Job ID = 6456041 SRX = SRX3159491 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:31:36 prefetch.2.10.7: 1) Downloading 'SRR6004221'... 2020-06-21T10:31:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:51 prefetch.2.10.7: 1) 'SRR6004221' was downloaded successfully 2020-06-21T10:34:51 prefetch.2.10.7: 'SRR6004221' has 0 unresolved dependencies Read 28224044 spots for SRR6004221/SRR6004221.sra Written 28224044 spots for SRR6004221/SRR6004221.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: 00:06:48 28224044 reads; of these: 28224044 (100.00%) were unpaired; of these: 2406648 (8.53%) aligned 0 times 20994240 (74.38%) aligned exactly 1 time 4823156 (17.09%) aligned >1 times 91.47% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 8553244 / 25817396 = 0.3313 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 19:48:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.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 19:48:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:23: 1000000 INFO @ Sun, 21 Jun 2020 19:48:28: 2000000 INFO @ Sun, 21 Jun 2020 19:48:33: 3000000 INFO @ Sun, 21 Jun 2020 19:48:37: 4000000 INFO @ Sun, 21 Jun 2020 19:48:42: 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 @ Sun, 21 Jun 2020 19:48:47: 6000000 INFO @ Sun, 21 Jun 2020 19:48:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.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 19:48:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:52: 7000000 INFO @ Sun, 21 Jun 2020 19:48:53: 1000000 INFO @ Sun, 21 Jun 2020 19:48:57: 8000000 INFO @ Sun, 21 Jun 2020 19:48:58: 2000000 INFO @ Sun, 21 Jun 2020 19:49:02: 9000000 INFO @ Sun, 21 Jun 2020 19:49:03: 3000000 INFO @ Sun, 21 Jun 2020 19:49:08: 10000000 INFO @ Sun, 21 Jun 2020 19:49:09: 4000000 INFO @ Sun, 21 Jun 2020 19:49:13: 11000000 INFO @ Sun, 21 Jun 2020 19:49:14: 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 19:49:18: 12000000 INFO @ Sun, 21 Jun 2020 19:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.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 19:49:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:20: 6000000 INFO @ Sun, 21 Jun 2020 19:49:23: 13000000 INFO @ Sun, 21 Jun 2020 19:49:23: 1000000 INFO @ Sun, 21 Jun 2020 19:49:26: 7000000 INFO @ Sun, 21 Jun 2020 19:49:28: 2000000 INFO @ Sun, 21 Jun 2020 19:49:28: 14000000 INFO @ Sun, 21 Jun 2020 19:49:32: 8000000 INFO @ Sun, 21 Jun 2020 19:49:33: 3000000 INFO @ Sun, 21 Jun 2020 19:49:33: 15000000 INFO @ Sun, 21 Jun 2020 19:49:37: 9000000 INFO @ Sun, 21 Jun 2020 19:49:38: 4000000 INFO @ Sun, 21 Jun 2020 19:49:39: 16000000 INFO @ Sun, 21 Jun 2020 19:49:43: 10000000 INFO @ Sun, 21 Jun 2020 19:49:43: 5000000 INFO @ Sun, 21 Jun 2020 19:49:44: 17000000 INFO @ Sun, 21 Jun 2020 19:49:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:49:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:49:45: #1 total tags in treatment: 17264152 INFO @ Sun, 21 Jun 2020 19:49:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:45: #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 19:49:46: #1 tags after filtering in treatment: 17264149 INFO @ Sun, 21 Jun 2020 19:49:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:47: #2 number of paired peaks: 880 WARNING @ Sun, 21 Jun 2020 19:49:47: Fewer paired peaks (880) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 880 pairs to build model! INFO @ Sun, 21 Jun 2020 19:49:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:47: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 19:49:47: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 21 Jun 2020 19:49:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.05_model.r INFO @ Sun, 21 Jun 2020 19:49:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:48: 6000000 INFO @ Sun, 21 Jun 2020 19:49:48: 11000000 INFO @ Sun, 21 Jun 2020 19:49:53: 7000000 INFO @ Sun, 21 Jun 2020 19:49:54: 12000000 INFO @ Sun, 21 Jun 2020 19:49:58: 8000000 INFO @ Sun, 21 Jun 2020 19:49:59: 13000000 INFO @ Sun, 21 Jun 2020 19:50:03: 9000000 INFO @ Sun, 21 Jun 2020 19:50:05: 14000000 INFO @ Sun, 21 Jun 2020 19:50:08: 10000000 INFO @ Sun, 21 Jun 2020 19:50:11: 15000000 INFO @ Sun, 21 Jun 2020 19:50:13: 11000000 INFO @ Sun, 21 Jun 2020 19:50:16: 16000000 INFO @ Sun, 21 Jun 2020 19:50:18: 12000000 INFO @ Sun, 21 Jun 2020 19:50:22: 17000000 INFO @ Sun, 21 Jun 2020 19:50:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:23: 13000000 INFO @ Sun, 21 Jun 2020 19:50:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:50:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:50:24: #1 total tags in treatment: 17264152 INFO @ Sun, 21 Jun 2020 19:50:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:24: #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 19:50:24: #1 tags after filtering in treatment: 17264149 INFO @ Sun, 21 Jun 2020 19:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:25: #2 number of paired peaks: 880 WARNING @ Sun, 21 Jun 2020 19:50:25: Fewer paired peaks (880) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 880 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:25: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 19:50:25: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 21 Jun 2020 19:50:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.10_model.r INFO @ Sun, 21 Jun 2020 19:50:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:29: 14000000 INFO @ Sun, 21 Jun 2020 19:50:34: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:50:38: 16000000 INFO @ Sun, 21 Jun 2020 19:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.05_summits.bed INFO @ Sun, 21 Jun 2020 19:50:41: Done! pass1 - making usageList (595 chroms): 2 millis pass2 - checking and writing primary data (5374 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:50:43: 17000000 INFO @ Sun, 21 Jun 2020 19:50:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:50:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:50:45: #1 total tags in treatment: 17264152 INFO @ Sun, 21 Jun 2020 19:50:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:45: #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 19:50:46: #1 tags after filtering in treatment: 17264149 INFO @ Sun, 21 Jun 2020 19:50:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:47: #2 number of paired peaks: 880 WARNING @ Sun, 21 Jun 2020 19:50:47: Fewer paired peaks (880) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 880 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:47: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 19:50:47: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sun, 21 Jun 2020 19:50:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.20_model.r INFO @ Sun, 21 Jun 2020 19:50:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.10_summits.bed INFO @ Sun, 21 Jun 2020 19:51:23: Done! pass1 - making usageList (503 chroms): 2 millis pass2 - checking and writing primary data (2541 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159491/SRX3159491.20_summits.bed INFO @ Sun, 21 Jun 2020 19:51:44: Done! pass1 - making usageList (392 chroms): 1 millis pass2 - checking and writing primary data (1104 records, 4 fields): 14 millis CompletedMACS2peakCalling