Job ID = 5720642 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,273,408 reads read : 20,273,408 reads written : 20,273,408 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289742.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: 00:05:13 20273408 reads; of these: 20273408 (100.00%) were unpaired; of these: 3523658 (17.38%) aligned 0 times 13532791 (66.75%) aligned exactly 1 time 3216959 (15.87%) aligned >1 times 82.62% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 5032854 / 16749750 = 0.3005 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 00:55:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.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 00:55:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:17: 1000000 INFO @ Thu, 16 Apr 2020 00:55:22: 2000000 INFO @ Thu, 16 Apr 2020 00:55:27: 3000000 INFO @ Thu, 16 Apr 2020 00:55:32: 4000000 INFO @ Thu, 16 Apr 2020 00:55:37: 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 00:55:42: 6000000 INFO @ Thu, 16 Apr 2020 00:55:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.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 00:55:42: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:42: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:47: 7000000 INFO @ Thu, 16 Apr 2020 00:55:48: 1000000 INFO @ Thu, 16 Apr 2020 00:55:52: 8000000 INFO @ Thu, 16 Apr 2020 00:55:54: 2000000 INFO @ Thu, 16 Apr 2020 00:55:57: 9000000 INFO @ Thu, 16 Apr 2020 00:56:00: 3000000 INFO @ Thu, 16 Apr 2020 00:56:03: 10000000 INFO @ Thu, 16 Apr 2020 00:56:06: 4000000 INFO @ Thu, 16 Apr 2020 00:56:08: 11000000 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 00:56:11: 5000000 INFO @ Thu, 16 Apr 2020 00:56:12: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:12: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:12: #1 total tags in treatment: 11716896 INFO @ Thu, 16 Apr 2020 00:56:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:12: #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 00:56:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.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 00:56:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:56:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:56:12: #1 tags after filtering in treatment: 11716896 INFO @ Thu, 16 Apr 2020 00:56:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:12: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:13: #2 number of paired peaks: 7993 INFO @ Thu, 16 Apr 2020 00:56:13: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:13: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:13: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:13: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:13: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 00:56:13: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 00:56:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.05_model.r INFO @ Thu, 16 Apr 2020 00:56:13: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:17: 6000000 INFO @ Thu, 16 Apr 2020 00:56:18: 1000000 INFO @ Thu, 16 Apr 2020 00:56:23: 7000000 INFO @ Thu, 16 Apr 2020 00:56:24: 2000000 INFO @ Thu, 16 Apr 2020 00:56:29: 8000000 INFO @ Thu, 16 Apr 2020 00:56:30: 3000000 INFO @ Thu, 16 Apr 2020 00:56:35: 9000000 INFO @ Thu, 16 Apr 2020 00:56:36: 4000000 INFO @ Thu, 16 Apr 2020 00:56:41: 10000000 INFO @ Thu, 16 Apr 2020 00:56:43: 5000000 INFO @ Thu, 16 Apr 2020 00:56:47: 11000000 INFO @ Thu, 16 Apr 2020 00:56:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:49: 6000000 INFO @ Thu, 16 Apr 2020 00:56:51: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:51: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:51: #1 total tags in treatment: 11716896 INFO @ Thu, 16 Apr 2020 00:56:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:51: #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 00:56:52: #1 tags after filtering in treatment: 11716896 INFO @ Thu, 16 Apr 2020 00:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:52: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:53: #2 number of paired peaks: 7993 INFO @ Thu, 16 Apr 2020 00:56:53: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:53: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:53: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:53: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:53: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 00:56:53: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 00:56:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.10_model.r INFO @ Thu, 16 Apr 2020 00:56:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:55: 7000000 INFO @ Thu, 16 Apr 2020 00:57:01: 8000000 INFO @ Thu, 16 Apr 2020 00:57:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.05_summits.bed INFO @ Thu, 16 Apr 2020 00:57:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12255 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:57:06: 9000000 INFO @ Thu, 16 Apr 2020 00:57:12: 10000000 INFO @ Thu, 16 Apr 2020 00:57:18: 11000000 INFO @ Thu, 16 Apr 2020 00:57:22: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:57:22: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:57:22: #1 total tags in treatment: 11716896 INFO @ Thu, 16 Apr 2020 00:57:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:57:22: #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 00:57:22: #1 tags after filtering in treatment: 11716896 INFO @ Thu, 16 Apr 2020 00:57:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:57:22: #1 finished! INFO @ Thu, 16 Apr 2020 00:57:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:57:24: #2 number of paired peaks: 7993 INFO @ Thu, 16 Apr 2020 00:57:24: start model_add_line... INFO @ Thu, 16 Apr 2020 00:57:24: start X-correlation... INFO @ Thu, 16 Apr 2020 00:57:24: end of X-cor INFO @ Thu, 16 Apr 2020 00:57:24: #2 finished! INFO @ Thu, 16 Apr 2020 00:57:24: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 00:57:24: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 00:57:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.20_model.r INFO @ Thu, 16 Apr 2020 00:57:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:57:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:57:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.10_summits.bed INFO @ Thu, 16 Apr 2020 00:57:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9228 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:57:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:58:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:58:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:58:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592465/SRX2592465.20_summits.bed INFO @ Thu, 16 Apr 2020 00:58:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6386 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。