Job ID = 6368913 SRX = SRX707297 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:35:46 prefetch.2.10.7: 1) Downloading 'SRR1582080'... 2020-06-16T00:35:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:40:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:40:08 prefetch.2.10.7: 1) 'SRR1582080' was downloaded successfully Read 34455150 spots for SRR1582080/SRR1582080.sra Written 34455150 spots for SRR1582080/SRR1582080.sra 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:45 34455150 reads; of these: 34455150 (100.00%) were unpaired; of these: 11912771 (34.57%) aligned 0 times 18177902 (52.76%) aligned exactly 1 time 4364477 (12.67%) aligned >1 times 65.43% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 14775141 / 22542379 = 0.6554 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 @ Tue, 16 Jun 2020 09:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:51:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:56: 1000000 INFO @ Tue, 16 Jun 2020 09:52:03: 2000000 INFO @ Tue, 16 Jun 2020 09:52:09: 3000000 INFO @ Tue, 16 Jun 2020 09:52:16: 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 @ Tue, 16 Jun 2020 09:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:52:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:23: 5000000 INFO @ Tue, 16 Jun 2020 09:52:27: 1000000 INFO @ Tue, 16 Jun 2020 09:52:30: 6000000 INFO @ Tue, 16 Jun 2020 09:52:34: 2000000 INFO @ Tue, 16 Jun 2020 09:52:37: 7000000 INFO @ Tue, 16 Jun 2020 09:52:42: 3000000 INFO @ Tue, 16 Jun 2020 09:52:43: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:43: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:43: #1 total tags in treatment: 7767238 INFO @ Tue, 16 Jun 2020 09:52:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:52:43: #1 tags after filtering in treatment: 7767238 INFO @ Tue, 16 Jun 2020 09:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:43: #2 number of paired peaks: 1135 INFO @ Tue, 16 Jun 2020 09:52:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:43: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 09:52:43: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 09:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.05_model.r INFO @ Tue, 16 Jun 2020 09:52:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:43: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 09:52:49: 4000000 INFO @ Tue, 16 Jun 2020 09:52:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:52:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:56: 5000000 INFO @ Tue, 16 Jun 2020 09:52:57: 1000000 INFO @ Tue, 16 Jun 2020 09:53:04: 6000000 INFO @ Tue, 16 Jun 2020 09:53:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:04: 2000000 INFO @ Tue, 16 Jun 2020 09:53:11: 7000000 INFO @ Tue, 16 Jun 2020 09:53:12: 3000000 INFO @ Tue, 16 Jun 2020 09:53:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:14: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (13126 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:17: #1 total tags in treatment: 7767238 INFO @ Tue, 16 Jun 2020 09:53:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:53:17: #1 tags after filtering in treatment: 7767238 INFO @ Tue, 16 Jun 2020 09:53:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:17: #2 number of paired peaks: 1135 INFO @ Tue, 16 Jun 2020 09:53:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:18: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 09:53:18: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 09:53:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.10_model.r INFO @ Tue, 16 Jun 2020 09:53:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:18: 4000000 INFO @ Tue, 16 Jun 2020 09:53:24: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:53:30: 6000000 INFO @ Tue, 16 Jun 2020 09:53:37: 7000000 INFO @ Tue, 16 Jun 2020 09:53:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:53:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:42: #1 total tags in treatment: 7767238 INFO @ Tue, 16 Jun 2020 09:53:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:53:42: #1 tags after filtering in treatment: 7767238 INFO @ Tue, 16 Jun 2020 09:53:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:43: #2 number of paired peaks: 1135 INFO @ Tue, 16 Jun 2020 09:53:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:43: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 09:53:43: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 09:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.20_model.r INFO @ Tue, 16 Jun 2020 09:53:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4877 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX707297/SRX707297.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1587 records, 4 fields): 2 millis CompletedMACS2peakCalling