Job ID = 14168784 SRX = SRX9910774 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24020355 spots for SRR13498845/SRR13498845.sra Written 24020355 spots for SRR13498845/SRR13498845.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169850 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:24 24020355 reads; of these: 24020355 (100.00%) were unpaired; of these: 3446747 (14.35%) aligned 0 times 13998535 (58.28%) aligned exactly 1 time 6575073 (27.37%) aligned >1 times 85.65% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5095544 / 20573608 = 0.2477 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 20:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.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 @ Fri, 10 Dec 2021 20:30:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:30:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:30:21: 1000000 INFO @ Fri, 10 Dec 2021 20:30:26: 2000000 INFO @ Fri, 10 Dec 2021 20:30:31: 3000000 INFO @ Fri, 10 Dec 2021 20:30:36: 4000000 INFO @ Fri, 10 Dec 2021 20:30:41: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 20:30:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.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 @ Fri, 10 Dec 2021 20:30:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:30:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:30:46: 6000000 INFO @ Fri, 10 Dec 2021 20:30:51: 1000000 INFO @ Fri, 10 Dec 2021 20:30:52: 7000000 INFO @ Fri, 10 Dec 2021 20:30:57: 2000000 INFO @ Fri, 10 Dec 2021 20:30:57: 8000000 INFO @ Fri, 10 Dec 2021 20:31:02: 9000000 INFO @ Fri, 10 Dec 2021 20:31:02: 3000000 INFO @ Fri, 10 Dec 2021 20:31:07: 4000000 INFO @ Fri, 10 Dec 2021 20:31:07: 10000000 INFO @ Fri, 10 Dec 2021 20:31:12: 5000000 INFO @ Fri, 10 Dec 2021 20:31:12: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 20:31:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.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 @ Fri, 10 Dec 2021 20:31:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:31:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:31:17: 6000000 INFO @ Fri, 10 Dec 2021 20:31:17: 12000000 INFO @ Fri, 10 Dec 2021 20:31:21: 1000000 INFO @ Fri, 10 Dec 2021 20:31:22: 13000000 INFO @ Fri, 10 Dec 2021 20:31:22: 7000000 INFO @ Fri, 10 Dec 2021 20:31:27: 2000000 INFO @ Fri, 10 Dec 2021 20:31:27: 8000000 INFO @ Fri, 10 Dec 2021 20:31:27: 14000000 INFO @ Fri, 10 Dec 2021 20:31:32: 3000000 INFO @ Fri, 10 Dec 2021 20:31:33: 9000000 INFO @ Fri, 10 Dec 2021 20:31:33: 15000000 INFO @ Fri, 10 Dec 2021 20:31:35: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 20:31:35: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 20:31:35: #1 total tags in treatment: 15478064 INFO @ Fri, 10 Dec 2021 20:31:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:31:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 20:31:35: #1 tags after filtering in treatment: 15478064 INFO @ Fri, 10 Dec 2021 20:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 20:31:35: #1 finished! INFO @ Fri, 10 Dec 2021 20:31:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:31:36: #2 number of paired peaks: 398 WARNING @ Fri, 10 Dec 2021 20:31:36: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Fri, 10 Dec 2021 20:31:36: start model_add_line... INFO @ Fri, 10 Dec 2021 20:31:37: start X-correlation... INFO @ Fri, 10 Dec 2021 20:31:37: end of X-cor INFO @ Fri, 10 Dec 2021 20:31:37: #2 finished! INFO @ Fri, 10 Dec 2021 20:31:37: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 20:31:37: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 20:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.05_model.r INFO @ Fri, 10 Dec 2021 20:31:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:31:37: 4000000 INFO @ Fri, 10 Dec 2021 20:31:38: 10000000 INFO @ Fri, 10 Dec 2021 20:31:42: 5000000 INFO @ Fri, 10 Dec 2021 20:31:43: 11000000 INFO @ Fri, 10 Dec 2021 20:31:47: 6000000 INFO @ Fri, 10 Dec 2021 20:31:48: 12000000 INFO @ Fri, 10 Dec 2021 20:31:52: 7000000 INFO @ Fri, 10 Dec 2021 20:31:53: 13000000 INFO @ Fri, 10 Dec 2021 20:31:58: 8000000 INFO @ Fri, 10 Dec 2021 20:31:58: 14000000 INFO @ Fri, 10 Dec 2021 20:32:03: 9000000 INFO @ Fri, 10 Dec 2021 20:32:03: 15000000 INFO @ Fri, 10 Dec 2021 20:32:06: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 20:32:06: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 20:32:06: #1 total tags in treatment: 15478064 INFO @ Fri, 10 Dec 2021 20:32:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:32:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 20:32:06: #1 tags after filtering in treatment: 15478064 INFO @ Fri, 10 Dec 2021 20:32:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 20:32:06: #1 finished! INFO @ Fri, 10 Dec 2021 20:32:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:32:07: #2 number of paired peaks: 398 WARNING @ Fri, 10 Dec 2021 20:32:07: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Fri, 10 Dec 2021 20:32:07: start model_add_line... INFO @ Fri, 10 Dec 2021 20:32:07: start X-correlation... INFO @ Fri, 10 Dec 2021 20:32:07: end of X-cor INFO @ Fri, 10 Dec 2021 20:32:07: #2 finished! INFO @ Fri, 10 Dec 2021 20:32:07: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 20:32:07: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 20:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.10_model.r INFO @ Fri, 10 Dec 2021 20:32:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:32:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:32:08: 10000000 INFO @ Fri, 10 Dec 2021 20:32:13: 11000000 INFO @ Fri, 10 Dec 2021 20:32:18: 12000000 INFO @ Fri, 10 Dec 2021 20:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.05_summits.bed INFO @ Fri, 10 Dec 2021 20:32:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3986 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:32:23: 13000000 INFO @ Fri, 10 Dec 2021 20:32:28: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:32:33: 15000000 INFO @ Fri, 10 Dec 2021 20:32:36: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 20:32:36: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 20:32:36: #1 total tags in treatment: 15478064 INFO @ Fri, 10 Dec 2021 20:32:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:32:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 20:32:36: #1 tags after filtering in treatment: 15478064 INFO @ Fri, 10 Dec 2021 20:32:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 20:32:36: #1 finished! INFO @ Fri, 10 Dec 2021 20:32:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:32:37: #2 number of paired peaks: 398 WARNING @ Fri, 10 Dec 2021 20:32:37: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Fri, 10 Dec 2021 20:32:37: start model_add_line... INFO @ Fri, 10 Dec 2021 20:32:37: start X-correlation... INFO @ Fri, 10 Dec 2021 20:32:37: end of X-cor INFO @ Fri, 10 Dec 2021 20:32:37: #2 finished! INFO @ Fri, 10 Dec 2021 20:32:37: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 20:32:37: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 20:32:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.20_model.r INFO @ Fri, 10 Dec 2021 20:32:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:32:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:32:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.10_summits.bed INFO @ Fri, 10 Dec 2021 20:32:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2699 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:33:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910774/SRX9910774.20_summits.bed INFO @ Fri, 10 Dec 2021 20:33:23: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1686 records, 4 fields): 4 millis CompletedMACS2peakCalling