Job ID = 5720701 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,691,066 reads read : 9,691,066 reads written : 9,691,066 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: 00:02:00 9691066 reads; of these: 9691066 (100.00%) were unpaired; of these: 504093 (5.20%) aligned 0 times 8535054 (88.07%) aligned exactly 1 time 651919 (6.73%) aligned >1 times 94.80% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 2137387 / 9186973 = 0.2327 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 01:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.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 01:09:07: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:09:07: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:09:12: 1000000 INFO @ Thu, 16 Apr 2020 01:09:17: 2000000 INFO @ Thu, 16 Apr 2020 01:09:22: 3000000 INFO @ Thu, 16 Apr 2020 01:09:28: 4000000 INFO @ Thu, 16 Apr 2020 01:09:33: 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 @ Thu, 16 Apr 2020 01:09:38: 6000000 INFO @ Thu, 16 Apr 2020 01:09:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.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 01:09:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:09:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:09:44: 7000000 INFO @ Thu, 16 Apr 2020 01:09:44: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:09:44: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:09:44: #1 total tags in treatment: 7049586 INFO @ Thu, 16 Apr 2020 01:09:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:09:44: #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 01:09:44: #1 tags after filtering in treatment: 7049586 INFO @ Thu, 16 Apr 2020 01:09:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:09:44: #1 finished! INFO @ Thu, 16 Apr 2020 01:09:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:09:44: 1000000 INFO @ Thu, 16 Apr 2020 01:09:45: #2 number of paired peaks: 8120 INFO @ Thu, 16 Apr 2020 01:09:45: start model_add_line... INFO @ Thu, 16 Apr 2020 01:09:45: start X-correlation... INFO @ Thu, 16 Apr 2020 01:09:45: end of X-cor INFO @ Thu, 16 Apr 2020 01:09:45: #2 finished! INFO @ Thu, 16 Apr 2020 01:09:45: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 01:09:45: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 01:09:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.05_model.r INFO @ Thu, 16 Apr 2020 01:09:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:09:50: 2000000 INFO @ Thu, 16 Apr 2020 01:09:55: 3000000 INFO @ Thu, 16 Apr 2020 01:10:01: 4000000 INFO @ Thu, 16 Apr 2020 01:10:05: #3 Call peaks for each chromosome... 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 01:10:06: 5000000 INFO @ Thu, 16 Apr 2020 01:10:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.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 01:10:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:10:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:10:12: 6000000 INFO @ Thu, 16 Apr 2020 01:10:13: 1000000 INFO @ Thu, 16 Apr 2020 01:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.05_summits.bed INFO @ Thu, 16 Apr 2020 01:10:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6615 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:10:18: 7000000 INFO @ Thu, 16 Apr 2020 01:10:18: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:10:18: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:10:18: #1 total tags in treatment: 7049586 INFO @ Thu, 16 Apr 2020 01:10:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:10:18: #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 01:10:18: #1 tags after filtering in treatment: 7049586 INFO @ Thu, 16 Apr 2020 01:10:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:10:18: #1 finished! INFO @ Thu, 16 Apr 2020 01:10:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:10:19: #2 number of paired peaks: 8120 INFO @ Thu, 16 Apr 2020 01:10:19: start model_add_line... INFO @ Thu, 16 Apr 2020 01:10:19: start X-correlation... INFO @ Thu, 16 Apr 2020 01:10:19: end of X-cor INFO @ Thu, 16 Apr 2020 01:10:19: #2 finished! INFO @ Thu, 16 Apr 2020 01:10:19: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 01:10:19: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 01:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.10_model.r INFO @ Thu, 16 Apr 2020 01:10:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:10:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:10:19: 2000000 INFO @ Thu, 16 Apr 2020 01:10:25: 3000000 INFO @ Thu, 16 Apr 2020 01:10:30: 4000000 INFO @ Thu, 16 Apr 2020 01:10:35: 5000000 INFO @ Thu, 16 Apr 2020 01:10:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:10:41: 6000000 INFO @ Thu, 16 Apr 2020 01:10:46: 7000000 INFO @ Thu, 16 Apr 2020 01:10:46: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:10:46: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:10:46: #1 total tags in treatment: 7049586 INFO @ Thu, 16 Apr 2020 01:10:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:10:46: #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 01:10:46: #1 tags after filtering in treatment: 7049586 INFO @ Thu, 16 Apr 2020 01:10:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:10:46: #1 finished! INFO @ Thu, 16 Apr 2020 01:10:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:10:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:10:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:10:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:10:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.10_summits.bed INFO @ Thu, 16 Apr 2020 01:10:47: Done! INFO @ Thu, 16 Apr 2020 01:10:47: #2 number of paired peaks: 8120 INFO @ Thu, 16 Apr 2020 01:10:47: start model_add_line... INFO @ Thu, 16 Apr 2020 01:10:48: start X-correlation... INFO @ Thu, 16 Apr 2020 01:10:48: end of X-cor INFO @ Thu, 16 Apr 2020 01:10:48: #2 finished! INFO @ Thu, 16 Apr 2020 01:10:48: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 01:10:48: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 01:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.20_model.r INFO @ Thu, 16 Apr 2020 01:10:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:10:48: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6111 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:11:07: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:11:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:11:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:11:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158165/SRX4158165.20_summits.bed INFO @ Thu, 16 Apr 2020 01:11:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5275 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。