Job ID = 5790698 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,937,937 reads read : 22,937,937 reads written : 22,937,937 rm: cannot remove ‘[DSE]RR*’: 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: 00:07:17 22937937 reads; of these: 22937937 (100.00%) were unpaired; of these: 6462659 (28.17%) aligned 0 times 11646118 (50.77%) aligned exactly 1 time 4829160 (21.05%) aligned >1 times 71.83% overall alignment rate Time searching: 00:07:18 Overall time: 00:07:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2539068 / 16475278 = 0.1541 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 @ Wed, 22 Apr 2020 06:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:35:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:35:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:35:21: 1000000 INFO @ Wed, 22 Apr 2020 06:35:26: 2000000 INFO @ Wed, 22 Apr 2020 06:35:32: 3000000 INFO @ Wed, 22 Apr 2020 06:35:37: 4000000 INFO @ Wed, 22 Apr 2020 06:35:42: 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 @ Wed, 22 Apr 2020 06:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:35:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:35:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:35:47: 6000000 INFO @ Wed, 22 Apr 2020 06:35:51: 1000000 INFO @ Wed, 22 Apr 2020 06:35:53: 7000000 INFO @ Wed, 22 Apr 2020 06:35:57: 2000000 INFO @ Wed, 22 Apr 2020 06:35:58: 8000000 INFO @ Wed, 22 Apr 2020 06:36:02: 3000000 INFO @ Wed, 22 Apr 2020 06:36:03: 9000000 INFO @ Wed, 22 Apr 2020 06:36:07: 4000000 INFO @ Wed, 22 Apr 2020 06:36:09: 10000000 INFO @ Wed, 22 Apr 2020 06:36:13: 5000000 BedGraph に変換中... INFO @ Wed, 22 Apr 2020 06:36:14: 11000000 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 @ Wed, 22 Apr 2020 06:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:36:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:36:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:36:18: 6000000 INFO @ Wed, 22 Apr 2020 06:36:20: 12000000 INFO @ Wed, 22 Apr 2020 06:36:21: 1000000 INFO @ Wed, 22 Apr 2020 06:36:23: 7000000 INFO @ Wed, 22 Apr 2020 06:36:25: 13000000 INFO @ Wed, 22 Apr 2020 06:36:26: 2000000 INFO @ Wed, 22 Apr 2020 06:36:28: 8000000 INFO @ Wed, 22 Apr 2020 06:36:30: 3000000 INFO @ Wed, 22 Apr 2020 06:36:31: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:36:31: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:36:31: #1 total tags in treatment: 13936210 INFO @ Wed, 22 Apr 2020 06:36:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:36:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:36:31: #1 tags after filtering in treatment: 13936040 INFO @ Wed, 22 Apr 2020 06:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:36:31: #1 finished! INFO @ Wed, 22 Apr 2020 06:36:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:36:33: #2 number of paired peaks: 11721 INFO @ Wed, 22 Apr 2020 06:36:33: start model_add_line... INFO @ Wed, 22 Apr 2020 06:36:33: start X-correlation... INFO @ Wed, 22 Apr 2020 06:36:33: end of X-cor INFO @ Wed, 22 Apr 2020 06:36:33: #2 finished! INFO @ Wed, 22 Apr 2020 06:36:33: #2 predicted fragment length is 202 bps INFO @ Wed, 22 Apr 2020 06:36:33: #2 alternative fragment length(s) may be 42,202 bps INFO @ Wed, 22 Apr 2020 06:36:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.05_model.r INFO @ Wed, 22 Apr 2020 06:36:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:36:33: 9000000 INFO @ Wed, 22 Apr 2020 06:36:35: 4000000 INFO @ Wed, 22 Apr 2020 06:36:39: 10000000 INFO @ Wed, 22 Apr 2020 06:36:40: 5000000 INFO @ Wed, 22 Apr 2020 06:36:44: 11000000 INFO @ Wed, 22 Apr 2020 06:36:45: 6000000 INFO @ Wed, 22 Apr 2020 06:36:49: 12000000 INFO @ Wed, 22 Apr 2020 06:36:50: 7000000 INFO @ Wed, 22 Apr 2020 06:36:54: 13000000 INFO @ Wed, 22 Apr 2020 06:36:54: 8000000 INFO @ Wed, 22 Apr 2020 06:36:59: 9000000 INFO @ Wed, 22 Apr 2020 06:37:00: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:37:00: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:37:00: #1 total tags in treatment: 13936210 INFO @ Wed, 22 Apr 2020 06:37:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:37:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:37:00: #1 tags after filtering in treatment: 13936040 INFO @ Wed, 22 Apr 2020 06:37:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:37:00: #1 finished! INFO @ Wed, 22 Apr 2020 06:37:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:37:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:37:02: #2 number of paired peaks: 11721 INFO @ Wed, 22 Apr 2020 06:37:02: start model_add_line... INFO @ Wed, 22 Apr 2020 06:37:02: start X-correlation... INFO @ Wed, 22 Apr 2020 06:37:02: end of X-cor INFO @ Wed, 22 Apr 2020 06:37:02: #2 finished! INFO @ Wed, 22 Apr 2020 06:37:02: #2 predicted fragment length is 202 bps INFO @ Wed, 22 Apr 2020 06:37:02: #2 alternative fragment length(s) may be 42,202 bps INFO @ Wed, 22 Apr 2020 06:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.10_model.r INFO @ Wed, 22 Apr 2020 06:37:02: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:37:04: 10000000 INFO @ Wed, 22 Apr 2020 06:37:05: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:37:09: 11000000 INFO @ Wed, 22 Apr 2020 06:37:14: 12000000 INFO @ Wed, 22 Apr 2020 06:37:18: 13000000 INFO @ Wed, 22 Apr 2020 06:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.05_summits.bed INFO @ Wed, 22 Apr 2020 06:37:21: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (2963 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:37:23: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:37:23: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:37:23: #1 total tags in treatment: 13936210 INFO @ Wed, 22 Apr 2020 06:37:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:37:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:37:23: #1 tags after filtering in treatment: 13936040 INFO @ Wed, 22 Apr 2020 06:37:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:37:23: #1 finished! INFO @ Wed, 22 Apr 2020 06:37:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:37:25: #2 number of paired peaks: 11721 INFO @ Wed, 22 Apr 2020 06:37:25: start model_add_line... INFO @ Wed, 22 Apr 2020 06:37:25: start X-correlation... INFO @ Wed, 22 Apr 2020 06:37:25: end of X-cor INFO @ Wed, 22 Apr 2020 06:37:25: #2 finished! INFO @ Wed, 22 Apr 2020 06:37:25: #2 predicted fragment length is 202 bps INFO @ Wed, 22 Apr 2020 06:37:25: #2 alternative fragment length(s) may be 42,202 bps INFO @ Wed, 22 Apr 2020 06:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.20_model.r INFO @ Wed, 22 Apr 2020 06:37:25: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:37:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:37:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:37:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.10_summits.bed INFO @ Wed, 22 Apr 2020 06:37:49: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (938 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:37:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761730/SRX5761730.20_summits.bed INFO @ Wed, 22 Apr 2020 06:38:14: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。