Job ID = 5720387 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,639,098 reads read : 20,639,098 reads written : 20,639,098 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289661.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: 00:06:10 20639098 reads; of these: 20639098 (100.00%) were unpaired; of these: 1800243 (8.72%) aligned 0 times 15242324 (73.85%) aligned exactly 1 time 3596531 (17.43%) aligned >1 times 91.28% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 8806737 / 18838855 = 0.4675 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 00:25:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.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 00:25:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:25:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:25:27: 1000000 INFO @ Thu, 16 Apr 2020 00:25:32: 2000000 INFO @ Thu, 16 Apr 2020 00:25:37: 3000000 INFO @ Thu, 16 Apr 2020 00:25:43: 4000000 INFO @ Thu, 16 Apr 2020 00:25:49: 5000000 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 00:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.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 00:25:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:25:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:25:55: 6000000 INFO @ Thu, 16 Apr 2020 00:25:58: 1000000 INFO @ Thu, 16 Apr 2020 00:26:01: 7000000 INFO @ Thu, 16 Apr 2020 00:26:04: 2000000 INFO @ Thu, 16 Apr 2020 00:26:07: 8000000 INFO @ Thu, 16 Apr 2020 00:26:10: 3000000 INFO @ Thu, 16 Apr 2020 00:26:13: 9000000 INFO @ Thu, 16 Apr 2020 00:26:16: 4000000 INFO @ Thu, 16 Apr 2020 00:26:18: 10000000 INFO @ Thu, 16 Apr 2020 00:26:19: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:26:19: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:26:19: #1 total tags in treatment: 10032118 INFO @ Thu, 16 Apr 2020 00:26:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:26:19: #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 00:26:19: #1 tags after filtering in treatment: 10032118 INFO @ Thu, 16 Apr 2020 00:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:26:19: #1 finished! INFO @ Thu, 16 Apr 2020 00:26:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:26:20: #2 number of paired peaks: 260 WARNING @ Thu, 16 Apr 2020 00:26:20: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Thu, 16 Apr 2020 00:26:20: start model_add_line... INFO @ Thu, 16 Apr 2020 00:26:20: start X-correlation... INFO @ Thu, 16 Apr 2020 00:26:20: end of X-cor INFO @ Thu, 16 Apr 2020 00:26:20: #2 finished! INFO @ Thu, 16 Apr 2020 00:26:20: #2 predicted fragment length is 164 bps INFO @ Thu, 16 Apr 2020 00:26:20: #2 alternative fragment length(s) may be 164 bps INFO @ Thu, 16 Apr 2020 00:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.05_model.r INFO @ Thu, 16 Apr 2020 00:26:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:26:20: #3 Pre-compute pvalue-qvalue table... 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 00:26:22: 5000000 INFO @ Thu, 16 Apr 2020 00:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.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 00:26:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:26:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:26:27: 1000000 INFO @ Thu, 16 Apr 2020 00:26:28: 6000000 INFO @ Thu, 16 Apr 2020 00:26:32: 2000000 INFO @ Thu, 16 Apr 2020 00:26:34: 7000000 INFO @ Thu, 16 Apr 2020 00:26:37: 3000000 INFO @ Thu, 16 Apr 2020 00:26:40: 8000000 INFO @ Thu, 16 Apr 2020 00:26:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:26:43: 4000000 INFO @ Thu, 16 Apr 2020 00:26:46: 9000000 INFO @ Thu, 16 Apr 2020 00:26:48: 5000000 INFO @ Thu, 16 Apr 2020 00:26:52: 10000000 INFO @ Thu, 16 Apr 2020 00:26:52: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:26:52: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:26:52: #1 total tags in treatment: 10032118 INFO @ Thu, 16 Apr 2020 00:26:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:26:52: #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 00:26:52: #1 tags after filtering in treatment: 10032118 INFO @ Thu, 16 Apr 2020 00:26:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:26:52: #1 finished! INFO @ Thu, 16 Apr 2020 00:26:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:26:53: 6000000 INFO @ Thu, 16 Apr 2020 00:26:53: #2 number of paired peaks: 260 WARNING @ Thu, 16 Apr 2020 00:26:53: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Thu, 16 Apr 2020 00:26:53: start model_add_line... INFO @ Thu, 16 Apr 2020 00:26:53: start X-correlation... INFO @ Thu, 16 Apr 2020 00:26:53: end of X-cor INFO @ Thu, 16 Apr 2020 00:26:53: #2 finished! INFO @ Thu, 16 Apr 2020 00:26:53: #2 predicted fragment length is 164 bps INFO @ Thu, 16 Apr 2020 00:26:53: #2 alternative fragment length(s) may be 164 bps INFO @ Thu, 16 Apr 2020 00:26:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.10_model.r INFO @ Thu, 16 Apr 2020 00:26:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:26:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:26:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:26:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:26:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.05_summits.bed INFO @ Thu, 16 Apr 2020 00:26:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (12236 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:26:58: 7000000 INFO @ Thu, 16 Apr 2020 00:27:03: 8000000 INFO @ Thu, 16 Apr 2020 00:27:08: 9000000 INFO @ Thu, 16 Apr 2020 00:27:13: 10000000 INFO @ Thu, 16 Apr 2020 00:27:13: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:27:13: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:27:13: #1 total tags in treatment: 10032118 INFO @ Thu, 16 Apr 2020 00:27:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:27:13: #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 00:27:13: #1 tags after filtering in treatment: 10032118 INFO @ Thu, 16 Apr 2020 00:27:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:27:13: #1 finished! INFO @ Thu, 16 Apr 2020 00:27:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:27:14: #2 number of paired peaks: 260 WARNING @ Thu, 16 Apr 2020 00:27:14: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Thu, 16 Apr 2020 00:27:14: start model_add_line... INFO @ Thu, 16 Apr 2020 00:27:14: start X-correlation... INFO @ Thu, 16 Apr 2020 00:27:14: end of X-cor INFO @ Thu, 16 Apr 2020 00:27:14: #2 finished! INFO @ Thu, 16 Apr 2020 00:27:14: #2 predicted fragment length is 164 bps INFO @ Thu, 16 Apr 2020 00:27:14: #2 alternative fragment length(s) may be 164 bps INFO @ Thu, 16 Apr 2020 00:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.20_model.r INFO @ Thu, 16 Apr 2020 00:27:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:27:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:27:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:27:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:27:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.10_summits.bed INFO @ Thu, 16 Apr 2020 00:27:27: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9997 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:27:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:27:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:27:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:27:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592384/SRX2592384.20_summits.bed INFO @ Thu, 16 Apr 2020 00:27:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (7462 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。