Job ID = 5720707 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,486,004 reads read : 1,486,004 reads written : 1,486,004 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:22 1486004 reads; of these: 1486004 (100.00%) were unpaired; of these: 81011 (5.45%) aligned 0 times 1211229 (81.51%) aligned exactly 1 time 193764 (13.04%) aligned >1 times 94.55% overall alignment rate Time searching: 00:00:22 Overall time: 00:00:22 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_rmdupse_core] 90944 / 1404993 = 0.0647 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 @ Thu, 16 Apr 2020 00:59:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.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 @ Thu, 16 Apr 2020 00:59:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:59:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:59:41: 1000000 INFO @ Thu, 16 Apr 2020 00:59:43: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 00:59:43: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 00:59:43: #1 total tags in treatment: 1314049 INFO @ Thu, 16 Apr 2020 00:59:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:59:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:59:43: #1 tags after filtering in treatment: 1314049 INFO @ Thu, 16 Apr 2020 00:59:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:59:43: #1 finished! INFO @ Thu, 16 Apr 2020 00:59:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:59:43: #2 number of paired peaks: 3895 INFO @ Thu, 16 Apr 2020 00:59:43: start model_add_line... INFO @ Thu, 16 Apr 2020 00:59:43: start X-correlation... INFO @ Thu, 16 Apr 2020 00:59:43: end of X-cor INFO @ Thu, 16 Apr 2020 00:59:43: #2 finished! INFO @ Thu, 16 Apr 2020 00:59:43: #2 predicted fragment length is 116 bps INFO @ Thu, 16 Apr 2020 00:59:43: #2 alternative fragment length(s) may be 116 bps INFO @ Thu, 16 Apr 2020 00:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.05_model.r INFO @ Thu, 16 Apr 2020 00:59:43: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:59:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.05_summits.bed INFO @ Thu, 16 Apr 2020 00:59:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2667 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 @ Thu, 16 Apr 2020 01:00:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.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 @ Thu, 16 Apr 2020 01:00:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:09: 1000000 INFO @ Thu, 16 Apr 2020 01:00:11: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:00:11: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:00:11: #1 total tags in treatment: 1314049 INFO @ Thu, 16 Apr 2020 01:00:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:00:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:00:11: #1 tags after filtering in treatment: 1314049 INFO @ Thu, 16 Apr 2020 01:00:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:00:11: #1 finished! INFO @ Thu, 16 Apr 2020 01:00:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:00:11: #2 number of paired peaks: 3895 INFO @ Thu, 16 Apr 2020 01:00:11: start model_add_line... INFO @ Thu, 16 Apr 2020 01:00:11: start X-correlation... INFO @ Thu, 16 Apr 2020 01:00:11: end of X-cor INFO @ Thu, 16 Apr 2020 01:00:11: #2 finished! INFO @ Thu, 16 Apr 2020 01:00:11: #2 predicted fragment length is 116 bps INFO @ Thu, 16 Apr 2020 01:00:11: #2 alternative fragment length(s) may be 116 bps INFO @ Thu, 16 Apr 2020 01:00:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.10_model.r INFO @ Thu, 16 Apr 2020 01:00:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:00:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:00:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.10_summits.bed INFO @ Thu, 16 Apr 2020 01:00:16: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1727 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Thu, 16 Apr 2020 01:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.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 @ Thu, 16 Apr 2020 01:00:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:40: 1000000 INFO @ Thu, 16 Apr 2020 01:00:41: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:00:41: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:00:41: #1 total tags in treatment: 1314049 INFO @ Thu, 16 Apr 2020 01:00:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:00:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:00:41: #1 tags after filtering in treatment: 1314049 INFO @ Thu, 16 Apr 2020 01:00:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:00:41: #1 finished! INFO @ Thu, 16 Apr 2020 01:00:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:00:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:00:41: #2 number of paired peaks: 3895 INFO @ Thu, 16 Apr 2020 01:00:41: start model_add_line... INFO @ Thu, 16 Apr 2020 01:00:41: start X-correlation... INFO @ Thu, 16 Apr 2020 01:00:41: end of X-cor INFO @ Thu, 16 Apr 2020 01:00:41: #2 finished! INFO @ Thu, 16 Apr 2020 01:00:41: #2 predicted fragment length is 116 bps INFO @ Thu, 16 Apr 2020 01:00:41: #2 alternative fragment length(s) may be 116 bps INFO @ Thu, 16 Apr 2020 01:00:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.20_model.r INFO @ Thu, 16 Apr 2020 01:00:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:00:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:00:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158171/SRX4158171.20_summits.bed INFO @ Thu, 16 Apr 2020 01:00:46: Done! BigWig に変換しました。 pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (973 records, 4 fields): 2 millis CompletedMACS2peakCalling