finished! INFO @ Thu, 16 Apr 2020 03:45:26: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 03:45:26: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 03:45:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.10_model.r INFO @ Thu, 16 Apr 2020 03:45:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:45:30: 11000000 INFO @ Thu, 16 Apr 2020 03:45:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:45:35: 12000000 INFO @ Thu, 16 Apr 2020 03:45:41: 13000000 INFO @ Thu, 16 Apr 2020 03:45:46: 14000000 INFO @ Thu, 16 Apr 2020 03:45:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:45:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:45:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.05_summits.bed INFO @ Thu, 16 Apr 2020 03:45:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5038 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:45:52: 15000000 INFO @ Thu, 16 Apr 2020 03:45:54: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:45:54: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:45:54: #1 total tags in treatment: 15395275 INFO @ Thu, 16 Apr 2020 03:45:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:45:54: #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 03:45:54: #1 tags after filtering in treatment: 15395275 INFO @ Thu, 16 Apr 2020 03:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:45:54: #1 finished! INFO @ Thu, 16 Apr 2020 03:45:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:45:55: #2 number of paired peaks: 356 WARNING @ Thu, 16 Apr 2020 03:45:55: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Thu, 16 Apr 2020 03:45:55: start model_add_line... INFO @ Thu, 16 Apr 2020 03:45:55: start X-correlation... INFO @ Thu, 16 Apr 2020 03:45:55: end of X-cor INFO @ Thu, 16 Apr 2020 03:45:55: #2 finished! INFO @ Thu, 16 Apr 2020 03:45:55: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 03:45:55: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 03:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.20_model.r INFO @ Thu, 16 Apr 2020 03:45:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:45:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:46:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:46:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:46:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.10_summits.bed INFO @ Thu, 16 Apr 2020 03:46:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2794 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:46:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386725/SRX6386725.20_summits.bed INFO @ Thu, 16 Apr 2020 03:46:43: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1521 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。