Job ID = 5720422 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,542,316 reads read : 21,542,316 reads written : 21,542,316 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289679.sra.cache’: No such file or directory 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: 00:06:28 21542316 reads; of these: 21542316 (100.00%) were unpaired; of these: 1430370 (6.64%) aligned 0 times 16229196 (75.34%) aligned exactly 1 time 3882750 (18.02%) aligned >1 times 93.36% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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_sort_core] merging from 12 files... [bam_rmdupse_core] 8126298 / 20111946 = 0.4041 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 @ Thu, 16 Apr 2020 00:35:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.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 @ Thu, 16 Apr 2020 00:35:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:35:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:35:45: 1000000 INFO @ Thu, 16 Apr 2020 00:35:51: 2000000 INFO @ Thu, 16 Apr 2020 00:35:57: 3000000 INFO @ Thu, 16 Apr 2020 00:36:03: 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 @ Thu, 16 Apr 2020 00:36:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.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 @ Thu, 16 Apr 2020 00:36:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:36:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:36:09: 5000000 INFO @ Thu, 16 Apr 2020 00:36:15: 1000000 INFO @ Thu, 16 Apr 2020 00:36:16: 6000000 INFO @ Thu, 16 Apr 2020 00:36:21: 2000000 INFO @ Thu, 16 Apr 2020 00:36:22: 7000000 INFO @ Thu, 16 Apr 2020 00:36:27: 3000000 INFO @ Thu, 16 Apr 2020 00:36:29: 8000000 INFO @ Thu, 16 Apr 2020 00:36:32: 4000000 INFO @ Thu, 16 Apr 2020 00:36:35: 9000000 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 @ Thu, 16 Apr 2020 00:36:38: 5000000 INFO @ Thu, 16 Apr 2020 00:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.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 @ Thu, 16 Apr 2020 00:36:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:36:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:36:42: 10000000 INFO @ Thu, 16 Apr 2020 00:36:44: 6000000 INFO @ Thu, 16 Apr 2020 00:36:45: 1000000 INFO @ Thu, 16 Apr 2020 00:36:48: 11000000 INFO @ Thu, 16 Apr 2020 00:36:50: 7000000 INFO @ Thu, 16 Apr 2020 00:36:51: 2000000 INFO @ Thu, 16 Apr 2020 00:36:55: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:36:55: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:36:55: #1 total tags in treatment: 11985648 INFO @ Thu, 16 Apr 2020 00:36:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:36:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:36:55: #1 tags after filtering in treatment: 11985648 INFO @ Thu, 16 Apr 2020 00:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:36:55: #1 finished! INFO @ Thu, 16 Apr 2020 00:36:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:36:56: 8000000 INFO @ Thu, 16 Apr 2020 00:36:56: #2 number of paired peaks: 1208 INFO @ Thu, 16 Apr 2020 00:36:56: start model_add_line... INFO @ Thu, 16 Apr 2020 00:36:57: start X-correlation... INFO @ Thu, 16 Apr 2020 00:36:57: end of X-cor INFO @ Thu, 16 Apr 2020 00:36:57: #2 finished! INFO @ Thu, 16 Apr 2020 00:36:57: #2 predicted fragment length is 186 bps INFO @ Thu, 16 Apr 2020 00:36:57: #2 alternative fragment length(s) may be 186 bps INFO @ Thu, 16 Apr 2020 00:36:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.05_model.r INFO @ Thu, 16 Apr 2020 00:36:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:36:57: 3000000 INFO @ Thu, 16 Apr 2020 00:37:02: 9000000 INFO @ Thu, 16 Apr 2020 00:37:03: 4000000 INFO @ Thu, 16 Apr 2020 00:37:08: 10000000 INFO @ Thu, 16 Apr 2020 00:37:08: 5000000 INFO @ Thu, 16 Apr 2020 00:37:14: 11000000 INFO @ Thu, 16 Apr 2020 00:37:14: 6000000 INFO @ Thu, 16 Apr 2020 00:37:19: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:37:19: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:37:19: #1 total tags in treatment: 11985648 INFO @ Thu, 16 Apr 2020 00:37:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:37:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:37:20: #1 tags after filtering in treatment: 11985648 INFO @ Thu, 16 Apr 2020 00:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:37:20: #1 finished! INFO @ Thu, 16 Apr 2020 00:37:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:37:20: 7000000 INFO @ Thu, 16 Apr 2020 00:37:21: #2 number of paired peaks: 1208 INFO @ Thu, 16 Apr 2020 00:37:21: start model_add_line... INFO @ Thu, 16 Apr 2020 00:37:21: start X-correlation... INFO @ Thu, 16 Apr 2020 00:37:21: end of X-cor INFO @ Thu, 16 Apr 2020 00:37:21: #2 finished! INFO @ Thu, 16 Apr 2020 00:37:21: #2 predicted fragment length is 186 bps INFO @ Thu, 16 Apr 2020 00:37:21: #2 alternative fragment length(s) may be 186 bps INFO @ Thu, 16 Apr 2020 00:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.10_model.r INFO @ Thu, 16 Apr 2020 00:37:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:37:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:37:25: 8000000 INFO @ Thu, 16 Apr 2020 00:37:31: 9000000 INFO @ Thu, 16 Apr 2020 00:37:36: 10000000 INFO @ Thu, 16 Apr 2020 00:37:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:37:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:37:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.05_summits.bed INFO @ Thu, 16 Apr 2020 00:37:39: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (22014 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:37:41: 11000000 INFO @ Thu, 16 Apr 2020 00:37:47: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:37:47: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:37:47: #1 total tags in treatment: 11985648 INFO @ Thu, 16 Apr 2020 00:37:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:37:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:37:47: #1 tags after filtering in treatment: 11985648 INFO @ Thu, 16 Apr 2020 00:37:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:37:47: #1 finished! INFO @ Thu, 16 Apr 2020 00:37:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:37:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:37:48: #2 number of paired peaks: 1208 INFO @ Thu, 16 Apr 2020 00:37:48: start model_add_line... INFO @ Thu, 16 Apr 2020 00:37:48: start X-correlation... INFO @ Thu, 16 Apr 2020 00:37:48: end of X-cor INFO @ Thu, 16 Apr 2020 00:37:48: #2 finished! INFO @ Thu, 16 Apr 2020 00:37:48: #2 predicted fragment length is 186 bps INFO @ Thu, 16 Apr 2020 00:37:48: #2 alternative fragment length(s) may be 186 bps INFO @ Thu, 16 Apr 2020 00:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.20_model.r INFO @ Thu, 16 Apr 2020 00:37:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:37:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:38:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:38:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:38:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.10_summits.bed INFO @ Thu, 16 Apr 2020 00:38:02: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (18536 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:38:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:38:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:38:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:38:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592402/SRX2592402.20_summits.bed INFO @ Thu, 16 Apr 2020 00:38:27: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (13198 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。