Job ID = 5720462 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,226,225 reads read : 19,226,225 reads written : 19,226,225 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289690.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: 00:05:46 19226225 reads; of these: 19226225 (100.00%) were unpaired; of these: 1371905 (7.14%) aligned 0 times 14100175 (73.34%) aligned exactly 1 time 3754145 (19.53%) aligned >1 times 92.86% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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] 7543064 / 17854320 = 0.4225 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 00:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.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 00:38:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:38:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:38:08: 1000000 INFO @ Thu, 16 Apr 2020 00:38:15: 2000000 INFO @ Thu, 16 Apr 2020 00:38:22: 3000000 INFO @ Thu, 16 Apr 2020 00:38:28: 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 00:38:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.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 00:38:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:38:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:38:36: 5000000 INFO @ Thu, 16 Apr 2020 00:38:39: 1000000 INFO @ Thu, 16 Apr 2020 00:38:43: 6000000 INFO @ Thu, 16 Apr 2020 00:38:46: 2000000 INFO @ Thu, 16 Apr 2020 00:38:51: 7000000 INFO @ Thu, 16 Apr 2020 00:38:54: 3000000 INFO @ Thu, 16 Apr 2020 00:38:58: 8000000 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 00:39:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.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 00:39:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:01: 4000000 INFO @ Thu, 16 Apr 2020 00:39:06: 9000000 INFO @ Thu, 16 Apr 2020 00:39:09: 1000000 INFO @ Thu, 16 Apr 2020 00:39:09: 5000000 INFO @ Thu, 16 Apr 2020 00:39:13: 10000000 INFO @ Thu, 16 Apr 2020 00:39:16: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:39:16: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:39:16: #1 total tags in treatment: 10311256 INFO @ Thu, 16 Apr 2020 00:39:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:39:16: #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 00:39:16: #1 tags after filtering in treatment: 10311256 INFO @ Thu, 16 Apr 2020 00:39:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:39:16: #1 finished! INFO @ Thu, 16 Apr 2020 00:39:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:39:16: 6000000 INFO @ Thu, 16 Apr 2020 00:39:16: 2000000 INFO @ Thu, 16 Apr 2020 00:39:17: #2 number of paired peaks: 491 WARNING @ Thu, 16 Apr 2020 00:39:17: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Thu, 16 Apr 2020 00:39:17: start model_add_line... INFO @ Thu, 16 Apr 2020 00:39:17: start X-correlation... INFO @ Thu, 16 Apr 2020 00:39:17: end of X-cor INFO @ Thu, 16 Apr 2020 00:39:17: #2 finished! INFO @ Thu, 16 Apr 2020 00:39:17: #2 predicted fragment length is 166 bps INFO @ Thu, 16 Apr 2020 00:39:17: #2 alternative fragment length(s) may be 166 bps INFO @ Thu, 16 Apr 2020 00:39:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.05_model.r INFO @ Thu, 16 Apr 2020 00:39:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:39:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:39:24: 7000000 INFO @ Thu, 16 Apr 2020 00:39:24: 3000000 INFO @ Thu, 16 Apr 2020 00:39:31: 8000000 INFO @ Thu, 16 Apr 2020 00:39:31: 4000000 INFO @ Thu, 16 Apr 2020 00:39:39: 9000000 INFO @ Thu, 16 Apr 2020 00:39:39: 5000000 INFO @ Thu, 16 Apr 2020 00:39:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:39:46: 10000000 INFO @ Thu, 16 Apr 2020 00:39:46: 6000000 INFO @ Thu, 16 Apr 2020 00:39:48: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:39:48: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:39:48: #1 total tags in treatment: 10311256 INFO @ Thu, 16 Apr 2020 00:39:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:39:48: #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 00:39:48: #1 tags after filtering in treatment: 10311256 INFO @ Thu, 16 Apr 2020 00:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:39:48: #1 finished! INFO @ Thu, 16 Apr 2020 00:39:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:39:49: #2 number of paired peaks: 491 WARNING @ Thu, 16 Apr 2020 00:39:49: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Thu, 16 Apr 2020 00:39:49: start model_add_line... INFO @ Thu, 16 Apr 2020 00:39:49: start X-correlation... INFO @ Thu, 16 Apr 2020 00:39:49: end of X-cor INFO @ Thu, 16 Apr 2020 00:39:49: #2 finished! INFO @ Thu, 16 Apr 2020 00:39:49: #2 predicted fragment length is 166 bps INFO @ Thu, 16 Apr 2020 00:39:49: #2 alternative fragment length(s) may be 166 bps INFO @ Thu, 16 Apr 2020 00:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.10_model.r INFO @ Thu, 16 Apr 2020 00:39:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:39:54: 7000000 INFO @ Thu, 16 Apr 2020 00:39:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:39:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:39:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.05_summits.bed INFO @ Thu, 16 Apr 2020 00:39:55: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (17927 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:40:01: 8000000 INFO @ Thu, 16 Apr 2020 00:40:08: 9000000 INFO @ Thu, 16 Apr 2020 00:40:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:40:14: 10000000 INFO @ Thu, 16 Apr 2020 00:40:17: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:40:17: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:40:17: #1 total tags in treatment: 10311256 INFO @ Thu, 16 Apr 2020 00:40:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:17: #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 00:40:17: #1 tags after filtering in treatment: 10311256 INFO @ Thu, 16 Apr 2020 00:40:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:17: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:18: #2 number of paired peaks: 491 WARNING @ Thu, 16 Apr 2020 00:40:18: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Thu, 16 Apr 2020 00:40:18: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:18: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:18: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:18: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:18: #2 predicted fragment length is 166 bps INFO @ Thu, 16 Apr 2020 00:40:18: #2 alternative fragment length(s) may be 166 bps INFO @ Thu, 16 Apr 2020 00:40:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.20_model.r INFO @ Thu, 16 Apr 2020 00:40:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:40:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:40:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:40:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.10_summits.bed INFO @ Thu, 16 Apr 2020 00:40:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14118 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:40:43: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592413/SRX2592413.20_summits.bed INFO @ Thu, 16 Apr 2020 00:40:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9798 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。