Job ID = 6497920 SRX = SRX2592454 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:37:01 prefetch.2.10.7: 1) Downloading 'SRR5289731'... 2020-06-25T22:37:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:39:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:39:53 prefetch.2.10.7: 1) 'SRR5289731' was downloaded successfully Read 16467723 spots for SRR5289731/SRR5289731.sra Written 16467723 spots for SRR5289731/SRR5289731.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: 00:07:05 16467723 reads; of these: 16467723 (100.00%) were unpaired; of these: 1783727 (10.83%) aligned 0 times 9197734 (55.85%) aligned exactly 1 time 5486262 (33.32%) aligned >1 times 89.17% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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 8 files... [bam_rmdupse_core] 5680510 / 14683996 = 0.3869 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 @ Fri, 26 Jun 2020 07:51:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.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, 26 Jun 2020 07:51:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:51:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:51:48: 1000000 INFO @ Fri, 26 Jun 2020 07:51:53: 2000000 INFO @ Fri, 26 Jun 2020 07:51:59: 3000000 INFO @ Fri, 26 Jun 2020 07:52:05: 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 @ Fri, 26 Jun 2020 07:52:10: 5000000 INFO @ Fri, 26 Jun 2020 07:52:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.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, 26 Jun 2020 07:52:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:17: 6000000 INFO @ Fri, 26 Jun 2020 07:52:19: 1000000 INFO @ Fri, 26 Jun 2020 07:52:23: 7000000 INFO @ Fri, 26 Jun 2020 07:52:27: 2000000 INFO @ Fri, 26 Jun 2020 07:52:30: 8000000 INFO @ Fri, 26 Jun 2020 07:52:34: 3000000 INFO @ Fri, 26 Jun 2020 07:52:36: 9000000 INFO @ Fri, 26 Jun 2020 07:52:36: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:52:36: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:52:36: #1 total tags in treatment: 9003486 INFO @ Fri, 26 Jun 2020 07:52:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:52:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:52:37: #1 tags after filtering in treatment: 9003486 INFO @ Fri, 26 Jun 2020 07:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:52:37: #1 finished! INFO @ Fri, 26 Jun 2020 07:52:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:52:38: #2 number of paired peaks: 253 WARNING @ Fri, 26 Jun 2020 07:52:38: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Fri, 26 Jun 2020 07:52:38: start model_add_line... INFO @ Fri, 26 Jun 2020 07:52:38: start X-correlation... INFO @ Fri, 26 Jun 2020 07:52:38: end of X-cor INFO @ Fri, 26 Jun 2020 07:52:38: #2 finished! INFO @ Fri, 26 Jun 2020 07:52:38: #2 predicted fragment length is 307 bps INFO @ Fri, 26 Jun 2020 07:52:38: #2 alternative fragment length(s) may be 307 bps INFO @ Fri, 26 Jun 2020 07:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.05_model.r INFO @ Fri, 26 Jun 2020 07:52:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:52:38: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 07:52:42: 4000000 INFO @ Fri, 26 Jun 2020 07:52:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.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, 26 Jun 2020 07:52:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:49: 1000000 INFO @ Fri, 26 Jun 2020 07:52:49: 5000000 INFO @ Fri, 26 Jun 2020 07:52:56: 2000000 INFO @ Fri, 26 Jun 2020 07:52:57: 6000000 INFO @ Fri, 26 Jun 2020 07:53:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:53:03: 3000000 INFO @ Fri, 26 Jun 2020 07:53:04: 7000000 INFO @ Fri, 26 Jun 2020 07:53:09: 4000000 INFO @ Fri, 26 Jun 2020 07:53:12: 8000000 INFO @ Fri, 26 Jun 2020 07:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.05_summits.bed INFO @ Fri, 26 Jun 2020 07:53:13: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14724 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:53:16: 5000000 INFO @ Fri, 26 Jun 2020 07:53:19: 9000000 INFO @ Fri, 26 Jun 2020 07:53:19: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:53:19: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:53:19: #1 total tags in treatment: 9003486 INFO @ Fri, 26 Jun 2020 07:53:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:53:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:53:19: #1 tags after filtering in treatment: 9003486 INFO @ Fri, 26 Jun 2020 07:53:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:53:19: #1 finished! INFO @ Fri, 26 Jun 2020 07:53:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:53:20: #2 number of paired peaks: 253 WARNING @ Fri, 26 Jun 2020 07:53:20: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Fri, 26 Jun 2020 07:53:20: start model_add_line... INFO @ Fri, 26 Jun 2020 07:53:20: start X-correlation... INFO @ Fri, 26 Jun 2020 07:53:20: end of X-cor INFO @ Fri, 26 Jun 2020 07:53:20: #2 finished! INFO @ Fri, 26 Jun 2020 07:53:20: #2 predicted fragment length is 307 bps INFO @ Fri, 26 Jun 2020 07:53:20: #2 alternative fragment length(s) may be 307 bps INFO @ Fri, 26 Jun 2020 07:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.10_model.r INFO @ Fri, 26 Jun 2020 07:53:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:53:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:53:28: 7000000 INFO @ Fri, 26 Jun 2020 07:53:35: 8000000 INFO @ Fri, 26 Jun 2020 07:53:40: 9000000 INFO @ Fri, 26 Jun 2020 07:53:41: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:53:41: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:53:41: #1 total tags in treatment: 9003486 INFO @ Fri, 26 Jun 2020 07:53:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:53:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:53:41: #1 tags after filtering in treatment: 9003486 INFO @ Fri, 26 Jun 2020 07:53:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:53:41: #1 finished! INFO @ Fri, 26 Jun 2020 07:53:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:53:42: #2 number of paired peaks: 253 WARNING @ Fri, 26 Jun 2020 07:53:42: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Fri, 26 Jun 2020 07:53:42: start model_add_line... INFO @ Fri, 26 Jun 2020 07:53:42: start X-correlation... INFO @ Fri, 26 Jun 2020 07:53:42: end of X-cor INFO @ Fri, 26 Jun 2020 07:53:42: #2 finished! INFO @ Fri, 26 Jun 2020 07:53:42: #2 predicted fragment length is 307 bps INFO @ Fri, 26 Jun 2020 07:53:42: #2 alternative fragment length(s) may be 307 bps INFO @ Fri, 26 Jun 2020 07:53:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.20_model.r INFO @ Fri, 26 Jun 2020 07:53:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:53:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:53:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.10_summits.bed INFO @ Fri, 26 Jun 2020 07:53:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11265 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:54:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:54:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:54:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:54:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592454/SRX2592454.20_summits.bed INFO @ Fri, 26 Jun 2020 07:54:18: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7878 records, 4 fields): 9 millis CompletedMACS2peakCalling