Job ID = 14167193 SRX = SRX10760658 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15370995 spots for SRR14408509/SRR14408509.sra Written 15370995 spots for SRR14408509/SRR14408509.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167739 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:23 15370995 reads; of these: 15370995 (100.00%) were unpaired; of these: 1820910 (11.85%) aligned 0 times 12180042 (79.24%) aligned exactly 1 time 1370043 (8.91%) aligned >1 times 88.15% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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] 3924761 / 13550085 = 0.2896 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 @ Fri, 10 Dec 2021 11:03:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.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 @ Fri, 10 Dec 2021 11:03:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:03:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:04:02: 1000000 INFO @ Fri, 10 Dec 2021 11:04:07: 2000000 INFO @ Fri, 10 Dec 2021 11:04:12: 3000000 INFO @ Fri, 10 Dec 2021 11:04:16: 4000000 INFO @ Fri, 10 Dec 2021 11:04:21: 5000000 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 @ Fri, 10 Dec 2021 11:04:26: 6000000 INFO @ Fri, 10 Dec 2021 11:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.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 @ Fri, 10 Dec 2021 11:04:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:04:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:04:31: 7000000 INFO @ Fri, 10 Dec 2021 11:04:32: 1000000 INFO @ Fri, 10 Dec 2021 11:04:36: 8000000 INFO @ Fri, 10 Dec 2021 11:04:37: 2000000 INFO @ Fri, 10 Dec 2021 11:04:41: 9000000 INFO @ Fri, 10 Dec 2021 11:04:42: 3000000 INFO @ Fri, 10 Dec 2021 11:04:44: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 11:04:44: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 11:04:44: #1 total tags in treatment: 9625324 INFO @ Fri, 10 Dec 2021 11:04:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:04:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:04:44: #1 tags after filtering in treatment: 9625324 INFO @ Fri, 10 Dec 2021 11:04:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:04:44: #1 finished! INFO @ Fri, 10 Dec 2021 11:04:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:04:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:04:45: #2 number of paired peaks: 9624 INFO @ Fri, 10 Dec 2021 11:04:45: start model_add_line... INFO @ Fri, 10 Dec 2021 11:04:45: start X-correlation... INFO @ Fri, 10 Dec 2021 11:04:45: end of X-cor INFO @ Fri, 10 Dec 2021 11:04:45: #2 finished! INFO @ Fri, 10 Dec 2021 11:04:45: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Dec 2021 11:04:45: #2 alternative fragment length(s) may be 177 bps INFO @ Fri, 10 Dec 2021 11:04:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.05_model.r INFO @ Fri, 10 Dec 2021 11:04:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:04:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:04:47: 4000000 INFO @ Fri, 10 Dec 2021 11:04:51: 5000000 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 @ Fri, 10 Dec 2021 11:04:56: 6000000 INFO @ Fri, 10 Dec 2021 11:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.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 @ Fri, 10 Dec 2021 11:04:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:04:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:05:01: 7000000 INFO @ Fri, 10 Dec 2021 11:05:03: 1000000 INFO @ Fri, 10 Dec 2021 11:05:06: 8000000 INFO @ Fri, 10 Dec 2021 11:05:09: 2000000 INFO @ Fri, 10 Dec 2021 11:05:11: 9000000 INFO @ Fri, 10 Dec 2021 11:05:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:05:14: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 11:05:14: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 11:05:14: #1 total tags in treatment: 9625324 INFO @ Fri, 10 Dec 2021 11:05:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:05:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:05:14: #1 tags after filtering in treatment: 9625324 INFO @ Fri, 10 Dec 2021 11:05:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:05:14: #1 finished! INFO @ Fri, 10 Dec 2021 11:05:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:05:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:05:14: 3000000 INFO @ Fri, 10 Dec 2021 11:05:15: #2 number of paired peaks: 9624 INFO @ Fri, 10 Dec 2021 11:05:15: start model_add_line... INFO @ Fri, 10 Dec 2021 11:05:15: start X-correlation... INFO @ Fri, 10 Dec 2021 11:05:15: end of X-cor INFO @ Fri, 10 Dec 2021 11:05:15: #2 finished! INFO @ Fri, 10 Dec 2021 11:05:15: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Dec 2021 11:05:15: #2 alternative fragment length(s) may be 177 bps INFO @ Fri, 10 Dec 2021 11:05:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.10_model.r INFO @ Fri, 10 Dec 2021 11:05:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:05:20: 4000000 INFO @ Fri, 10 Dec 2021 11:05:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:05:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:05:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.05_summits.bed INFO @ Fri, 10 Dec 2021 11:05:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14044 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:05:26: 5000000 INFO @ Fri, 10 Dec 2021 11:05:31: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:05:37: 7000000 INFO @ Fri, 10 Dec 2021 11:05:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:05:43: 8000000 INFO @ Fri, 10 Dec 2021 11:05:48: 9000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:05:52: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 11:05:52: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 11:05:52: #1 total tags in treatment: 9625324 INFO @ Fri, 10 Dec 2021 11:05:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:05:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:05:52: #1 tags after filtering in treatment: 9625324 INFO @ Fri, 10 Dec 2021 11:05:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:05:52: #1 finished! INFO @ Fri, 10 Dec 2021 11:05:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:05:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:05:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:05:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.10_summits.bed INFO @ Fri, 10 Dec 2021 11:05:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (10960 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:05:53: #2 number of paired peaks: 9624 INFO @ Fri, 10 Dec 2021 11:05:53: start model_add_line... INFO @ Fri, 10 Dec 2021 11:05:54: start X-correlation... INFO @ Fri, 10 Dec 2021 11:05:54: end of X-cor INFO @ Fri, 10 Dec 2021 11:05:54: #2 finished! INFO @ Fri, 10 Dec 2021 11:05:54: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Dec 2021 11:05:54: #2 alternative fragment length(s) may be 177 bps INFO @ Fri, 10 Dec 2021 11:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.20_model.r INFO @ Fri, 10 Dec 2021 11:05:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:06:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:06:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:06:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:06:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10760658/SRX10760658.20_summits.bed INFO @ Fri, 10 Dec 2021 11:06:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7757 records, 4 fields): 8 millis CompletedMACS2peakCalling