Job ID = 6498659 SRX = SRX681769 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:49:30 prefetch.2.10.7: 1) Downloading 'SRR1552238'... 2020-06-25T23:49:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:50:33 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:50:33 prefetch.2.10.7: 'SRR1552238' is valid 2020-06-25T23:50:33 prefetch.2.10.7: 1) 'SRR1552238' was downloaded successfully Read 5455192 spots for SRR1552238/SRR1552238.sra Written 5455192 spots for SRR1552238/SRR1552238.sra 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: 00:01:17 5455192 reads; of these: 5455192 (100.00%) were unpaired; of these: 264050 (4.84%) aligned 0 times 4299928 (78.82%) aligned exactly 1 time 891214 (16.34%) aligned >1 times 95.16% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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_rmdupse_core] 459812 / 5191142 = 0.0886 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 @ Fri, 26 Jun 2020 08:53:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.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, 26 Jun 2020 08:53:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:53:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:53:31: 1000000 INFO @ Fri, 26 Jun 2020 08:53:37: 2000000 INFO @ Fri, 26 Jun 2020 08:53:42: 3000000 INFO @ Fri, 26 Jun 2020 08:53:48: 4000000 INFO @ Fri, 26 Jun 2020 08:53:52: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:53:52: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:53:52: #1 total tags in treatment: 4731330 INFO @ Fri, 26 Jun 2020 08:53:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:53:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:53:52: #1 tags after filtering in treatment: 4731330 INFO @ Fri, 26 Jun 2020 08:53:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:53:52: #1 finished! INFO @ Fri, 26 Jun 2020 08:53:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:53:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:53:52: #2 number of paired peaks: 1823 INFO @ Fri, 26 Jun 2020 08:53:52: start model_add_line... INFO @ Fri, 26 Jun 2020 08:53:52: start X-correlation... INFO @ Fri, 26 Jun 2020 08:53:52: end of X-cor INFO @ Fri, 26 Jun 2020 08:53:52: #2 finished! INFO @ Fri, 26 Jun 2020 08:53:52: #2 predicted fragment length is 138 bps INFO @ Fri, 26 Jun 2020 08:53:52: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 26 Jun 2020 08:53:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.05_model.r INFO @ Fri, 26 Jun 2020 08:53:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:53:52: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 08:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.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, 26 Jun 2020 08:53:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:53:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:54:01: 1000000 INFO @ Fri, 26 Jun 2020 08:54:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:54:07: 2000000 INFO @ Fri, 26 Jun 2020 08:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.05_summits.bed INFO @ Fri, 26 Jun 2020 08:54:09: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1066 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:54:12: 3000000 INFO @ Fri, 26 Jun 2020 08:54:18: 4000000 INFO @ Fri, 26 Jun 2020 08:54:21: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:54:21: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:54:21: #1 total tags in treatment: 4731330 INFO @ Fri, 26 Jun 2020 08:54:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:54:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:54:22: #1 tags after filtering in treatment: 4731330 INFO @ Fri, 26 Jun 2020 08:54:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:54:22: #1 finished! INFO @ Fri, 26 Jun 2020 08:54:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:54:22: #2 number of paired peaks: 1823 INFO @ Fri, 26 Jun 2020 08:54:22: start model_add_line... INFO @ Fri, 26 Jun 2020 08:54:22: start X-correlation... INFO @ Fri, 26 Jun 2020 08:54:22: end of X-cor INFO @ Fri, 26 Jun 2020 08:54:22: #2 finished! INFO @ Fri, 26 Jun 2020 08:54:22: #2 predicted fragment length is 138 bps INFO @ Fri, 26 Jun 2020 08:54:22: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 26 Jun 2020 08:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.10_model.r INFO @ Fri, 26 Jun 2020 08:54:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:54:22: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 08:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.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, 26 Jun 2020 08:54:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:54:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:54:32: 1000000 INFO @ Fri, 26 Jun 2020 08:54:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.10_summits.bed INFO @ Fri, 26 Jun 2020 08:54:38: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (421 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:54:39: 2000000 INFO @ Fri, 26 Jun 2020 08:54:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:54:51: 4000000 INFO @ Fri, 26 Jun 2020 08:54:56: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:54:56: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:54:56: #1 total tags in treatment: 4731330 INFO @ Fri, 26 Jun 2020 08:54:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:54:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:54:56: #1 tags after filtering in treatment: 4731330 INFO @ Fri, 26 Jun 2020 08:54:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:54:56: #1 finished! INFO @ Fri, 26 Jun 2020 08:54:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:54:56: #2 number of paired peaks: 1823 INFO @ Fri, 26 Jun 2020 08:54:56: start model_add_line... INFO @ Fri, 26 Jun 2020 08:54:56: start X-correlation... INFO @ Fri, 26 Jun 2020 08:54:56: end of X-cor INFO @ Fri, 26 Jun 2020 08:54:56: #2 finished! INFO @ Fri, 26 Jun 2020 08:54:56: #2 predicted fragment length is 138 bps INFO @ Fri, 26 Jun 2020 08:54:56: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 26 Jun 2020 08:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.20_model.r INFO @ Fri, 26 Jun 2020 08:54:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:54:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:55:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681769/SRX681769.20_summits.bed INFO @ Fri, 26 Jun 2020 08:55:13: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 1 millis CompletedMACS2peakCalling