Job ID = 5720367 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,104,275 reads read : 4,104,275 reads written : 4,104,275 spots read : 4,062,160 reads read : 4,062,160 reads written : 4,062,160 spots read : 4,121,144 reads read : 4,121,144 reads written : 4,121,144 spots read : 4,042,671 reads read : 4,042,671 reads written : 4,042,671 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:16 16330250 reads; of these: 16330250 (100.00%) were unpaired; of these: 4095589 (25.08%) aligned 0 times 8971414 (54.94%) aligned exactly 1 time 3263247 (19.98%) aligned >1 times 74.92% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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] 5517254 / 12234661 = 0.4510 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 00:16:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.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 00:16:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:16:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:16:36: 1000000 INFO @ Thu, 16 Apr 2020 00:16:41: 2000000 INFO @ Thu, 16 Apr 2020 00:16:46: 3000000 INFO @ Thu, 16 Apr 2020 00:16:51: 4000000 INFO @ Thu, 16 Apr 2020 00:16:56: 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 00:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.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 00:17:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:17:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:17:01: 6000000 INFO @ Thu, 16 Apr 2020 00:17:05: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:17:05: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:17:05: #1 total tags in treatment: 6717407 INFO @ Thu, 16 Apr 2020 00:17:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:17:05: #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 00:17:05: #1 tags after filtering in treatment: 6717407 INFO @ Thu, 16 Apr 2020 00:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:17:05: #1 finished! INFO @ Thu, 16 Apr 2020 00:17:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:17:05: #2 number of paired peaks: 2699 INFO @ Thu, 16 Apr 2020 00:17:05: start model_add_line... INFO @ Thu, 16 Apr 2020 00:17:05: start X-correlation... INFO @ Thu, 16 Apr 2020 00:17:05: end of X-cor INFO @ Thu, 16 Apr 2020 00:17:05: #2 finished! INFO @ Thu, 16 Apr 2020 00:17:05: #2 predicted fragment length is 184 bps INFO @ Thu, 16 Apr 2020 00:17:05: #2 alternative fragment length(s) may be 184 bps INFO @ Thu, 16 Apr 2020 00:17:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.05_model.r INFO @ Thu, 16 Apr 2020 00:17:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:17:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:17:06: 1000000 INFO @ Thu, 16 Apr 2020 00:17:11: 2000000 INFO @ Thu, 16 Apr 2020 00:17:16: 3000000 INFO @ Thu, 16 Apr 2020 00:17:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:17:22: 4000000 INFO @ Thu, 16 Apr 2020 00:17:27: 5000000 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 00:17:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:17:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:17:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.05_summits.bed INFO @ Thu, 16 Apr 2020 00:17:30: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8558 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:17:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.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 00:17:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:17:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:17:32: 6000000 INFO @ Thu, 16 Apr 2020 00:17:36: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:17:36: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:17:36: #1 total tags in treatment: 6717407 INFO @ Thu, 16 Apr 2020 00:17:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:17:36: #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 00:17:36: #1 tags after filtering in treatment: 6717407 INFO @ Thu, 16 Apr 2020 00:17:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:17:36: #1 finished! INFO @ Thu, 16 Apr 2020 00:17:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:17:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:17:37: #2 number of paired peaks: 2699 INFO @ Thu, 16 Apr 2020 00:17:37: start model_add_line... INFO @ Thu, 16 Apr 2020 00:17:37: start X-correlation... INFO @ Thu, 16 Apr 2020 00:17:37: end of X-cor INFO @ Thu, 16 Apr 2020 00:17:37: #2 finished! INFO @ Thu, 16 Apr 2020 00:17:37: #2 predicted fragment length is 184 bps INFO @ Thu, 16 Apr 2020 00:17:37: #2 alternative fragment length(s) may be 184 bps INFO @ Thu, 16 Apr 2020 00:17:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.10_model.r INFO @ Thu, 16 Apr 2020 00:17:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:17:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:17:37: 1000000 INFO @ Thu, 16 Apr 2020 00:17:43: 2000000 INFO @ Thu, 16 Apr 2020 00:17:49: 3000000 INFO @ Thu, 16 Apr 2020 00:17:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:17:55: 4000000 INFO @ Thu, 16 Apr 2020 00:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:18:01: 5000000 INFO @ Thu, 16 Apr 2020 00:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.10_summits.bed INFO @ Thu, 16 Apr 2020 00:18:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5331 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:18:07: 6000000 INFO @ Thu, 16 Apr 2020 00:18:11: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:18:11: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:18:11: #1 total tags in treatment: 6717407 INFO @ Thu, 16 Apr 2020 00:18:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:18:11: #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 00:18:11: #1 tags after filtering in treatment: 6717407 INFO @ Thu, 16 Apr 2020 00:18:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:18:11: #1 finished! INFO @ Thu, 16 Apr 2020 00:18:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:18:12: #2 number of paired peaks: 2699 INFO @ Thu, 16 Apr 2020 00:18:12: start model_add_line... INFO @ Thu, 16 Apr 2020 00:18:12: start X-correlation... INFO @ Thu, 16 Apr 2020 00:18:12: end of X-cor INFO @ Thu, 16 Apr 2020 00:18:12: #2 finished! INFO @ Thu, 16 Apr 2020 00:18:12: #2 predicted fragment length is 184 bps INFO @ Thu, 16 Apr 2020 00:18:12: #2 alternative fragment length(s) may be 184 bps INFO @ Thu, 16 Apr 2020 00:18:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.20_model.r INFO @ Thu, 16 Apr 2020 00:18:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:18:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:18:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:18:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:18:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:18:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3548051/ERX3548051.20_summits.bed INFO @ Thu, 16 Apr 2020 00:18:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2642 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。