Job ID = 5790702 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,490,518 reads read : 24,490,518 reads written : 24,490,518 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:47 24490518 reads; of these: 24490518 (100.00%) were unpaired; of these: 4227035 (17.26%) aligned 0 times 14724596 (60.12%) aligned exactly 1 time 5538887 (22.62%) aligned >1 times 82.74% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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] 5364299 / 20263483 = 0.2647 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 06:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.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 06:37:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:37:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:37:55: 1000000 INFO @ Wed, 22 Apr 2020 06:38:01: 2000000 INFO @ Wed, 22 Apr 2020 06:38:06: 3000000 INFO @ Wed, 22 Apr 2020 06:38:12: 4000000 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 06:38:17: 5000000 INFO @ Wed, 22 Apr 2020 06:38:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.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 06:38:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:38:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:38:23: 6000000 INFO @ Wed, 22 Apr 2020 06:38:26: 1000000 INFO @ Wed, 22 Apr 2020 06:38:29: 7000000 INFO @ Wed, 22 Apr 2020 06:38:32: 2000000 INFO @ Wed, 22 Apr 2020 06:38:35: 8000000 INFO @ Wed, 22 Apr 2020 06:38:38: 3000000 INFO @ Wed, 22 Apr 2020 06:38:41: 9000000 INFO @ Wed, 22 Apr 2020 06:38:44: 4000000 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 06:38:48: 10000000 INFO @ Wed, 22 Apr 2020 06:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.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 06:38:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:38:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:38:50: 5000000 INFO @ Wed, 22 Apr 2020 06:38:54: 11000000 INFO @ Wed, 22 Apr 2020 06:38:56: 1000000 INFO @ Wed, 22 Apr 2020 06:38:57: 6000000 INFO @ Wed, 22 Apr 2020 06:39:00: 12000000 INFO @ Wed, 22 Apr 2020 06:39:02: 2000000 INFO @ Wed, 22 Apr 2020 06:39:03: 7000000 INFO @ Wed, 22 Apr 2020 06:39:06: 13000000 INFO @ Wed, 22 Apr 2020 06:39:08: 3000000 INFO @ Wed, 22 Apr 2020 06:39:09: 8000000 INFO @ Wed, 22 Apr 2020 06:39:12: 14000000 INFO @ Wed, 22 Apr 2020 06:39:14: 4000000 INFO @ Wed, 22 Apr 2020 06:39:15: 9000000 INFO @ Wed, 22 Apr 2020 06:39:18: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:39:18: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:39:18: #1 total tags in treatment: 14899184 INFO @ Wed, 22 Apr 2020 06:39:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:39:18: #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 06:39:18: #1 tags after filtering in treatment: 14899035 INFO @ Wed, 22 Apr 2020 06:39:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:39:18: #1 finished! INFO @ Wed, 22 Apr 2020 06:39:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:39:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:39:20: 5000000 INFO @ Wed, 22 Apr 2020 06:39:21: #2 number of paired peaks: 46451 INFO @ Wed, 22 Apr 2020 06:39:21: start model_add_line... INFO @ Wed, 22 Apr 2020 06:39:21: start X-correlation... INFO @ Wed, 22 Apr 2020 06:39:21: end of X-cor INFO @ Wed, 22 Apr 2020 06:39:21: #2 finished! INFO @ Wed, 22 Apr 2020 06:39:21: #2 predicted fragment length is 173 bps INFO @ Wed, 22 Apr 2020 06:39:21: #2 alternative fragment length(s) may be 173 bps INFO @ Wed, 22 Apr 2020 06:39:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.05_model.r INFO @ Wed, 22 Apr 2020 06:39:21: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:39:22: 10000000 INFO @ Wed, 22 Apr 2020 06:39:27: 6000000 INFO @ Wed, 22 Apr 2020 06:39:28: 11000000 INFO @ Wed, 22 Apr 2020 06:39:33: 7000000 INFO @ Wed, 22 Apr 2020 06:39:34: 12000000 INFO @ Wed, 22 Apr 2020 06:39:39: 8000000 INFO @ Wed, 22 Apr 2020 06:39:40: 13000000 INFO @ Wed, 22 Apr 2020 06:39:45: 9000000 INFO @ Wed, 22 Apr 2020 06:39:46: 14000000 INFO @ Wed, 22 Apr 2020 06:39:52: 10000000 INFO @ Wed, 22 Apr 2020 06:39:52: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:39:52: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:39:52: #1 total tags in treatment: 14899184 INFO @ Wed, 22 Apr 2020 06:39:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:39:52: #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 06:39:53: #1 tags after filtering in treatment: 14899035 INFO @ Wed, 22 Apr 2020 06:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:39:53: #1 finished! INFO @ Wed, 22 Apr 2020 06:39:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:39:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:39:55: #2 number of paired peaks: 46451 INFO @ Wed, 22 Apr 2020 06:39:55: start model_add_line... INFO @ Wed, 22 Apr 2020 06:39:55: start X-correlation... INFO @ Wed, 22 Apr 2020 06:39:55: end of X-cor INFO @ Wed, 22 Apr 2020 06:39:55: #2 finished! INFO @ Wed, 22 Apr 2020 06:39:55: #2 predicted fragment length is 173 bps INFO @ Wed, 22 Apr 2020 06:39:55: #2 alternative fragment length(s) may be 173 bps INFO @ Wed, 22 Apr 2020 06:39:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.10_model.r INFO @ Wed, 22 Apr 2020 06:39:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:39:57: 11000000 INFO @ Wed, 22 Apr 2020 06:40:03: 12000000 INFO @ Wed, 22 Apr 2020 06:40:09: 13000000 INFO @ Wed, 22 Apr 2020 06:40:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:40:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:40:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.05_summits.bed INFO @ Wed, 22 Apr 2020 06:40:13: Done! INFO @ Wed, 22 Apr 2020 06:40:14: 14000000 pass1 - making usageList (127 chroms): 3 millis pass2 - checking and writing primary data (19513 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:40:20: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:40:20: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:40:20: #1 total tags in treatment: 14899184 INFO @ Wed, 22 Apr 2020 06:40:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:40:20: #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 06:40:20: #1 tags after filtering in treatment: 14899035 INFO @ Wed, 22 Apr 2020 06:40:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:40:20: #1 finished! INFO @ Wed, 22 Apr 2020 06:40:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:40:23: #2 number of paired peaks: 46451 INFO @ Wed, 22 Apr 2020 06:40:23: start model_add_line... INFO @ Wed, 22 Apr 2020 06:40:23: start X-correlation... INFO @ Wed, 22 Apr 2020 06:40:23: end of X-cor INFO @ Wed, 22 Apr 2020 06:40:23: #2 finished! INFO @ Wed, 22 Apr 2020 06:40:23: #2 predicted fragment length is 173 bps INFO @ Wed, 22 Apr 2020 06:40:23: #2 alternative fragment length(s) may be 173 bps INFO @ Wed, 22 Apr 2020 06:40:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.20_model.r INFO @ Wed, 22 Apr 2020 06:40:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:40:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:40:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:40:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:40:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.10_summits.bed INFO @ Wed, 22 Apr 2020 06:40:47: Done! pass1 - making usageList (84 chroms): 2 millis pass2 - checking and writing primary data (11625 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:40:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761733/SRX5761733.20_summits.bed INFO @ Wed, 22 Apr 2020 06:41:16: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (6499 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。