Job ID = 5720685 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,046,457 reads read : 20,046,457 reads written : 20,046,457 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289777.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:45 20046457 reads; of these: 20046457 (100.00%) were unpaired; of these: 2305585 (11.50%) aligned 0 times 15710011 (78.37%) aligned exactly 1 time 2030861 (10.13%) aligned >1 times 88.50% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 5538141 / 17740872 = 0.3122 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 01:04:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.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 01:04:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:04:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:04:43: 1000000 INFO @ Thu, 16 Apr 2020 01:04:50: 2000000 INFO @ Thu, 16 Apr 2020 01:04:56: 3000000 INFO @ Thu, 16 Apr 2020 01:05:01: 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 01:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.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 01:05:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:05:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:05:08: 5000000 INFO @ Thu, 16 Apr 2020 01:05:13: 1000000 INFO @ Thu, 16 Apr 2020 01:05:14: 6000000 INFO @ Thu, 16 Apr 2020 01:05:21: 2000000 INFO @ Thu, 16 Apr 2020 01:05:22: 7000000 INFO @ Thu, 16 Apr 2020 01:05:28: 8000000 INFO @ Thu, 16 Apr 2020 01:05:30: 3000000 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 01:05:34: 9000000 INFO @ Thu, 16 Apr 2020 01:05:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.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 01:05:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:05:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:05:38: 4000000 INFO @ Thu, 16 Apr 2020 01:05:40: 10000000 INFO @ Thu, 16 Apr 2020 01:05:43: 1000000 INFO @ Thu, 16 Apr 2020 01:05:46: 11000000 INFO @ Thu, 16 Apr 2020 01:05:46: 5000000 INFO @ Thu, 16 Apr 2020 01:05:51: 2000000 INFO @ Thu, 16 Apr 2020 01:05:52: 12000000 INFO @ Thu, 16 Apr 2020 01:05:54: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:05:54: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:05:54: #1 total tags in treatment: 12202731 INFO @ Thu, 16 Apr 2020 01:05:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:05:54: #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 01:05:54: #1 tags after filtering in treatment: 12202731 INFO @ Thu, 16 Apr 2020 01:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:05:54: #1 finished! INFO @ Thu, 16 Apr 2020 01:05:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:05:55: 6000000 INFO @ Thu, 16 Apr 2020 01:05:55: #2 number of paired peaks: 8937 INFO @ Thu, 16 Apr 2020 01:05:55: start model_add_line... INFO @ Thu, 16 Apr 2020 01:05:56: start X-correlation... INFO @ Thu, 16 Apr 2020 01:05:56: end of X-cor INFO @ Thu, 16 Apr 2020 01:05:56: #2 finished! INFO @ Thu, 16 Apr 2020 01:05:56: #2 predicted fragment length is 211 bps INFO @ Thu, 16 Apr 2020 01:05:56: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 16 Apr 2020 01:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.05_model.r INFO @ Thu, 16 Apr 2020 01:05:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:05:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:06:00: 3000000 INFO @ Thu, 16 Apr 2020 01:06:03: 7000000 INFO @ Thu, 16 Apr 2020 01:06:08: 4000000 INFO @ Thu, 16 Apr 2020 01:06:11: 8000000 INFO @ Thu, 16 Apr 2020 01:06:16: 5000000 INFO @ Thu, 16 Apr 2020 01:06:19: 9000000 INFO @ Thu, 16 Apr 2020 01:06:25: 6000000 INFO @ Thu, 16 Apr 2020 01:06:28: 10000000 INFO @ Thu, 16 Apr 2020 01:06:33: 7000000 INFO @ Thu, 16 Apr 2020 01:06:36: 11000000 INFO @ Thu, 16 Apr 2020 01:06:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:06:41: 8000000 INFO @ Thu, 16 Apr 2020 01:06:44: 12000000 INFO @ Thu, 16 Apr 2020 01:06:45: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:06:45: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:06:45: #1 total tags in treatment: 12202731 INFO @ Thu, 16 Apr 2020 01:06:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:06:45: #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 01:06:46: #1 tags after filtering in treatment: 12202731 INFO @ Thu, 16 Apr 2020 01:06:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:06:46: #1 finished! INFO @ Thu, 16 Apr 2020 01:06:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:06:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:06:47: #2 number of paired peaks: 8937 INFO @ Thu, 16 Apr 2020 01:06:47: start model_add_line... INFO @ Thu, 16 Apr 2020 01:06:48: start X-correlation... INFO @ Thu, 16 Apr 2020 01:06:48: end of X-cor INFO @ Thu, 16 Apr 2020 01:06:48: #2 finished! INFO @ Thu, 16 Apr 2020 01:06:48: #2 predicted fragment length is 211 bps INFO @ Thu, 16 Apr 2020 01:06:48: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 16 Apr 2020 01:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.10_model.r INFO @ Thu, 16 Apr 2020 01:06:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:06:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:06:49: 9000000 INFO @ Thu, 16 Apr 2020 01:06:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:06:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:06:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.05_summits.bed INFO @ Thu, 16 Apr 2020 01:06:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12269 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:06:57: 10000000 INFO @ Thu, 16 Apr 2020 01:07:05: 11000000 INFO @ Thu, 16 Apr 2020 01:07:13: 12000000 INFO @ Thu, 16 Apr 2020 01:07:15: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:07:15: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:07:15: #1 total tags in treatment: 12202731 INFO @ Thu, 16 Apr 2020 01:07:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:07:15: #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 01:07:15: #1 tags after filtering in treatment: 12202731 INFO @ Thu, 16 Apr 2020 01:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:07:15: #1 finished! INFO @ Thu, 16 Apr 2020 01:07:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:07:17: #2 number of paired peaks: 8937 INFO @ Thu, 16 Apr 2020 01:07:17: start model_add_line... INFO @ Thu, 16 Apr 2020 01:07:17: start X-correlation... INFO @ Thu, 16 Apr 2020 01:07:17: end of X-cor INFO @ Thu, 16 Apr 2020 01:07:17: #2 finished! INFO @ Thu, 16 Apr 2020 01:07:17: #2 predicted fragment length is 211 bps INFO @ Thu, 16 Apr 2020 01:07:17: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 16 Apr 2020 01:07:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.20_model.r INFO @ Thu, 16 Apr 2020 01:07:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:07:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:07:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.10_summits.bed INFO @ Thu, 16 Apr 2020 01:07:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9951 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:08:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592500/SRX2592500.20_summits.bed INFO @ Thu, 16 Apr 2020 01:08:15: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7339 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。