Job ID = 5790691 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,637,268 reads read : 29,637,268 reads written : 29,637,268 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: 00:10:05 29637268 reads; of these: 29637268 (100.00%) were unpaired; of these: 6811275 (22.98%) aligned 0 times 15379080 (51.89%) aligned exactly 1 time 7446913 (25.13%) aligned >1 times 77.02% overall alignment rate Time searching: 00:10:06 Overall time: 00:10:06 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] 7997195 / 22825993 = 0.3504 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 06:34:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.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 06:34:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:34:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:34:32: 1000000 INFO @ Wed, 22 Apr 2020 06:34:37: 2000000 INFO @ Wed, 22 Apr 2020 06:34:42: 3000000 INFO @ Wed, 22 Apr 2020 06:34:47: 4000000 INFO @ Wed, 22 Apr 2020 06:34:52: 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 06:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.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 06:34:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:34:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:34:57: 6000000 INFO @ Wed, 22 Apr 2020 06:35:02: 7000000 INFO @ Wed, 22 Apr 2020 06:35:03: 1000000 INFO @ Wed, 22 Apr 2020 06:35:08: 8000000 INFO @ Wed, 22 Apr 2020 06:35:09: 2000000 INFO @ Wed, 22 Apr 2020 06:35:14: 9000000 INFO @ Wed, 22 Apr 2020 06:35:15: 3000000 INFO @ Wed, 22 Apr 2020 06:35:19: 10000000 INFO @ Wed, 22 Apr 2020 06:35:21: 4000000 INFO @ Wed, 22 Apr 2020 06:35:25: 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 @ Wed, 22 Apr 2020 06:35:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.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 06:35:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:35:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:35:27: 5000000 INFO @ Wed, 22 Apr 2020 06:35:30: 12000000 INFO @ Wed, 22 Apr 2020 06:35:32: 1000000 INFO @ Wed, 22 Apr 2020 06:35:33: 6000000 INFO @ Wed, 22 Apr 2020 06:35:36: 13000000 INFO @ Wed, 22 Apr 2020 06:35:38: 2000000 INFO @ Wed, 22 Apr 2020 06:35:39: 7000000 INFO @ Wed, 22 Apr 2020 06:35:42: 14000000 INFO @ Wed, 22 Apr 2020 06:35:44: 3000000 INFO @ Wed, 22 Apr 2020 06:35:45: 8000000 INFO @ Wed, 22 Apr 2020 06:35:47: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:35:47: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:35:47: #1 total tags in treatment: 14828798 INFO @ Wed, 22 Apr 2020 06:35:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:35:47: #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 06:35:47: #1 tags after filtering in treatment: 14828663 INFO @ Wed, 22 Apr 2020 06:35:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:35:47: #1 finished! INFO @ Wed, 22 Apr 2020 06:35:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:35:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:35:49: #2 number of paired peaks: 22672 INFO @ Wed, 22 Apr 2020 06:35:49: start model_add_line... INFO @ Wed, 22 Apr 2020 06:35:49: start X-correlation... INFO @ Wed, 22 Apr 2020 06:35:49: end of X-cor INFO @ Wed, 22 Apr 2020 06:35:49: #2 finished! INFO @ Wed, 22 Apr 2020 06:35:49: #2 predicted fragment length is 193 bps INFO @ Wed, 22 Apr 2020 06:35:49: #2 alternative fragment length(s) may be 193 bps INFO @ Wed, 22 Apr 2020 06:35:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.05_model.r INFO @ Wed, 22 Apr 2020 06:35:49: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:35:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:35:49: 4000000 INFO @ Wed, 22 Apr 2020 06:35:51: 9000000 INFO @ Wed, 22 Apr 2020 06:35:55: 5000000 INFO @ Wed, 22 Apr 2020 06:35:57: 10000000 INFO @ Wed, 22 Apr 2020 06:36:01: 6000000 INFO @ Wed, 22 Apr 2020 06:36:03: 11000000 INFO @ Wed, 22 Apr 2020 06:36:06: 7000000 INFO @ Wed, 22 Apr 2020 06:36:10: 12000000 INFO @ Wed, 22 Apr 2020 06:36:12: 8000000 INFO @ Wed, 22 Apr 2020 06:36:16: 13000000 INFO @ Wed, 22 Apr 2020 06:36:17: 9000000 INFO @ Wed, 22 Apr 2020 06:36:23: 14000000 INFO @ Wed, 22 Apr 2020 06:36:23: 10000000 INFO @ Wed, 22 Apr 2020 06:36:23: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:36:28: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:36:28: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:36:28: #1 total tags in treatment: 14828798 INFO @ Wed, 22 Apr 2020 06:36:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:36:28: #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 06:36:29: 11000000 INFO @ Wed, 22 Apr 2020 06:36:29: #1 tags after filtering in treatment: 14828663 INFO @ Wed, 22 Apr 2020 06:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:36:29: #1 finished! INFO @ Wed, 22 Apr 2020 06:36:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:36:31: #2 number of paired peaks: 22672 INFO @ Wed, 22 Apr 2020 06:36:31: start model_add_line... INFO @ Wed, 22 Apr 2020 06:36:31: start X-correlation... INFO @ Wed, 22 Apr 2020 06:36:31: end of X-cor INFO @ Wed, 22 Apr 2020 06:36:31: #2 finished! INFO @ Wed, 22 Apr 2020 06:36:31: #2 predicted fragment length is 193 bps INFO @ Wed, 22 Apr 2020 06:36:31: #2 alternative fragment length(s) may be 193 bps INFO @ Wed, 22 Apr 2020 06:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.10_model.r INFO @ Wed, 22 Apr 2020 06:36:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:36:34: 12000000 INFO @ Wed, 22 Apr 2020 06:36:39: 13000000 INFO @ Wed, 22 Apr 2020 06:36:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:36:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:36:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.05_summits.bed INFO @ Wed, 22 Apr 2020 06:36:41: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (6083 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:36:44: 14000000 INFO @ Wed, 22 Apr 2020 06:36:49: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:36:49: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:36:49: #1 total tags in treatment: 14828798 INFO @ Wed, 22 Apr 2020 06:36:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:36:49: #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 06:36:49: #1 tags after filtering in treatment: 14828663 INFO @ Wed, 22 Apr 2020 06:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:36:49: #1 finished! INFO @ Wed, 22 Apr 2020 06:36:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:36:51: #2 number of paired peaks: 22672 INFO @ Wed, 22 Apr 2020 06:36:51: start model_add_line... INFO @ Wed, 22 Apr 2020 06:36:51: start X-correlation... INFO @ Wed, 22 Apr 2020 06:36:51: end of X-cor INFO @ Wed, 22 Apr 2020 06:36:51: #2 finished! INFO @ Wed, 22 Apr 2020 06:36:51: #2 predicted fragment length is 193 bps INFO @ Wed, 22 Apr 2020 06:36:51: #2 alternative fragment length(s) may be 193 bps INFO @ Wed, 22 Apr 2020 06:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.20_model.r INFO @ Wed, 22 Apr 2020 06:36:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:37:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:37:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:37:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:37:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.10_summits.bed INFO @ Wed, 22 Apr 2020 06:37:23: Done! pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (1936 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:37:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:37:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:37:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:37:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761723/SRX5761723.20_summits.bed INFO @ Wed, 22 Apr 2020 06:37:43: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。