Job ID = 6452967 SRX = SRX084385 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:55:15 prefetch.2.10.7: 1) Downloading 'SRR314831'... 2020-06-21T07:55:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:57:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:57:51 prefetch.2.10.7: 'SRR314831' is valid 2020-06-21T07:57:51 prefetch.2.10.7: 1) 'SRR314831' was downloaded successfully Read 22822197 spots for SRR314831/SRR314831.sra Written 22822197 spots for SRR314831/SRR314831.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: 00:04:12 22822197 reads; of these: 22822197 (100.00%) were unpaired; of these: 2060212 (9.03%) aligned 0 times 17595928 (77.10%) aligned exactly 1 time 3166057 (13.87%) aligned >1 times 90.97% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 11751659 / 20761985 = 0.5660 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 @ Sun, 21 Jun 2020 17:06:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:06:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:06:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:06:43: 1000000 INFO @ Sun, 21 Jun 2020 17:06:47: 2000000 INFO @ Sun, 21 Jun 2020 17:06:52: 3000000 INFO @ Sun, 21 Jun 2020 17:06:57: 4000000 INFO @ Sun, 21 Jun 2020 17:07:01: 5000000 INFO @ Sun, 21 Jun 2020 17:07:06: 6000000 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 @ Sun, 21 Jun 2020 17:07:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:07:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:07:11: 7000000 INFO @ Sun, 21 Jun 2020 17:07:13: 1000000 INFO @ Sun, 21 Jun 2020 17:07:16: 8000000 INFO @ Sun, 21 Jun 2020 17:07:18: 2000000 INFO @ Sun, 21 Jun 2020 17:07:22: 9000000 INFO @ Sun, 21 Jun 2020 17:07:22: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:07:22: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:07:22: #1 total tags in treatment: 9010326 INFO @ Sun, 21 Jun 2020 17:07:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:07:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:07:22: #1 tags after filtering in treatment: 9010318 INFO @ Sun, 21 Jun 2020 17:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:07:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:07:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:07:23: 3000000 INFO @ Sun, 21 Jun 2020 17:07:23: #2 number of paired peaks: 5461 INFO @ Sun, 21 Jun 2020 17:07:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:07:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:07:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:07:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:07:23: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 17:07:23: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 17:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.05_model.r INFO @ Sun, 21 Jun 2020 17:07:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:07:28: 4000000 INFO @ Sun, 21 Jun 2020 17:07:32: 5000000 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 @ Sun, 21 Jun 2020 17:07:37: 6000000 INFO @ Sun, 21 Jun 2020 17:07:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:07:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:07:42: 7000000 INFO @ Sun, 21 Jun 2020 17:07:43: 1000000 INFO @ Sun, 21 Jun 2020 17:07:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:07:48: 8000000 INFO @ Sun, 21 Jun 2020 17:07:48: 2000000 INFO @ Sun, 21 Jun 2020 17:07:53: 9000000 INFO @ Sun, 21 Jun 2020 17:07:53: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:07:53: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:07:53: #1 total tags in treatment: 9010326 INFO @ Sun, 21 Jun 2020 17:07:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:07:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:07:53: 3000000 INFO @ Sun, 21 Jun 2020 17:07:53: #1 tags after filtering in treatment: 9010318 INFO @ Sun, 21 Jun 2020 17:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:07:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:07:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:07:54: #2 number of paired peaks: 5461 INFO @ Sun, 21 Jun 2020 17:07:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:07:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:07:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:07:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:07:54: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 17:07:54: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 17:07:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.10_model.r INFO @ Sun, 21 Jun 2020 17:07:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:07:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:07:58: 4000000 INFO @ Sun, 21 Jun 2020 17:07:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:07:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:07:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.05_summits.bed INFO @ Sun, 21 Jun 2020 17:07:58: Done! pass1 - making usageList (419 chroms): 3 millis pass2 - checking and writing primary data (13225 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:08:03: 5000000 INFO @ Sun, 21 Jun 2020 17:08:08: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:08:12: 7000000 INFO @ Sun, 21 Jun 2020 17:08:18: 8000000 INFO @ Sun, 21 Jun 2020 17:08:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:08:23: 9000000 INFO @ Sun, 21 Jun 2020 17:08:23: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:08:23: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:08:23: #1 total tags in treatment: 9010326 INFO @ Sun, 21 Jun 2020 17:08:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:08:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:08:23: #1 tags after filtering in treatment: 9010318 INFO @ Sun, 21 Jun 2020 17:08:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:08:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:08:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:08:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:08:24: #2 number of paired peaks: 5461 INFO @ Sun, 21 Jun 2020 17:08:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:08:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:08:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:08:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:08:24: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 17:08:24: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 17:08:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.20_model.r INFO @ Sun, 21 Jun 2020 17:08:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:08:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:08:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:08:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:08:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.10_summits.bed INFO @ Sun, 21 Jun 2020 17:08:31: Done! pass1 - making usageList (235 chroms): 2 millis pass2 - checking and writing primary data (9807 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:08:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX084385/SRX084385.20_summits.bed INFO @ Sun, 21 Jun 2020 17:09:01: Done! pass1 - making usageList (157 chroms): 2 millis pass2 - checking and writing primary data (7000 records, 4 fields): 12 millis CompletedMACS2peakCalling