Job ID = 5720583 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,054,423 reads read : 10,054,423 reads written : 10,054,423 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289713.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: 00:02:46 10054423 reads; of these: 10054423 (100.00%) were unpaired; of these: 990240 (9.85%) aligned 0 times 7845836 (78.03%) aligned exactly 1 time 1218347 (12.12%) aligned >1 times 90.15% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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_rmdupse_core] 2749974 / 9064183 = 0.3034 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 00:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.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 00:40:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:22: 1000000 INFO @ Thu, 16 Apr 2020 00:40:27: 2000000 INFO @ Thu, 16 Apr 2020 00:40:32: 3000000 INFO @ Thu, 16 Apr 2020 00:40:37: 4000000 INFO @ Thu, 16 Apr 2020 00:40:42: 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 00:40:47: 6000000 INFO @ Thu, 16 Apr 2020 00:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.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 00:40:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:48: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:40:48: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:40:48: #1 total tags in treatment: 6314209 INFO @ Thu, 16 Apr 2020 00:40:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:48: #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 00:40:48: #1 tags after filtering in treatment: 6314209 INFO @ Thu, 16 Apr 2020 00:40:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:48: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:49: #2 number of paired peaks: 418 WARNING @ Thu, 16 Apr 2020 00:40:49: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Thu, 16 Apr 2020 00:40:49: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:49: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:49: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:49: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:49: #2 predicted fragment length is 224 bps INFO @ Thu, 16 Apr 2020 00:40:49: #2 alternative fragment length(s) may be 224 bps INFO @ Thu, 16 Apr 2020 00:40:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.05_model.r INFO @ Thu, 16 Apr 2020 00:40:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:40:52: 1000000 INFO @ Thu, 16 Apr 2020 00:40:57: 2000000 INFO @ Thu, 16 Apr 2020 00:41:02: 3000000 INFO @ Thu, 16 Apr 2020 00:41:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:41:07: 4000000 INFO @ Thu, 16 Apr 2020 00:41:12: 5000000 BedGraph に変換中... INFO @ Thu, 16 Apr 2020 00:41:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.05_peaks.xls 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 00:41:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.05_summits.bed INFO @ Thu, 16 Apr 2020 00:41:14: Done! INFO @ Thu, 16 Apr 2020 00:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.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 00:41:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:41:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:41:17: 6000000 pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12902 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:41:19: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:41:19: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:41:19: #1 total tags in treatment: 6314209 INFO @ Thu, 16 Apr 2020 00:41:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:19: #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 00:41:19: #1 tags after filtering in treatment: 6314209 INFO @ Thu, 16 Apr 2020 00:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:19: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:20: #2 number of paired peaks: 418 WARNING @ Thu, 16 Apr 2020 00:41:20: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:20: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:20: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:20: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:20: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:20: #2 predicted fragment length is 224 bps INFO @ Thu, 16 Apr 2020 00:41:20: #2 alternative fragment length(s) may be 224 bps INFO @ Thu, 16 Apr 2020 00:41:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.10_model.r INFO @ Thu, 16 Apr 2020 00:41:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:22: 1000000 INFO @ Thu, 16 Apr 2020 00:41:27: 2000000 INFO @ Thu, 16 Apr 2020 00:41:32: 3000000 INFO @ Thu, 16 Apr 2020 00:41:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:41:37: 4000000 INFO @ Thu, 16 Apr 2020 00:41:42: 5000000 INFO @ Thu, 16 Apr 2020 00:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.10_summits.bed INFO @ Thu, 16 Apr 2020 00:41:43: Done! INFO @ Thu, 16 Apr 2020 00:41:47: 6000000 pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8801 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:41:48: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:41:48: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:41:48: #1 total tags in treatment: 6314209 INFO @ Thu, 16 Apr 2020 00:41:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:48: #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 00:41:48: #1 tags after filtering in treatment: 6314209 INFO @ Thu, 16 Apr 2020 00:41:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:48: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:49: #2 number of paired peaks: 418 WARNING @ Thu, 16 Apr 2020 00:41:49: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:49: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:49: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:49: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:49: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:49: #2 predicted fragment length is 224 bps INFO @ Thu, 16 Apr 2020 00:41:49: #2 alternative fragment length(s) may be 224 bps INFO @ Thu, 16 Apr 2020 00:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.20_model.r INFO @ Thu, 16 Apr 2020 00:41:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:42:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592436/SRX2592436.20_summits.bed INFO @ Thu, 16 Apr 2020 00:42:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5528 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。