Job ID = 5720651 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,958,488 reads read : 16,958,488 reads written : 16,958,488 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289748.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: 00:04:25 16958488 reads; of these: 16958488 (100.00%) were unpaired; of these: 3458565 (20.39%) aligned 0 times 10889140 (64.21%) aligned exactly 1 time 2610783 (15.40%) aligned >1 times 79.61% overall alignment rate Time searching: 00:04:25 Overall time: 00:04:25 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] 4299448 / 13499923 = 0.3185 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 00:55:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.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 00:55:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:28: 1000000 INFO @ Thu, 16 Apr 2020 00:55:33: 2000000 INFO @ Thu, 16 Apr 2020 00:55:38: 3000000 INFO @ Thu, 16 Apr 2020 00:55:42: 4000000 INFO @ Thu, 16 Apr 2020 00:55:47: 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 00:55:52: 6000000 INFO @ Thu, 16 Apr 2020 00:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.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 00:55:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:57: 7000000 INFO @ Thu, 16 Apr 2020 00:55:59: 1000000 INFO @ Thu, 16 Apr 2020 00:56:02: 8000000 INFO @ Thu, 16 Apr 2020 00:56:04: 2000000 INFO @ Thu, 16 Apr 2020 00:56:08: 9000000 INFO @ Thu, 16 Apr 2020 00:56:09: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:09: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:09: #1 total tags in treatment: 9200475 INFO @ Thu, 16 Apr 2020 00:56:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:09: #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 00:56:09: #1 tags after filtering in treatment: 9200475 INFO @ Thu, 16 Apr 2020 00:56:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:09: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:10: 3000000 INFO @ Thu, 16 Apr 2020 00:56:10: #2 number of paired peaks: 8658 INFO @ Thu, 16 Apr 2020 00:56:10: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:10: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:10: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:10: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:10: #2 predicted fragment length is 221 bps INFO @ Thu, 16 Apr 2020 00:56:10: #2 alternative fragment length(s) may be 221 bps INFO @ Thu, 16 Apr 2020 00:56:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.05_model.r INFO @ Thu, 16 Apr 2020 00:56:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:15: 4000000 INFO @ Thu, 16 Apr 2020 00:56:21: 5000000 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 00:56:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.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 00:56:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:56:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:56:27: 6000000 INFO @ Thu, 16 Apr 2020 00:56:29: 1000000 INFO @ Thu, 16 Apr 2020 00:56:34: 7000000 INFO @ Thu, 16 Apr 2020 00:56:34: 2000000 INFO @ Thu, 16 Apr 2020 00:56:40: 3000000 INFO @ Thu, 16 Apr 2020 00:56:40: 8000000 INFO @ Thu, 16 Apr 2020 00:56:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:45: 4000000 INFO @ Thu, 16 Apr 2020 00:56:47: 9000000 INFO @ Thu, 16 Apr 2020 00:56:48: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:48: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:48: #1 total tags in treatment: 9200475 INFO @ Thu, 16 Apr 2020 00:56:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:48: #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 00:56:48: #1 tags after filtering in treatment: 9200475 INFO @ Thu, 16 Apr 2020 00:56:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:48: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:49: #2 number of paired peaks: 8658 INFO @ Thu, 16 Apr 2020 00:56:49: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:49: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:49: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:49: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:49: #2 predicted fragment length is 221 bps INFO @ Thu, 16 Apr 2020 00:56:49: #2 alternative fragment length(s) may be 221 bps INFO @ Thu, 16 Apr 2020 00:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.10_model.r INFO @ Thu, 16 Apr 2020 00:56:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:51: 5000000 INFO @ Thu, 16 Apr 2020 00:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.05_summits.bed INFO @ Thu, 16 Apr 2020 00:56:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9626 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:56:56: 6000000 INFO @ Thu, 16 Apr 2020 00:57:02: 7000000 INFO @ Thu, 16 Apr 2020 00:57:07: 8000000 INFO @ Thu, 16 Apr 2020 00:57:12: 9000000 INFO @ Thu, 16 Apr 2020 00:57:13: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:57:13: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:57:13: #1 total tags in treatment: 9200475 INFO @ Thu, 16 Apr 2020 00:57:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:57:13: #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 00:57:14: #1 tags after filtering in treatment: 9200475 INFO @ Thu, 16 Apr 2020 00:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:57:14: #1 finished! INFO @ Thu, 16 Apr 2020 00:57:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:57:15: #2 number of paired peaks: 8658 INFO @ Thu, 16 Apr 2020 00:57:15: start model_add_line... INFO @ Thu, 16 Apr 2020 00:57:15: start X-correlation... INFO @ Thu, 16 Apr 2020 00:57:15: end of X-cor INFO @ Thu, 16 Apr 2020 00:57:15: #2 finished! INFO @ Thu, 16 Apr 2020 00:57:15: #2 predicted fragment length is 221 bps INFO @ Thu, 16 Apr 2020 00:57:15: #2 alternative fragment length(s) may be 221 bps INFO @ Thu, 16 Apr 2020 00:57:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.20_model.r INFO @ Thu, 16 Apr 2020 00:57:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:57:21: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.10_summits.bed INFO @ Thu, 16 Apr 2020 00:57:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8065 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:57:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592471/SRX2592471.20_summits.bed INFO @ Thu, 16 Apr 2020 00:57:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6233 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。