Job ID = 6456648 SRX = SRX3873746 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:11:09 prefetch.2.10.7: 1) Downloading 'SRR6927811'... 2020-06-21T11:11:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:12:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:12:35 prefetch.2.10.7: 'SRR6927811' is valid 2020-06-21T11:12:35 prefetch.2.10.7: 1) 'SRR6927811' was downloaded successfully 2020-06-21T11:12:35 prefetch.2.10.7: 'SRR6927811' has 0 unresolved dependencies Read 13100545 spots for SRR6927811/SRR6927811.sra Written 13100545 spots for SRR6927811/SRR6927811.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: 00:02:56 13100545 reads; of these: 13100545 (100.00%) were unpaired; of these: 1144535 (8.74%) aligned 0 times 10248595 (78.23%) aligned exactly 1 time 1707415 (13.03%) aligned >1 times 91.26% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 3383222 / 11956010 = 0.2830 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 20:19:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.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 20:19:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:22: 1000000 INFO @ Sun, 21 Jun 2020 20:19:27: 2000000 INFO @ Sun, 21 Jun 2020 20:19:32: 3000000 INFO @ Sun, 21 Jun 2020 20:19:37: 4000000 INFO @ Sun, 21 Jun 2020 20:19:43: 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 20:19:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.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 20:19:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:48: 6000000 INFO @ Sun, 21 Jun 2020 20:19:52: 1000000 INFO @ Sun, 21 Jun 2020 20:19:54: 7000000 INFO @ Sun, 21 Jun 2020 20:19:58: 2000000 INFO @ Sun, 21 Jun 2020 20:20:00: 8000000 INFO @ Sun, 21 Jun 2020 20:20:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:03: #1 total tags in treatment: 8572788 INFO @ Sun, 21 Jun 2020 20:20:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:03: #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 20:20:04: #1 tags after filtering in treatment: 8572471 INFO @ Sun, 21 Jun 2020 20:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:04: 3000000 INFO @ Sun, 21 Jun 2020 20:20:05: #2 number of paired peaks: 8951 INFO @ Sun, 21 Jun 2020 20:20:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:05: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 20:20:05: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 21 Jun 2020 20:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.05_model.r INFO @ Sun, 21 Jun 2020 20:20:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:20:09: 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 20:20:15: 5000000 INFO @ Sun, 21 Jun 2020 20:20:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.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 20:20:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:20:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:20:21: 6000000 INFO @ Sun, 21 Jun 2020 20:20:22: 1000000 INFO @ Sun, 21 Jun 2020 20:20:26: 7000000 INFO @ Sun, 21 Jun 2020 20:20:28: 2000000 INFO @ Sun, 21 Jun 2020 20:20:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:20:32: 8000000 INFO @ Sun, 21 Jun 2020 20:20:34: 3000000 INFO @ Sun, 21 Jun 2020 20:20:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:36: #1 total tags in treatment: 8572788 INFO @ Sun, 21 Jun 2020 20:20:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:36: #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 20:20:36: #1 tags after filtering in treatment: 8572471 INFO @ Sun, 21 Jun 2020 20:20:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:37: #2 number of paired peaks: 8951 INFO @ Sun, 21 Jun 2020 20:20:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:37: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 20:20:37: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 21 Jun 2020 20:20:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.10_model.r INFO @ Sun, 21 Jun 2020 20:20:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:20:39: 4000000 INFO @ Sun, 21 Jun 2020 20:20:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.05_summits.bed INFO @ Sun, 21 Jun 2020 20:20:41: Done! pass1 - making usageList (154 chroms): 2 millis pass2 - checking and writing primary data (9737 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:20:45: 5000000 INFO @ Sun, 21 Jun 2020 20:20:50: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:20:55: 7000000 INFO @ Sun, 21 Jun 2020 20:21:01: 8000000 INFO @ Sun, 21 Jun 2020 20:21:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:21:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:21:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:21:04: #1 total tags in treatment: 8572788 INFO @ Sun, 21 Jun 2020 20:21:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:21:04: #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 20:21:04: #1 tags after filtering in treatment: 8572471 INFO @ Sun, 21 Jun 2020 20:21:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:21:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:21:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:21:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:21:05: #2 number of paired peaks: 8951 INFO @ Sun, 21 Jun 2020 20:21:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:21:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:21:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:21:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:21:05: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 20:21:05: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 21 Jun 2020 20:21:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.20_model.r INFO @ Sun, 21 Jun 2020 20:21:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:21:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.10_summits.bed INFO @ Sun, 21 Jun 2020 20:21:13: Done! pass1 - making usageList (139 chroms): 1 millis pass2 - checking and writing primary data (8030 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:21:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:21:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:21:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:21:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873746/SRX3873746.20_summits.bed INFO @ Sun, 21 Jun 2020 20:21:42: Done! pass1 - making usageList (116 chroms): 2 millis pass2 - checking and writing primary data (5979 records, 4 fields): 10 millis CompletedMACS2peakCalling