Job ID = 6453790 SRX = SRX1490782 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:48:19 prefetch.2.10.7: 1) Downloading 'SRR3031649'... 2020-06-21T08:48:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:49:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:49:32 prefetch.2.10.7: 'SRR3031649' is valid 2020-06-21T08:49:32 prefetch.2.10.7: 1) 'SRR3031649' was downloaded successfully Read 11707941 spots for SRR3031649/SRR3031649.sra Written 11707941 spots for SRR3031649/SRR3031649.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:52 11707941 reads; of these: 11707941 (100.00%) were unpaired; of these: 4954872 (42.32%) aligned 0 times 6144004 (52.48%) aligned exactly 1 time 609065 (5.20%) aligned >1 times 57.68% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 3651239 / 6753069 = 0.5407 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 17:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.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 17:53:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:45: 1000000 INFO @ Sun, 21 Jun 2020 17:53:50: 2000000 INFO @ Sun, 21 Jun 2020 17:53:55: 3000000 INFO @ Sun, 21 Jun 2020 17:53:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:53:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:53:56: #1 total tags in treatment: 3101830 INFO @ Sun, 21 Jun 2020 17:53:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:56: #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 17:53:56: #1 tags after filtering in treatment: 3101632 INFO @ Sun, 21 Jun 2020 17:53:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:56: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:57: #2 number of paired peaks: 6370 INFO @ Sun, 21 Jun 2020 17:53:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:57: #2 predicted fragment length is 203 bps INFO @ Sun, 21 Jun 2020 17:53:57: #2 alternative fragment length(s) may be 4,203 bps INFO @ Sun, 21 Jun 2020 17:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.05_model.r INFO @ Sun, 21 Jun 2020 17:53:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:08: #3 Call peaks for each chromosome... 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 17:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.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 17:54:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.05_summits.bed INFO @ Sun, 21 Jun 2020 17:54:12: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (2264 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:54:15: 1000000 INFO @ Sun, 21 Jun 2020 17:54:20: 2000000 INFO @ Sun, 21 Jun 2020 17:54:25: 3000000 INFO @ Sun, 21 Jun 2020 17:54:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:54:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:54:26: #1 total tags in treatment: 3101830 INFO @ Sun, 21 Jun 2020 17:54:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:26: #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 17:54:26: #1 tags after filtering in treatment: 3101632 INFO @ Sun, 21 Jun 2020 17:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:26: #2 number of paired peaks: 6370 INFO @ Sun, 21 Jun 2020 17:54:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:26: #2 predicted fragment length is 203 bps INFO @ Sun, 21 Jun 2020 17:54:26: #2 alternative fragment length(s) may be 4,203 bps INFO @ Sun, 21 Jun 2020 17:54:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.10_model.r INFO @ Sun, 21 Jun 2020 17:54:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:37: #3 Call peaks for each chromosome... 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 17:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.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 17:54:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.10_summits.bed INFO @ Sun, 21 Jun 2020 17:54:41: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (1465 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:54:46: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:54:52: 2000000 INFO @ Sun, 21 Jun 2020 17:54:57: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:54:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:54:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:54:58: #1 total tags in treatment: 3101830 INFO @ Sun, 21 Jun 2020 17:54:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:58: #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 17:54:58: #1 tags after filtering in treatment: 3101632 INFO @ Sun, 21 Jun 2020 17:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:59: #2 number of paired peaks: 6370 INFO @ Sun, 21 Jun 2020 17:54:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:59: #2 predicted fragment length is 203 bps INFO @ Sun, 21 Jun 2020 17:54:59: #2 alternative fragment length(s) may be 4,203 bps INFO @ Sun, 21 Jun 2020 17:54:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.20_model.r INFO @ Sun, 21 Jun 2020 17:54:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490782/SRX1490782.20_summits.bed INFO @ Sun, 21 Jun 2020 17:55:14: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (850 records, 4 fields): 6 millis CompletedMACS2peakCalling