Job ID = 5720654 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,076,180 reads read : 14,076,180 reads written : 14,076,180 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289751.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: 00:03:03 14076180 reads; of these: 14076180 (100.00%) were unpaired; of these: 4088956 (29.05%) aligned 0 times 8291014 (58.90%) aligned exactly 1 time 1696210 (12.05%) aligned >1 times 70.95% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 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] 2337219 / 9987224 = 0.2340 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 00:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.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 00:53:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:00: 1000000 INFO @ Thu, 16 Apr 2020 00:54:05: 2000000 INFO @ Thu, 16 Apr 2020 00:54:10: 3000000 INFO @ Thu, 16 Apr 2020 00:54:14: 4000000 INFO @ Thu, 16 Apr 2020 00:54:19: 5000000 INFO @ Thu, 16 Apr 2020 00:54:24: 6000000 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 00:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.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 00:54:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:28: 7000000 INFO @ Thu, 16 Apr 2020 00:54:30: 1000000 INFO @ Thu, 16 Apr 2020 00:54:32: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:54:32: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:54:32: #1 total tags in treatment: 7650005 INFO @ Thu, 16 Apr 2020 00:54:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:54:32: #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 00:54:32: #1 tags after filtering in treatment: 7650005 INFO @ Thu, 16 Apr 2020 00:54:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:54:32: #1 finished! INFO @ Thu, 16 Apr 2020 00:54:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:54:33: #2 number of paired peaks: 7762 INFO @ Thu, 16 Apr 2020 00:54:33: start model_add_line... INFO @ Thu, 16 Apr 2020 00:54:33: start X-correlation... INFO @ Thu, 16 Apr 2020 00:54:33: end of X-cor INFO @ Thu, 16 Apr 2020 00:54:33: #2 finished! INFO @ Thu, 16 Apr 2020 00:54:33: #2 predicted fragment length is 204 bps INFO @ Thu, 16 Apr 2020 00:54:33: #2 alternative fragment length(s) may be 204 bps INFO @ Thu, 16 Apr 2020 00:54:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.05_model.r INFO @ Thu, 16 Apr 2020 00:54:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:54:35: 2000000 INFO @ Thu, 16 Apr 2020 00:54:40: 3000000 INFO @ Thu, 16 Apr 2020 00:54:45: 4000000 INFO @ Thu, 16 Apr 2020 00:54:49: 5000000 INFO @ Thu, 16 Apr 2020 00:54:54: 6000000 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 00:54:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.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 00:54:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:54:59: 7000000 INFO @ Thu, 16 Apr 2020 00:55:01: 1000000 INFO @ Thu, 16 Apr 2020 00:55:02: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:02: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:02: #1 total tags in treatment: 7650005 INFO @ Thu, 16 Apr 2020 00:55:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:02: #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 00:55:02: #1 tags after filtering in treatment: 7650005 INFO @ Thu, 16 Apr 2020 00:55:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:02: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:03: #2 number of paired peaks: 7762 INFO @ Thu, 16 Apr 2020 00:55:03: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:03: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:03: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:03: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:03: #2 predicted fragment length is 204 bps INFO @ Thu, 16 Apr 2020 00:55:03: #2 alternative fragment length(s) may be 204 bps INFO @ Thu, 16 Apr 2020 00:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.10_model.r INFO @ Thu, 16 Apr 2020 00:55:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:55:05: 2000000 INFO @ Thu, 16 Apr 2020 00:55:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:55:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:55:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.05_summits.bed INFO @ Thu, 16 Apr 2020 00:55:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9287 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:55:10: 3000000 INFO @ Thu, 16 Apr 2020 00:55:15: 4000000 INFO @ Thu, 16 Apr 2020 00:55:20: 5000000 INFO @ Thu, 16 Apr 2020 00:55:25: 6000000 INFO @ Thu, 16 Apr 2020 00:55:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:55:29: 7000000 INFO @ Thu, 16 Apr 2020 00:55:32: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:32: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:32: #1 total tags in treatment: 7650005 INFO @ Thu, 16 Apr 2020 00:55:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:32: #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 00:55:33: #1 tags after filtering in treatment: 7650005 INFO @ Thu, 16 Apr 2020 00:55:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:33: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:34: #2 number of paired peaks: 7762 INFO @ Thu, 16 Apr 2020 00:55:34: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:34: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:34: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:34: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:34: #2 predicted fragment length is 204 bps INFO @ Thu, 16 Apr 2020 00:55:34: #2 alternative fragment length(s) may be 204 bps INFO @ Thu, 16 Apr 2020 00:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.20_model.r INFO @ Thu, 16 Apr 2020 00:55:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:55:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:55:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:55:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.10_summits.bed INFO @ Thu, 16 Apr 2020 00:55:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7302 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:55:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592474/SRX2592474.20_summits.bed INFO @ Thu, 16 Apr 2020 00:56:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5234 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。