Job ID = 6456269 SRX = SRX331419 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:36:29 prefetch.2.10.7: 1) Downloading 'SRR947656'... 2020-06-21T10:36:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:26 prefetch.2.10.7: 1) 'SRR947656' was downloaded successfully Read 21083661 spots for SRR947656/SRR947656.sra Written 21083661 spots for SRR947656/SRR947656.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: 00:05:10 21083661 reads; of these: 21083661 (100.00%) were unpaired; of these: 3070921 (14.57%) aligned 0 times 14334393 (67.99%) aligned exactly 1 time 3678347 (17.45%) aligned >1 times 85.43% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6927154 / 18012740 = 0.3846 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 @ Sun, 21 Jun 2020 19:50:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.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 @ Sun, 21 Jun 2020 19:50:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:46: 1000000 INFO @ Sun, 21 Jun 2020 19:50:52: 2000000 INFO @ Sun, 21 Jun 2020 19:50:57: 3000000 INFO @ Sun, 21 Jun 2020 19:51:03: 4000000 INFO @ Sun, 21 Jun 2020 19:51:08: 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 @ Sun, 21 Jun 2020 19:51:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.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 @ Sun, 21 Jun 2020 19:51:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:14: 6000000 INFO @ Sun, 21 Jun 2020 19:51:17: 1000000 INFO @ Sun, 21 Jun 2020 19:51:21: 7000000 INFO @ Sun, 21 Jun 2020 19:51:23: 2000000 INFO @ Sun, 21 Jun 2020 19:51:27: 8000000 INFO @ Sun, 21 Jun 2020 19:51:30: 3000000 INFO @ Sun, 21 Jun 2020 19:51:33: 9000000 INFO @ Sun, 21 Jun 2020 19:51:36: 4000000 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 @ Sun, 21 Jun 2020 19:51:39: 10000000 INFO @ Sun, 21 Jun 2020 19:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.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 @ Sun, 21 Jun 2020 19:51:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:42: 5000000 INFO @ Sun, 21 Jun 2020 19:51:46: 11000000 INFO @ Sun, 21 Jun 2020 19:51:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:46: #1 total tags in treatment: 11085586 INFO @ Sun, 21 Jun 2020 19:51:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:51:47: #1 tags after filtering in treatment: 11085422 INFO @ Sun, 21 Jun 2020 19:51:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:47: 1000000 INFO @ Sun, 21 Jun 2020 19:51:48: #2 number of paired peaks: 10307 INFO @ Sun, 21 Jun 2020 19:51:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:48: 6000000 INFO @ Sun, 21 Jun 2020 19:51:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:48: #2 predicted fragment length is 238 bps INFO @ Sun, 21 Jun 2020 19:51:48: #2 alternative fragment length(s) may be 238 bps INFO @ Sun, 21 Jun 2020 19:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.05_model.r INFO @ Sun, 21 Jun 2020 19:51:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:54: 2000000 INFO @ Sun, 21 Jun 2020 19:51:55: 7000000 INFO @ Sun, 21 Jun 2020 19:52:00: 3000000 INFO @ Sun, 21 Jun 2020 19:52:01: 8000000 INFO @ Sun, 21 Jun 2020 19:52:06: 4000000 INFO @ Sun, 21 Jun 2020 19:52:08: 9000000 INFO @ Sun, 21 Jun 2020 19:52:12: 5000000 INFO @ Sun, 21 Jun 2020 19:52:14: 10000000 INFO @ Sun, 21 Jun 2020 19:52:19: 6000000 INFO @ Sun, 21 Jun 2020 19:52:21: 11000000 INFO @ Sun, 21 Jun 2020 19:52:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:52:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:52:21: #1 total tags in treatment: 11085586 INFO @ Sun, 21 Jun 2020 19:52:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:52:22: #1 tags after filtering in treatment: 11085422 INFO @ Sun, 21 Jun 2020 19:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:23: #2 number of paired peaks: 10307 INFO @ Sun, 21 Jun 2020 19:52:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:23: #2 predicted fragment length is 238 bps INFO @ Sun, 21 Jun 2020 19:52:23: #2 alternative fragment length(s) may be 238 bps INFO @ Sun, 21 Jun 2020 19:52:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.10_model.r INFO @ Sun, 21 Jun 2020 19:52:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:52:25: 7000000 INFO @ Sun, 21 Jun 2020 19:52:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:31: 8000000 INFO @ Sun, 21 Jun 2020 19:52:37: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:52:43: 10000000 INFO @ Sun, 21 Jun 2020 19:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.05_summits.bed INFO @ Sun, 21 Jun 2020 19:52:44: Done! pass1 - making usageList (223 chroms): 2 millis pass2 - checking and writing primary data (8515 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:52:48: 11000000 INFO @ Sun, 21 Jun 2020 19:52:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:52:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:52:49: #1 total tags in treatment: 11085586 INFO @ Sun, 21 Jun 2020 19:52:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:52:49: #1 tags after filtering in treatment: 11085422 INFO @ Sun, 21 Jun 2020 19:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:51: #2 number of paired peaks: 10307 INFO @ Sun, 21 Jun 2020 19:52:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:51: #2 predicted fragment length is 238 bps INFO @ Sun, 21 Jun 2020 19:52:51: #2 alternative fragment length(s) may be 238 bps INFO @ Sun, 21 Jun 2020 19:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.20_model.r INFO @ Sun, 21 Jun 2020 19:52:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.10_summits.bed INFO @ Sun, 21 Jun 2020 19:53:18: Done! pass1 - making usageList (183 chroms): 2 millis pass2 - checking and writing primary data (7610 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:53:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331419/SRX331419.20_summits.bed INFO @ Sun, 21 Jun 2020 19:53:46: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (6454 records, 4 fields): 11 millis CompletedMACS2peakCalling