Job ID = 6458004 SRX = SRX4933907 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:08:36 prefetch.2.10.7: 1) Downloading 'SRR8107298'... 2020-06-21T12:08:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:11:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:11:05 prefetch.2.10.7: 1) 'SRR8107298' was downloaded successfully Read 16687520 spots for SRR8107298/SRR8107298.sra Written 16687520 spots for SRR8107298/SRR8107298.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: 00:04:16 16687520 reads; of these: 16687520 (100.00%) were unpaired; of these: 2314112 (13.87%) aligned 0 times 11295301 (67.69%) aligned exactly 1 time 3078107 (18.45%) aligned >1 times 86.13% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 9048219 / 14373408 = 0.6295 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 21:19:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.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 21:19:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:00: 1000000 INFO @ Sun, 21 Jun 2020 21:20:07: 2000000 INFO @ Sun, 21 Jun 2020 21:20:14: 3000000 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 21:20:21: 4000000 INFO @ Sun, 21 Jun 2020 21:20:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.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 21:20:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:29: 5000000 INFO @ Sun, 21 Jun 2020 21:20:30: 1000000 INFO @ Sun, 21 Jun 2020 21:20:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:20:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:20:31: #1 total tags in treatment: 5325189 INFO @ Sun, 21 Jun 2020 21:20:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:31: #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 21:20:32: #1 tags after filtering in treatment: 5325175 INFO @ Sun, 21 Jun 2020 21:20:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:32: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:32: #2 number of paired peaks: 2565 INFO @ Sun, 21 Jun 2020 21:20:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:33: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:33: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:33: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 21:20:33: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sun, 21 Jun 2020 21:20:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.05_model.r INFO @ Sun, 21 Jun 2020 21:20:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:20:38: 2000000 INFO @ Sun, 21 Jun 2020 21:20:45: 3000000 INFO @ Sun, 21 Jun 2020 21:20:46: #3 Call peaks for each chromosome... 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 21:20:52: 4000000 INFO @ Sun, 21 Jun 2020 21:20:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.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 21:20:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:20:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.05_summits.bed INFO @ Sun, 21 Jun 2020 21:20:53: Done! pass1 - making usageList (608 chroms): 1 millis pass2 - checking and writing primary data (1664 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:21:00: 5000000 INFO @ Sun, 21 Jun 2020 21:21:01: 1000000 INFO @ Sun, 21 Jun 2020 21:21:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:21:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:21:03: #1 total tags in treatment: 5325189 INFO @ Sun, 21 Jun 2020 21:21:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:03: #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 21:21:03: #1 tags after filtering in treatment: 5325175 INFO @ Sun, 21 Jun 2020 21:21:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:03: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:04: #2 number of paired peaks: 2565 INFO @ Sun, 21 Jun 2020 21:21:04: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:04: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:04: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:04: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:04: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 21:21:04: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sun, 21 Jun 2020 21:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.10_model.r INFO @ Sun, 21 Jun 2020 21:21:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:08: 2000000 INFO @ Sun, 21 Jun 2020 21:21:15: 3000000 INFO @ Sun, 21 Jun 2020 21:21:18: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:21:22: 4000000 INFO @ Sun, 21 Jun 2020 21:21:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.10_summits.bed INFO @ Sun, 21 Jun 2020 21:21:25: Done! pass1 - making usageList (491 chroms): 2 millis pass2 - checking and writing primary data (1113 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:21:29: 5000000 INFO @ Sun, 21 Jun 2020 21:21:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:21:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:21:32: #1 total tags in treatment: 5325189 INFO @ Sun, 21 Jun 2020 21:21:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:32: #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 21:21:32: #1 tags after filtering in treatment: 5325175 INFO @ Sun, 21 Jun 2020 21:21:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:32: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:33: #2 number of paired peaks: 2565 INFO @ Sun, 21 Jun 2020 21:21:33: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:33: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:33: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:33: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:33: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 21:21:33: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sun, 21 Jun 2020 21:21:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.20_model.r INFO @ Sun, 21 Jun 2020 21:21:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:21:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933907/SRX4933907.20_summits.bed INFO @ Sun, 21 Jun 2020 21:21:54: Done! pass1 - making usageList (244 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 10 millis CompletedMACS2peakCalling