Job ID = 5720545 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,352,586 reads read : 30,352,586 reads written : 30,352,586 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289695.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: 00:08:24 30352586 reads; of these: 30352586 (100.00%) were unpaired; of these: 2508115 (8.26%) aligned 0 times 22663929 (74.67%) aligned exactly 1 time 5180542 (17.07%) aligned >1 times 91.74% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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] 9381644 / 27844471 = 0.3369 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 00:45:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.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 00:45:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:45:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:45:24: 1000000 INFO @ Thu, 16 Apr 2020 00:45:29: 2000000 INFO @ Thu, 16 Apr 2020 00:45:33: 3000000 INFO @ Thu, 16 Apr 2020 00:45:38: 4000000 INFO @ Thu, 16 Apr 2020 00:45:42: 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 00:45:47: 6000000 INFO @ Thu, 16 Apr 2020 00:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.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 00:45:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:45:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:45:51: 7000000 INFO @ Thu, 16 Apr 2020 00:45:54: 1000000 INFO @ Thu, 16 Apr 2020 00:45:56: 8000000 INFO @ Thu, 16 Apr 2020 00:45:58: 2000000 INFO @ Thu, 16 Apr 2020 00:46:01: 9000000 INFO @ Thu, 16 Apr 2020 00:46:03: 3000000 INFO @ Thu, 16 Apr 2020 00:46:05: 10000000 INFO @ Thu, 16 Apr 2020 00:46:07: 4000000 INFO @ Thu, 16 Apr 2020 00:46:10: 11000000 INFO @ Thu, 16 Apr 2020 00:46:12: 5000000 INFO @ Thu, 16 Apr 2020 00:46:14: 12000000 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 00:46:17: 6000000 INFO @ Thu, 16 Apr 2020 00:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.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 00:46:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:46:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:46:19: 13000000 INFO @ Thu, 16 Apr 2020 00:46:21: 7000000 INFO @ Thu, 16 Apr 2020 00:46:23: 1000000 INFO @ Thu, 16 Apr 2020 00:46:24: 14000000 INFO @ Thu, 16 Apr 2020 00:46:26: 8000000 INFO @ Thu, 16 Apr 2020 00:46:28: 2000000 INFO @ Thu, 16 Apr 2020 00:46:28: 15000000 INFO @ Thu, 16 Apr 2020 00:46:30: 9000000 INFO @ Thu, 16 Apr 2020 00:46:33: 3000000 INFO @ Thu, 16 Apr 2020 00:46:33: 16000000 INFO @ Thu, 16 Apr 2020 00:46:35: 10000000 INFO @ Thu, 16 Apr 2020 00:46:37: 4000000 INFO @ Thu, 16 Apr 2020 00:46:38: 17000000 INFO @ Thu, 16 Apr 2020 00:46:40: 11000000 INFO @ Thu, 16 Apr 2020 00:46:42: 5000000 INFO @ Thu, 16 Apr 2020 00:46:42: 18000000 INFO @ Thu, 16 Apr 2020 00:46:44: 12000000 INFO @ Thu, 16 Apr 2020 00:46:44: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:46:44: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:46:44: #1 total tags in treatment: 18462827 INFO @ Thu, 16 Apr 2020 00:46:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:44: #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 00:46:45: #1 tags after filtering in treatment: 18462827 INFO @ Thu, 16 Apr 2020 00:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:45: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:46: #2 number of paired peaks: 2885 INFO @ Thu, 16 Apr 2020 00:46:46: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:46: 6000000 INFO @ Thu, 16 Apr 2020 00:46:47: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:47: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:47: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:47: #2 predicted fragment length is 190 bps INFO @ Thu, 16 Apr 2020 00:46:47: #2 alternative fragment length(s) may be 3,190 bps INFO @ Thu, 16 Apr 2020 00:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.05_model.r INFO @ Thu, 16 Apr 2020 00:46:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:49: 13000000 INFO @ Thu, 16 Apr 2020 00:46:51: 7000000 INFO @ Thu, 16 Apr 2020 00:46:54: 14000000 INFO @ Thu, 16 Apr 2020 00:46:56: 8000000 INFO @ Thu, 16 Apr 2020 00:46:58: 15000000 INFO @ Thu, 16 Apr 2020 00:47:00: 9000000 INFO @ Thu, 16 Apr 2020 00:47:03: 16000000 INFO @ Thu, 16 Apr 2020 00:47:05: 10000000 INFO @ Thu, 16 Apr 2020 00:47:07: 17000000 INFO @ Thu, 16 Apr 2020 00:47:10: 11000000 INFO @ Thu, 16 Apr 2020 00:47:12: 18000000 INFO @ Thu, 16 Apr 2020 00:47:14: 12000000 INFO @ Thu, 16 Apr 2020 00:47:14: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:47:14: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:47:14: #1 total tags in treatment: 18462827 INFO @ Thu, 16 Apr 2020 00:47:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:47:14: #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 00:47:15: #1 tags after filtering in treatment: 18462827 INFO @ Thu, 16 Apr 2020 00:47:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:47:15: #1 finished! INFO @ Thu, 16 Apr 2020 00:47:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:47:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:47:16: #2 number of paired peaks: 2885 INFO @ Thu, 16 Apr 2020 00:47:16: start model_add_line... INFO @ Thu, 16 Apr 2020 00:47:16: start X-correlation... INFO @ Thu, 16 Apr 2020 00:47:16: end of X-cor INFO @ Thu, 16 Apr 2020 00:47:16: #2 finished! INFO @ Thu, 16 Apr 2020 00:47:16: #2 predicted fragment length is 190 bps INFO @ Thu, 16 Apr 2020 00:47:16: #2 alternative fragment length(s) may be 3,190 bps INFO @ Thu, 16 Apr 2020 00:47:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.10_model.r INFO @ Thu, 16 Apr 2020 00:47:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:47:19: 13000000 INFO @ Thu, 16 Apr 2020 00:47:23: 14000000 INFO @ Thu, 16 Apr 2020 00:47:28: 15000000 INFO @ Thu, 16 Apr 2020 00:47:33: 16000000 INFO @ Thu, 16 Apr 2020 00:47:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:47:37: 17000000 INFO @ Thu, 16 Apr 2020 00:47:42: 18000000 INFO @ Thu, 16 Apr 2020 00:47:44: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:47:44: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:47:44: #1 total tags in treatment: 18462827 INFO @ Thu, 16 Apr 2020 00:47:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:47:44: #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 00:47:44: #1 tags after filtering in treatment: 18462827 INFO @ Thu, 16 Apr 2020 00:47:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:47:44: #1 finished! INFO @ Thu, 16 Apr 2020 00:47:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:47:46: #2 number of paired peaks: 2885 INFO @ Thu, 16 Apr 2020 00:47:46: start model_add_line... INFO @ Thu, 16 Apr 2020 00:47:46: start X-correlation... INFO @ Thu, 16 Apr 2020 00:47:46: end of X-cor INFO @ Thu, 16 Apr 2020 00:47:46: #2 finished! INFO @ Thu, 16 Apr 2020 00:47:46: #2 predicted fragment length is 190 bps INFO @ Thu, 16 Apr 2020 00:47:46: #2 alternative fragment length(s) may be 3,190 bps INFO @ Thu, 16 Apr 2020 00:47:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.20_model.r INFO @ Thu, 16 Apr 2020 00:47:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:47:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.05_summits.bed INFO @ Thu, 16 Apr 2020 00:47:53: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16337 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:48:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:48:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:48:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:48:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.10_summits.bed INFO @ Thu, 16 Apr 2020 00:48:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11779 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:48:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592418/SRX2592418.20_summits.bed INFO @ Thu, 16 Apr 2020 00:48:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6086 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。