Job ID = 5790662 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,211,412 reads read : 36,211,412 reads written : 36,211,412 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:07 36211412 reads; of these: 36211412 (100.00%) were unpaired; of these: 7764374 (21.44%) aligned 0 times 21991957 (60.73%) aligned exactly 1 time 6455081 (17.83%) aligned >1 times 78.56% overall alignment rate Time searching: 00:13:11 Overall time: 00:13:11 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] 8026877 / 28447038 = 0.2822 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 05:46:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.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 05:46:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:46:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:46:49: 1000000 INFO @ Wed, 22 Apr 2020 05:46:55: 2000000 INFO @ Wed, 22 Apr 2020 05:47:00: 3000000 INFO @ Wed, 22 Apr 2020 05:47:06: 4000000 INFO @ Wed, 22 Apr 2020 05:47:11: 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 05:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.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 05:47:14: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:47:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:47:17: 6000000 INFO @ Wed, 22 Apr 2020 05:47:20: 1000000 INFO @ Wed, 22 Apr 2020 05:47:23: 7000000 INFO @ Wed, 22 Apr 2020 05:47:26: 2000000 INFO @ Wed, 22 Apr 2020 05:47:29: 8000000 INFO @ Wed, 22 Apr 2020 05:47:32: 3000000 INFO @ Wed, 22 Apr 2020 05:47:35: 9000000 INFO @ Wed, 22 Apr 2020 05:47:39: 4000000 INFO @ Wed, 22 Apr 2020 05:47:41: 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 05:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.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 05:47:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:47:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:47:45: 5000000 INFO @ Wed, 22 Apr 2020 05:47:47: 11000000 INFO @ Wed, 22 Apr 2020 05:47:51: 1000000 INFO @ Wed, 22 Apr 2020 05:47:51: 6000000 INFO @ Wed, 22 Apr 2020 05:47:53: 12000000 INFO @ Wed, 22 Apr 2020 05:47:58: 2000000 INFO @ Wed, 22 Apr 2020 05:47:58: 7000000 INFO @ Wed, 22 Apr 2020 05:48:00: 13000000 INFO @ Wed, 22 Apr 2020 05:48:05: 8000000 INFO @ Wed, 22 Apr 2020 05:48:05: 3000000 INFO @ Wed, 22 Apr 2020 05:48:06: 14000000 INFO @ Wed, 22 Apr 2020 05:48:11: 9000000 INFO @ Wed, 22 Apr 2020 05:48:12: 4000000 INFO @ Wed, 22 Apr 2020 05:48:13: 15000000 INFO @ Wed, 22 Apr 2020 05:48:18: 10000000 INFO @ Wed, 22 Apr 2020 05:48:19: 5000000 INFO @ Wed, 22 Apr 2020 05:48:19: 16000000 INFO @ Wed, 22 Apr 2020 05:48:25: 11000000 INFO @ Wed, 22 Apr 2020 05:48:26: 6000000 INFO @ Wed, 22 Apr 2020 05:48:26: 17000000 INFO @ Wed, 22 Apr 2020 05:48:31: 12000000 INFO @ Wed, 22 Apr 2020 05:48:33: 18000000 INFO @ Wed, 22 Apr 2020 05:48:33: 7000000 INFO @ Wed, 22 Apr 2020 05:48:38: 13000000 INFO @ Wed, 22 Apr 2020 05:48:39: 19000000 INFO @ Wed, 22 Apr 2020 05:48:40: 8000000 INFO @ Wed, 22 Apr 2020 05:48:44: 14000000 INFO @ Wed, 22 Apr 2020 05:48:46: 20000000 INFO @ Wed, 22 Apr 2020 05:48:47: 9000000 INFO @ Wed, 22 Apr 2020 05:48:49: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:48:49: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:48:49: #1 total tags in treatment: 20420161 INFO @ Wed, 22 Apr 2020 05:48:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:48:49: #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 05:48:49: #1 tags after filtering in treatment: 20420018 INFO @ Wed, 22 Apr 2020 05:48:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:48:49: #1 finished! INFO @ Wed, 22 Apr 2020 05:48:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:48:51: 15000000 INFO @ Wed, 22 Apr 2020 05:48:51: #2 number of paired peaks: 23522 INFO @ Wed, 22 Apr 2020 05:48:51: start model_add_line... INFO @ Wed, 22 Apr 2020 05:48:52: start X-correlation... INFO @ Wed, 22 Apr 2020 05:48:52: end of X-cor INFO @ Wed, 22 Apr 2020 05:48:52: #2 finished! INFO @ Wed, 22 Apr 2020 05:48:52: #2 predicted fragment length is 169 bps INFO @ Wed, 22 Apr 2020 05:48:52: #2 alternative fragment length(s) may be 169 bps INFO @ Wed, 22 Apr 2020 05:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.05_model.r INFO @ Wed, 22 Apr 2020 05:48:52: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:48:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:48:54: 10000000 INFO @ Wed, 22 Apr 2020 05:48:58: 16000000 INFO @ Wed, 22 Apr 2020 05:49:01: 11000000 INFO @ Wed, 22 Apr 2020 05:49:04: 17000000 INFO @ Wed, 22 Apr 2020 05:49:07: 12000000 INFO @ Wed, 22 Apr 2020 05:49:11: 18000000 INFO @ Wed, 22 Apr 2020 05:49:14: 13000000 INFO @ Wed, 22 Apr 2020 05:49:17: 19000000 INFO @ Wed, 22 Apr 2020 05:49:21: 14000000 INFO @ Wed, 22 Apr 2020 05:49:24: 20000000 INFO @ Wed, 22 Apr 2020 05:49:27: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:49:27: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:49:27: #1 total tags in treatment: 20420161 INFO @ Wed, 22 Apr 2020 05:49:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:49:27: #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 05:49:27: #1 tags after filtering in treatment: 20420018 INFO @ Wed, 22 Apr 2020 05:49:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:49:27: #1 finished! INFO @ Wed, 22 Apr 2020 05:49:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:49:28: 15000000 INFO @ Wed, 22 Apr 2020 05:49:30: #2 number of paired peaks: 23522 INFO @ Wed, 22 Apr 2020 05:49:30: start model_add_line... INFO @ Wed, 22 Apr 2020 05:49:30: start X-correlation... INFO @ Wed, 22 Apr 2020 05:49:30: end of X-cor INFO @ Wed, 22 Apr 2020 05:49:30: #2 finished! INFO @ Wed, 22 Apr 2020 05:49:30: #2 predicted fragment length is 169 bps INFO @ Wed, 22 Apr 2020 05:49:30: #2 alternative fragment length(s) may be 169 bps INFO @ Wed, 22 Apr 2020 05:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.10_model.r INFO @ Wed, 22 Apr 2020 05:49:30: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:49:35: 16000000 INFO @ Wed, 22 Apr 2020 05:49:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:49:41: 17000000 INFO @ Wed, 22 Apr 2020 05:49:48: 18000000 INFO @ Wed, 22 Apr 2020 05:49:54: 19000000 INFO @ Wed, 22 Apr 2020 05:50:00: 20000000 INFO @ Wed, 22 Apr 2020 05:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.05_summits.bed INFO @ Wed, 22 Apr 2020 05:50:01: Done! pass1 - making usageList (127 chroms): 3 millis pass2 - checking and writing primary data (19636 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:50:03: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 05:50:03: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 05:50:03: #1 total tags in treatment: 20420161 INFO @ Wed, 22 Apr 2020 05:50:03: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:50:03: #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 05:50:04: #1 tags after filtering in treatment: 20420018 INFO @ Wed, 22 Apr 2020 05:50:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:50:04: #1 finished! INFO @ Wed, 22 Apr 2020 05:50:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:50:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:50:06: #2 number of paired peaks: 23522 INFO @ Wed, 22 Apr 2020 05:50:06: start model_add_line... INFO @ Wed, 22 Apr 2020 05:50:06: start X-correlation... INFO @ Wed, 22 Apr 2020 05:50:06: end of X-cor INFO @ Wed, 22 Apr 2020 05:50:06: #2 finished! INFO @ Wed, 22 Apr 2020 05:50:06: #2 predicted fragment length is 169 bps INFO @ Wed, 22 Apr 2020 05:50:06: #2 alternative fragment length(s) may be 169 bps INFO @ Wed, 22 Apr 2020 05:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.20_model.r INFO @ Wed, 22 Apr 2020 05:50:06: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:50:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:50:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:50:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:50:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.10_summits.bed INFO @ Wed, 22 Apr 2020 05:50:40: Done! pass1 - making usageList (109 chroms): 3 millis pass2 - checking and writing primary data (16930 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:50:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 05:51:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761698/SRX5761698.20_summits.bed INFO @ Wed, 22 Apr 2020 05:51:15: Done! pass1 - making usageList (87 chroms): 5 millis pass2 - checking and writing primary data (14097 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。