Job ID = 6453737 SRX = SRX1433375 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:39:47 prefetch.2.10.7: 1) Downloading 'SRR2919840'... 2020-06-21T08:39:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:44:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:44:36 prefetch.2.10.7: 1) 'SRR2919840' was downloaded successfully Read 29269261 spots for SRR2919840/SRR2919840.sra Written 29269261 spots for SRR2919840/SRR2919840.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: 00:04:54 29269261 reads; of these: 29269261 (100.00%) were unpaired; of these: 19977575 (68.25%) aligned 0 times 7157064 (24.45%) aligned exactly 1 time 2134622 (7.29%) aligned >1 times 31.75% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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_rmdupse_core] 3360046 / 9291686 = 0.3616 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 17:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.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 17:53:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:20: 1000000 INFO @ Sun, 21 Jun 2020 17:53:26: 2000000 INFO @ Sun, 21 Jun 2020 17:53:32: 3000000 INFO @ Sun, 21 Jun 2020 17:53:38: 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 17:53:44: 5000000 INFO @ Sun, 21 Jun 2020 17:53:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.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 17:53:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:53:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:53:51: #1 total tags in treatment: 5931640 INFO @ Sun, 21 Jun 2020 17:53:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:51: #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 17:53:51: #1 tags after filtering in treatment: 5931478 INFO @ Sun, 21 Jun 2020 17:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:51: 1000000 INFO @ Sun, 21 Jun 2020 17:53:52: #2 number of paired peaks: 1175 INFO @ Sun, 21 Jun 2020 17:53:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:52: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:53:52: #2 alternative fragment length(s) may be 4,126,131,139 bps INFO @ Sun, 21 Jun 2020 17:53:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.05_model.r INFO @ Sun, 21 Jun 2020 17:53:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:57: 2000000 INFO @ Sun, 21 Jun 2020 17:54:03: 3000000 INFO @ Sun, 21 Jun 2020 17:54:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:10: 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 17:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.05_summits.bed INFO @ Sun, 21 Jun 2020 17:54:13: Done! pass1 - making usageList (326 chroms): 1 millis pass2 - checking and writing primary data (1155 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:54:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.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 17:54:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:17: 5000000 INFO @ Sun, 21 Jun 2020 17:54:23: 1000000 INFO @ Sun, 21 Jun 2020 17:54:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:54:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:54:24: #1 total tags in treatment: 5931640 INFO @ Sun, 21 Jun 2020 17:54:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:24: #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 17:54:24: #1 tags after filtering in treatment: 5931478 INFO @ Sun, 21 Jun 2020 17:54:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:25: #2 number of paired peaks: 1175 INFO @ Sun, 21 Jun 2020 17:54:25: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:25: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:25: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:25: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:25: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:54:25: #2 alternative fragment length(s) may be 4,126,131,139 bps INFO @ Sun, 21 Jun 2020 17:54:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.10_model.r INFO @ Sun, 21 Jun 2020 17:54:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:30: 2000000 INFO @ Sun, 21 Jun 2020 17:54:38: 3000000 INFO @ Sun, 21 Jun 2020 17:54:39: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:54:45: 4000000 INFO @ Sun, 21 Jun 2020 17:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.10_summits.bed INFO @ Sun, 21 Jun 2020 17:54:47: Done! pass1 - making usageList (138 chroms): 1 millis pass2 - checking and writing primary data (407 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:54:52: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:54:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:54:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:54:59: #1 total tags in treatment: 5931640 INFO @ Sun, 21 Jun 2020 17:54:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:59: #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 17:55:00: #1 tags after filtering in treatment: 5931478 INFO @ Sun, 21 Jun 2020 17:55:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:00: #2 number of paired peaks: 1175 INFO @ Sun, 21 Jun 2020 17:55:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:00: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:55:00: #2 alternative fragment length(s) may be 4,126,131,139 bps INFO @ Sun, 21 Jun 2020 17:55:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.20_model.r INFO @ Sun, 21 Jun 2020 17:55:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433375/SRX1433375.20_summits.bed INFO @ Sun, 21 Jun 2020 17:55:22: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 5 millis CompletedMACS2peakCalling