Job ID = 14171283 SRX = SRX9986135 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16499325 spots for SRR13591554/SRR13591554.sra Written 16499325 spots for SRR13591554/SRR13591554.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171737 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:56 16499325 reads; of these: 16499325 (100.00%) were unpaired; of these: 573748 (3.48%) aligned 0 times 3818308 (23.14%) aligned exactly 1 time 12107269 (73.38%) aligned >1 times 96.52% overall alignment rate Time searching: 00:07:57 Overall time: 00:07:57 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] 10948636 / 15925577 = 0.6875 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.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 @ Sat, 11 Dec 2021 11:05:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:05:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:05:31: 1000000 INFO @ Sat, 11 Dec 2021 11:05:36: 2000000 INFO @ Sat, 11 Dec 2021 11:05:42: 3000000 INFO @ Sat, 11 Dec 2021 11:05:47: 4000000 INFO @ Sat, 11 Dec 2021 11:05:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:05:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:05:53: #1 total tags in treatment: 4976941 INFO @ Sat, 11 Dec 2021 11:05:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:05:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:05:53: #1 tags after filtering in treatment: 4976941 INFO @ Sat, 11 Dec 2021 11:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:05:53: #1 finished! INFO @ Sat, 11 Dec 2021 11:05:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:05:53: #2 looking for paired plus/minus strand peaks... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:05:53: #2 number of paired peaks: 1446 INFO @ Sat, 11 Dec 2021 11:05:53: start model_add_line... INFO @ Sat, 11 Dec 2021 11:05:53: start X-correlation... INFO @ Sat, 11 Dec 2021 11:05:53: end of X-cor INFO @ Sat, 11 Dec 2021 11:05:53: #2 finished! INFO @ Sat, 11 Dec 2021 11:05:53: #2 predicted fragment length is 141 bps INFO @ Sat, 11 Dec 2021 11:05:53: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 11 Dec 2021 11:05:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.05_model.r INFO @ Sat, 11 Dec 2021 11:05:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:05:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:05:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.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 @ Sat, 11 Dec 2021 11:05:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:05:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:06:00: 1000000 INFO @ Sat, 11 Dec 2021 11:06:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:06:06: 2000000 INFO @ Sat, 11 Dec 2021 11:06:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:06:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:06:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.05_summits.bed INFO @ Sat, 11 Dec 2021 11:06:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8782 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:06:11: 3000000 INFO @ Sat, 11 Dec 2021 11:06:17: 4000000 INFO @ Sat, 11 Dec 2021 11:06:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:06:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:06:22: #1 total tags in treatment: 4976941 INFO @ Sat, 11 Dec 2021 11:06:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:06:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:06:22: #1 tags after filtering in treatment: 4976941 INFO @ Sat, 11 Dec 2021 11:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:06:22: #1 finished! INFO @ Sat, 11 Dec 2021 11:06:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:06:23: #2 number of paired peaks: 1446 INFO @ Sat, 11 Dec 2021 11:06:23: start model_add_line... INFO @ Sat, 11 Dec 2021 11:06:23: start X-correlation... INFO @ Sat, 11 Dec 2021 11:06:23: end of X-cor INFO @ Sat, 11 Dec 2021 11:06:23: #2 finished! INFO @ Sat, 11 Dec 2021 11:06:23: #2 predicted fragment length is 141 bps INFO @ Sat, 11 Dec 2021 11:06:23: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 11 Dec 2021 11:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.10_model.r INFO @ Sat, 11 Dec 2021 11:06:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:06:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:06:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.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 @ Sat, 11 Dec 2021 11:06:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:06:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:06:30: 1000000 INFO @ Sat, 11 Dec 2021 11:06:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:06:36: 2000000 INFO @ Sat, 11 Dec 2021 11:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.10_summits.bed INFO @ Sat, 11 Dec 2021 11:06:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4247 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:06:41: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:06:47: 4000000 INFO @ Sat, 11 Dec 2021 11:06:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:06:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:06:53: #1 total tags in treatment: 4976941 INFO @ Sat, 11 Dec 2021 11:06:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:06:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:06:53: #1 tags after filtering in treatment: 4976941 INFO @ Sat, 11 Dec 2021 11:06:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:06:53: #1 finished! INFO @ Sat, 11 Dec 2021 11:06:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:06:53: #2 number of paired peaks: 1446 INFO @ Sat, 11 Dec 2021 11:06:53: start model_add_line... INFO @ Sat, 11 Dec 2021 11:06:53: start X-correlation... INFO @ Sat, 11 Dec 2021 11:06:53: end of X-cor INFO @ Sat, 11 Dec 2021 11:06:53: #2 finished! INFO @ Sat, 11 Dec 2021 11:06:53: #2 predicted fragment length is 141 bps INFO @ Sat, 11 Dec 2021 11:06:53: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 11 Dec 2021 11:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.20_model.r INFO @ Sat, 11 Dec 2021 11:06:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:06:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:07:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986135/SRX9986135.20_summits.bed INFO @ Sat, 11 Dec 2021 11:07:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1614 records, 4 fields): 3 millis CompletedMACS2peakCalling