Job ID = 6458853 SRX = SRX5717024 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:53:52 prefetch.2.10.7: 1) Downloading 'SRR8936396'... 2020-06-21T12:53:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:57:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:57:57 prefetch.2.10.7: 'SRR8936396' is valid 2020-06-21T12:57:57 prefetch.2.10.7: 1) 'SRR8936396' was downloaded successfully Read 16046712 spots for SRR8936396/SRR8936396.sra Written 16046712 spots for SRR8936396/SRR8936396.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: 00:03:55 16046712 reads; of these: 16046712 (100.00%) were unpaired; of these: 1902481 (11.86%) aligned 0 times 10982089 (68.44%) aligned exactly 1 time 3162142 (19.71%) aligned >1 times 88.14% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 4171533 / 14144231 = 0.2949 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 22:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.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 22:06:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:06: 1000000 INFO @ Sun, 21 Jun 2020 22:06:12: 2000000 INFO @ Sun, 21 Jun 2020 22:06:18: 3000000 INFO @ Sun, 21 Jun 2020 22:06:23: 4000000 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 22:06:29: 5000000 INFO @ Sun, 21 Jun 2020 22:06:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.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 22:06:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:35: 6000000 INFO @ Sun, 21 Jun 2020 22:06:36: 1000000 INFO @ Sun, 21 Jun 2020 22:06:41: 7000000 INFO @ Sun, 21 Jun 2020 22:06:42: 2000000 INFO @ Sun, 21 Jun 2020 22:06:47: 8000000 INFO @ Sun, 21 Jun 2020 22:06:48: 3000000 INFO @ Sun, 21 Jun 2020 22:06:53: 9000000 INFO @ Sun, 21 Jun 2020 22:06:54: 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 22:06:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:06:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:06:59: #1 total tags in treatment: 9972698 INFO @ Sun, 21 Jun 2020 22:06:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:59: #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 22:06:59: #1 tags after filtering in treatment: 9972561 INFO @ Sun, 21 Jun 2020 22:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:59: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:00: 5000000 INFO @ Sun, 21 Jun 2020 22:07:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.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 22:07:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:00: #2 number of paired peaks: 3444 INFO @ Sun, 21 Jun 2020 22:07:00: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:01: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 22:07:01: #2 alternative fragment length(s) may be 0,14,64,159,188,204,242,275,279 bps INFO @ Sun, 21 Jun 2020 22:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.05_model.r INFO @ Sun, 21 Jun 2020 22:07:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:07:06: 6000000 INFO @ Sun, 21 Jun 2020 22:07:06: 1000000 INFO @ Sun, 21 Jun 2020 22:07:13: 2000000 INFO @ Sun, 21 Jun 2020 22:07:13: 7000000 INFO @ Sun, 21 Jun 2020 22:07:19: 8000000 INFO @ Sun, 21 Jun 2020 22:07:19: 3000000 INFO @ Sun, 21 Jun 2020 22:07:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:26: 9000000 INFO @ Sun, 21 Jun 2020 22:07:26: 4000000 INFO @ Sun, 21 Jun 2020 22:07:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:07:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:07:32: #1 total tags in treatment: 9972698 INFO @ Sun, 21 Jun 2020 22:07:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:32: #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 22:07:32: 5000000 INFO @ Sun, 21 Jun 2020 22:07:32: #1 tags after filtering in treatment: 9972561 INFO @ Sun, 21 Jun 2020 22:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:32: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:33: #2 number of paired peaks: 3444 INFO @ Sun, 21 Jun 2020 22:07:33: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:34: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 22:07:34: #2 alternative fragment length(s) may be 0,14,64,159,188,204,242,275,279 bps INFO @ Sun, 21 Jun 2020 22:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.10_model.r INFO @ Sun, 21 Jun 2020 22:07:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:07:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.05_summits.bed INFO @ Sun, 21 Jun 2020 22:07:37: Done! pass1 - making usageList (441 chroms): 2 millis pass2 - checking and writing primary data (2281 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:07:38: 6000000 INFO @ Sun, 21 Jun 2020 22:07:44: 7000000 INFO @ Sun, 21 Jun 2020 22:07:50: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:07:56: 9000000 INFO @ Sun, 21 Jun 2020 22:07:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:08:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:08:01: #1 total tags in treatment: 9972698 INFO @ Sun, 21 Jun 2020 22:08:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:08:01: #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 22:08:02: #1 tags after filtering in treatment: 9972561 INFO @ Sun, 21 Jun 2020 22:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:08:02: #1 finished! INFO @ Sun, 21 Jun 2020 22:08:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:08:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:08:03: #2 number of paired peaks: 3444 INFO @ Sun, 21 Jun 2020 22:08:03: start model_add_line... INFO @ Sun, 21 Jun 2020 22:08:03: start X-correlation... INFO @ Sun, 21 Jun 2020 22:08:03: end of X-cor INFO @ Sun, 21 Jun 2020 22:08:03: #2 finished! INFO @ Sun, 21 Jun 2020 22:08:03: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 22:08:03: #2 alternative fragment length(s) may be 0,14,64,159,188,204,242,275,279 bps INFO @ Sun, 21 Jun 2020 22:08:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.20_model.r INFO @ Sun, 21 Jun 2020 22:08:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:08:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.10_summits.bed INFO @ Sun, 21 Jun 2020 22:08:08: Done! pass1 - making usageList (265 chroms): 1 millis pass2 - checking and writing primary data (619 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:08:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717024/SRX5717024.20_summits.bed INFO @ Sun, 21 Jun 2020 22:08:38: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 4 millis CompletedMACS2peakCalling