Job ID = 5790633 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,409,675 reads read : 37,409,675 reads written : 37,409,675 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR4018122.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:34 37409675 reads; of these: 37409675 (100.00%) were unpaired; of these: 9145757 (24.45%) aligned 0 times 22914782 (61.25%) aligned exactly 1 time 5349136 (14.30%) aligned >1 times 75.55% overall alignment rate Time searching: 00:20:37 Overall time: 00:20:37 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 12 files... [bam_rmdupse_core] 6358829 / 28263918 = 0.2250 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 04:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.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 04:48:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 04:48:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 04:48:22: 1000000 INFO @ Wed, 22 Apr 2020 04:48:27: 2000000 INFO @ Wed, 22 Apr 2020 04:48:33: 3000000 INFO @ Wed, 22 Apr 2020 04:48:38: 4000000 INFO @ Wed, 22 Apr 2020 04:48:44: 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 04:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.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 04:48:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 04:48:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 04:48:49: 6000000 INFO @ Wed, 22 Apr 2020 04:48:52: 1000000 INFO @ Wed, 22 Apr 2020 04:48:55: 7000000 INFO @ Wed, 22 Apr 2020 04:48:58: 2000000 INFO @ Wed, 22 Apr 2020 04:49:01: 8000000 INFO @ Wed, 22 Apr 2020 04:49:04: 3000000 INFO @ Wed, 22 Apr 2020 04:49:07: 9000000 INFO @ Wed, 22 Apr 2020 04:49:10: 4000000 INFO @ Wed, 22 Apr 2020 04:49:13: 10000000 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 04:49:16: 5000000 INFO @ Wed, 22 Apr 2020 04:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.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 04:49:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 04:49:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 04:49:19: 11000000 INFO @ Wed, 22 Apr 2020 04:49:22: 6000000 INFO @ Wed, 22 Apr 2020 04:49:23: 1000000 INFO @ Wed, 22 Apr 2020 04:49:25: 12000000 INFO @ Wed, 22 Apr 2020 04:49:28: 7000000 INFO @ Wed, 22 Apr 2020 04:49:29: 2000000 INFO @ Wed, 22 Apr 2020 04:49:30: 13000000 INFO @ Wed, 22 Apr 2020 04:49:34: 8000000 INFO @ Wed, 22 Apr 2020 04:49:35: 3000000 INFO @ Wed, 22 Apr 2020 04:49:36: 14000000 INFO @ Wed, 22 Apr 2020 04:49:40: 9000000 INFO @ Wed, 22 Apr 2020 04:49:41: 4000000 INFO @ Wed, 22 Apr 2020 04:49:42: 15000000 INFO @ Wed, 22 Apr 2020 04:49:45: 10000000 INFO @ Wed, 22 Apr 2020 04:49:47: 5000000 INFO @ Wed, 22 Apr 2020 04:49:48: 16000000 INFO @ Wed, 22 Apr 2020 04:49:51: 11000000 INFO @ Wed, 22 Apr 2020 04:49:52: 6000000 INFO @ Wed, 22 Apr 2020 04:49:54: 17000000 INFO @ Wed, 22 Apr 2020 04:49:57: 12000000 INFO @ Wed, 22 Apr 2020 04:49:58: 7000000 INFO @ Wed, 22 Apr 2020 04:50:00: 18000000 INFO @ Wed, 22 Apr 2020 04:50:03: 13000000 INFO @ Wed, 22 Apr 2020 04:50:04: 8000000 INFO @ Wed, 22 Apr 2020 04:50:05: 19000000 INFO @ Wed, 22 Apr 2020 04:50:09: 14000000 INFO @ Wed, 22 Apr 2020 04:50:10: 9000000 INFO @ Wed, 22 Apr 2020 04:50:11: 20000000 INFO @ Wed, 22 Apr 2020 04:50:15: 15000000 INFO @ Wed, 22 Apr 2020 04:50:16: 10000000 INFO @ Wed, 22 Apr 2020 04:50:17: 21000000 INFO @ Wed, 22 Apr 2020 04:50:21: 16000000 INFO @ Wed, 22 Apr 2020 04:50:22: 11000000 INFO @ Wed, 22 Apr 2020 04:50:23: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 04:50:23: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 04:50:23: #1 total tags in treatment: 21905089 INFO @ Wed, 22 Apr 2020 04:50:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 04:50:23: #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 04:50:23: #1 tags after filtering in treatment: 21904950 INFO @ Wed, 22 Apr 2020 04:50:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 04:50:23: #1 finished! INFO @ Wed, 22 Apr 2020 04:50:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 04:50:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 04:50:27: #2 number of paired peaks: 63951 INFO @ Wed, 22 Apr 2020 04:50:27: start model_add_line... INFO @ Wed, 22 Apr 2020 04:50:27: 17000000 INFO @ Wed, 22 Apr 2020 04:50:27: start X-correlation... INFO @ Wed, 22 Apr 2020 04:50:27: end of X-cor INFO @ Wed, 22 Apr 2020 04:50:27: #2 finished! INFO @ Wed, 22 Apr 2020 04:50:27: #2 predicted fragment length is 161 bps INFO @ Wed, 22 Apr 2020 04:50:27: #2 alternative fragment length(s) may be 161 bps INFO @ Wed, 22 Apr 2020 04:50:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.05_model.r INFO @ Wed, 22 Apr 2020 04:50:27: #3 Call peaks... INFO @ Wed, 22 Apr 2020 04:50:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 04:50:28: 12000000 INFO @ Wed, 22 Apr 2020 04:50:33: 18000000 INFO @ Wed, 22 Apr 2020 04:50:34: 13000000 INFO @ Wed, 22 Apr 2020 04:50:38: 19000000 INFO @ Wed, 22 Apr 2020 04:50:39: 14000000 INFO @ Wed, 22 Apr 2020 04:50:44: 20000000 INFO @ Wed, 22 Apr 2020 04:50:45: 15000000 INFO @ Wed, 22 Apr 2020 04:50:50: 21000000 INFO @ Wed, 22 Apr 2020 04:50:51: 16000000 INFO @ Wed, 22 Apr 2020 04:50:56: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 04:50:56: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 04:50:56: #1 total tags in treatment: 21905089 INFO @ Wed, 22 Apr 2020 04:50:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 04:50:56: #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 04:50:56: #1 tags after filtering in treatment: 21904950 INFO @ Wed, 22 Apr 2020 04:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 04:50:56: #1 finished! INFO @ Wed, 22 Apr 2020 04:50:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 04:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 04:50:57: 17000000 INFO @ Wed, 22 Apr 2020 04:50:59: #2 number of paired peaks: 63951 INFO @ Wed, 22 Apr 2020 04:50:59: start model_add_line... INFO @ Wed, 22 Apr 2020 04:51:00: start X-correlation... INFO @ Wed, 22 Apr 2020 04:51:00: end of X-cor INFO @ Wed, 22 Apr 2020 04:51:00: #2 finished! INFO @ Wed, 22 Apr 2020 04:51:00: #2 predicted fragment length is 161 bps INFO @ Wed, 22 Apr 2020 04:51:00: #2 alternative fragment length(s) may be 161 bps INFO @ Wed, 22 Apr 2020 04:51:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.10_model.r INFO @ Wed, 22 Apr 2020 04:51:00: #3 Call peaks... INFO @ Wed, 22 Apr 2020 04:51:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 04:51:03: 18000000 INFO @ Wed, 22 Apr 2020 04:51:08: 19000000 INFO @ Wed, 22 Apr 2020 04:51:14: 20000000 INFO @ Wed, 22 Apr 2020 04:51:17: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 04:51:19: 21000000 INFO @ Wed, 22 Apr 2020 04:51:24: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 04:51:24: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 04:51:24: #1 total tags in treatment: 21905089 INFO @ Wed, 22 Apr 2020 04:51:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 04:51:24: #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 04:51:25: #1 tags after filtering in treatment: 21904950 INFO @ Wed, 22 Apr 2020 04:51:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 04:51:25: #1 finished! INFO @ Wed, 22 Apr 2020 04:51:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 04:51:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 04:51:28: #2 number of paired peaks: 63951 INFO @ Wed, 22 Apr 2020 04:51:28: start model_add_line... INFO @ Wed, 22 Apr 2020 04:51:28: start X-correlation... INFO @ Wed, 22 Apr 2020 04:51:28: end of X-cor INFO @ Wed, 22 Apr 2020 04:51:28: #2 finished! INFO @ Wed, 22 Apr 2020 04:51:28: #2 predicted fragment length is 161 bps INFO @ Wed, 22 Apr 2020 04:51:28: #2 alternative fragment length(s) may be 161 bps INFO @ Wed, 22 Apr 2020 04:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.20_model.r INFO @ Wed, 22 Apr 2020 04:51:28: #3 Call peaks... INFO @ Wed, 22 Apr 2020 04:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 04:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.05_peaks.xls INFO @ Wed, 22 Apr 2020 04:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 04:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.05_summits.bed INFO @ Wed, 22 Apr 2020 04:51:43: Done! pass1 - making usageList (139 chroms): 5 millis pass2 - checking and writing primary data (30324 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 04:51:50: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 04:52:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.10_peaks.xls INFO @ Wed, 22 Apr 2020 04:52:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 04:52:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.10_summits.bed INFO @ Wed, 22 Apr 2020 04:52:16: Done! pass1 - making usageList (95 chroms): 3 millis pass2 - checking and writing primary data (14296 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 04:52:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 04:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.20_peaks.xls INFO @ Wed, 22 Apr 2020 04:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 04:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX2011880/SRX2011880.20_summits.bed INFO @ Wed, 22 Apr 2020 04:52:44: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (4229 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。