Job ID = 6456453 SRX = SRX3404051 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:52:01 prefetch.2.10.7: 1) Downloading 'SRR6303528'... 2020-06-21T10:52:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:54:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:54:32 prefetch.2.10.7: 1) 'SRR6303528' was downloaded successfully 2020-06-21T10:54:32 prefetch.2.10.7: 'SRR6303528' has 0 unresolved dependencies Read 28263295 spots for SRR6303528/SRR6303528.sra Written 28263295 spots for SRR6303528/SRR6303528.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: 00:08:16 28263295 reads; of these: 28263295 (100.00%) were unpaired; of these: 763207 (2.70%) aligned 0 times 19847909 (70.23%) aligned exactly 1 time 7652179 (27.07%) aligned >1 times 97.30% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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 12 files... [bam_rmdupse_core] 5534709 / 27500088 = 0.2013 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 20:10:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.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 20:10:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:37: 1000000 INFO @ Sun, 21 Jun 2020 20:10:43: 2000000 INFO @ Sun, 21 Jun 2020 20:10:48: 3000000 INFO @ Sun, 21 Jun 2020 20:10:54: 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 @ Sun, 21 Jun 2020 20:11:00: 5000000 INFO @ Sun, 21 Jun 2020 20:11:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.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 20:11:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:06: 6000000 INFO @ Sun, 21 Jun 2020 20:11:07: 1000000 INFO @ Sun, 21 Jun 2020 20:11:12: 7000000 INFO @ Sun, 21 Jun 2020 20:11:13: 2000000 INFO @ Sun, 21 Jun 2020 20:11:19: 8000000 INFO @ Sun, 21 Jun 2020 20:11:19: 3000000 INFO @ Sun, 21 Jun 2020 20:11:25: 9000000 INFO @ Sun, 21 Jun 2020 20:11:26: 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 @ Sun, 21 Jun 2020 20:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.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 20:11:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:31: 10000000 INFO @ Sun, 21 Jun 2020 20:11:32: 5000000 INFO @ Sun, 21 Jun 2020 20:11:37: 1000000 INFO @ Sun, 21 Jun 2020 20:11:38: 11000000 INFO @ Sun, 21 Jun 2020 20:11:38: 6000000 INFO @ Sun, 21 Jun 2020 20:11:44: 2000000 INFO @ Sun, 21 Jun 2020 20:11:44: 12000000 INFO @ Sun, 21 Jun 2020 20:11:44: 7000000 INFO @ Sun, 21 Jun 2020 20:11:50: 3000000 INFO @ Sun, 21 Jun 2020 20:11:50: 13000000 INFO @ Sun, 21 Jun 2020 20:11:51: 8000000 INFO @ Sun, 21 Jun 2020 20:11:56: 4000000 INFO @ Sun, 21 Jun 2020 20:11:57: 14000000 INFO @ Sun, 21 Jun 2020 20:11:57: 9000000 INFO @ Sun, 21 Jun 2020 20:12:02: 5000000 INFO @ Sun, 21 Jun 2020 20:12:03: 15000000 INFO @ Sun, 21 Jun 2020 20:12:03: 10000000 INFO @ Sun, 21 Jun 2020 20:12:09: 6000000 INFO @ Sun, 21 Jun 2020 20:12:09: 16000000 INFO @ Sun, 21 Jun 2020 20:12:10: 11000000 INFO @ Sun, 21 Jun 2020 20:12:15: 7000000 INFO @ Sun, 21 Jun 2020 20:12:16: 17000000 INFO @ Sun, 21 Jun 2020 20:12:16: 12000000 INFO @ Sun, 21 Jun 2020 20:12:22: 8000000 INFO @ Sun, 21 Jun 2020 20:12:22: 18000000 INFO @ Sun, 21 Jun 2020 20:12:22: 13000000 INFO @ Sun, 21 Jun 2020 20:12:28: 9000000 INFO @ Sun, 21 Jun 2020 20:12:29: 14000000 INFO @ Sun, 21 Jun 2020 20:12:29: 19000000 INFO @ Sun, 21 Jun 2020 20:12:34: 10000000 INFO @ Sun, 21 Jun 2020 20:12:35: 15000000 INFO @ Sun, 21 Jun 2020 20:12:36: 20000000 INFO @ Sun, 21 Jun 2020 20:12:41: 11000000 INFO @ Sun, 21 Jun 2020 20:12:41: 16000000 INFO @ Sun, 21 Jun 2020 20:12:42: 21000000 INFO @ Sun, 21 Jun 2020 20:12:47: 12000000 INFO @ Sun, 21 Jun 2020 20:12:48: 17000000 INFO @ Sun, 21 Jun 2020 20:12:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:12:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:12:49: #1 total tags in treatment: 21965379 INFO @ Sun, 21 Jun 2020 20:12:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:49: #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 20:12:49: #1 tags after filtering in treatment: 21965320 INFO @ Sun, 21 Jun 2020 20:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:51: #2 number of paired peaks: 1480 INFO @ Sun, 21 Jun 2020 20:12:51: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:51: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:51: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:51: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:51: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 20:12:51: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 20:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.05_model.r INFO @ Sun, 21 Jun 2020 20:12:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:53: 13000000 INFO @ Sun, 21 Jun 2020 20:12:54: 18000000 INFO @ Sun, 21 Jun 2020 20:13:00: 14000000 INFO @ Sun, 21 Jun 2020 20:13:01: 19000000 INFO @ Sun, 21 Jun 2020 20:13:06: 15000000 INFO @ Sun, 21 Jun 2020 20:13:07: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:13:12: 16000000 INFO @ Sun, 21 Jun 2020 20:13:13: 21000000 INFO @ Sun, 21 Jun 2020 20:13:18: 17000000 INFO @ Sun, 21 Jun 2020 20:13:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:13:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:13:20: #1 total tags in treatment: 21965379 INFO @ Sun, 21 Jun 2020 20:13:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:13:20: #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 20:13:21: #1 tags after filtering in treatment: 21965320 INFO @ Sun, 21 Jun 2020 20:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:13:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:13:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:13:22: #2 number of paired peaks: 1480 INFO @ Sun, 21 Jun 2020 20:13:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:13:22: start X-correlation... INFO @ Sun, 21 Jun 2020 20:13:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:13:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:13:22: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 20:13:22: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 20:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.10_model.r INFO @ Sun, 21 Jun 2020 20:13:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:13:25: 18000000 INFO @ Sun, 21 Jun 2020 20:13:31: 19000000 INFO @ Sun, 21 Jun 2020 20:13:37: 20000000 INFO @ Sun, 21 Jun 2020 20:13:42: 21000000 INFO @ Sun, 21 Jun 2020 20:13:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:13:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:13:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:13:48: #1 total tags in treatment: 21965379 INFO @ Sun, 21 Jun 2020 20:13:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:13:48: #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 20:13:49: #1 tags after filtering in treatment: 21965320 INFO @ Sun, 21 Jun 2020 20:13:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:13:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:13:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:13:51: #2 number of paired peaks: 1480 INFO @ Sun, 21 Jun 2020 20:13:51: start model_add_line... INFO @ Sun, 21 Jun 2020 20:13:51: start X-correlation... INFO @ Sun, 21 Jun 2020 20:13:51: end of X-cor INFO @ Sun, 21 Jun 2020 20:13:51: #2 finished! INFO @ Sun, 21 Jun 2020 20:13:51: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 20:13:51: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 20:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.20_model.r INFO @ Sun, 21 Jun 2020 20:13:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:13:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:14:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:14:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:14:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.05_summits.bed INFO @ Sun, 21 Jun 2020 20:14:09: Done! pass1 - making usageList (669 chroms): 2 millis pass2 - checking and writing primary data (5328 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:14:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:14:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:14:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:14:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.10_summits.bed INFO @ Sun, 21 Jun 2020 20:14:39: Done! pass1 - making usageList (563 chroms): 1 millis pass2 - checking and writing primary data (4240 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:14:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:15:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:15:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:15:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404051/SRX3404051.20_summits.bed INFO @ Sun, 21 Jun 2020 20:15:08: Done! pass1 - making usageList (387 chroms): 2 millis pass2 - checking and writing primary data (3120 records, 4 fields): 16 millis CompletedMACS2peakCalling