Job ID = 5720674 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,753,737 reads read : 18,753,737 reads written : 18,753,737 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289768.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: 00:04:15 18753737 reads; of these: 18753737 (100.00%) were unpaired; of these: 3453279 (18.41%) aligned 0 times 13386385 (71.38%) aligned exactly 1 time 1914073 (10.21%) aligned >1 times 81.59% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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 8 files... [bam_rmdupse_core] 4764648 / 15300458 = 0.3114 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 01:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.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 01:00:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:05: 1000000 INFO @ Thu, 16 Apr 2020 01:00:11: 2000000 INFO @ Thu, 16 Apr 2020 01:00:16: 3000000 INFO @ Thu, 16 Apr 2020 01:00:22: 4000000 INFO @ Thu, 16 Apr 2020 01:00:27: 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 @ Thu, 16 Apr 2020 01:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.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 01:00:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:33: 6000000 INFO @ Thu, 16 Apr 2020 01:00:36: 1000000 INFO @ Thu, 16 Apr 2020 01:00:39: 7000000 INFO @ Thu, 16 Apr 2020 01:00:42: 2000000 INFO @ Thu, 16 Apr 2020 01:00:45: 8000000 INFO @ Thu, 16 Apr 2020 01:00:48: 3000000 INFO @ Thu, 16 Apr 2020 01:00:51: 9000000 INFO @ Thu, 16 Apr 2020 01:00:53: 4000000 INFO @ Thu, 16 Apr 2020 01:00:57: 10000000 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 01:00:59: 5000000 INFO @ Thu, 16 Apr 2020 01:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.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 01:01:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:00: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:01:00: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:01:00: #1 total tags in treatment: 10535810 INFO @ Thu, 16 Apr 2020 01:01:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:00: #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 01:01:00: #1 tags after filtering in treatment: 10535810 INFO @ Thu, 16 Apr 2020 01:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:00: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:01: #2 number of paired peaks: 7408 INFO @ Thu, 16 Apr 2020 01:01:01: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:01: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:01: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:01: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:01: #2 predicted fragment length is 204 bps INFO @ Thu, 16 Apr 2020 01:01:01: #2 alternative fragment length(s) may be 204 bps INFO @ Thu, 16 Apr 2020 01:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.05_model.r INFO @ Thu, 16 Apr 2020 01:01:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:01:06: 6000000 INFO @ Thu, 16 Apr 2020 01:01:06: 1000000 INFO @ Thu, 16 Apr 2020 01:01:11: 7000000 INFO @ Thu, 16 Apr 2020 01:01:12: 2000000 INFO @ Thu, 16 Apr 2020 01:01:17: 8000000 INFO @ Thu, 16 Apr 2020 01:01:18: 3000000 INFO @ Thu, 16 Apr 2020 01:01:23: 9000000 INFO @ Thu, 16 Apr 2020 01:01:24: 4000000 INFO @ Thu, 16 Apr 2020 01:01:29: 10000000 INFO @ Thu, 16 Apr 2020 01:01:29: 5000000 INFO @ Thu, 16 Apr 2020 01:01:33: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:01:33: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:01:33: #1 total tags in treatment: 10535810 INFO @ Thu, 16 Apr 2020 01:01:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:33: #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 01:01:33: #1 tags after filtering in treatment: 10535810 INFO @ Thu, 16 Apr 2020 01:01:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:33: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:01:34: #2 number of paired peaks: 7408 INFO @ Thu, 16 Apr 2020 01:01:34: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:34: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:34: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:34: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:34: #2 predicted fragment length is 204 bps INFO @ Thu, 16 Apr 2020 01:01:34: #2 alternative fragment length(s) may be 204 bps INFO @ Thu, 16 Apr 2020 01:01:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.10_model.r INFO @ Thu, 16 Apr 2020 01:01:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:01:35: 6000000 INFO @ Thu, 16 Apr 2020 01:01:41: 7000000 INFO @ Thu, 16 Apr 2020 01:01:47: 8000000 INFO @ Thu, 16 Apr 2020 01:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.05_summits.bed INFO @ Thu, 16 Apr 2020 01:01:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10950 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:01:52: 9000000 INFO @ Thu, 16 Apr 2020 01:01:58: 10000000 INFO @ Thu, 16 Apr 2020 01:02:01: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:02:01: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:02:01: #1 total tags in treatment: 10535810 INFO @ Thu, 16 Apr 2020 01:02:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:01: #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 01:02:01: #1 tags after filtering in treatment: 10535810 INFO @ Thu, 16 Apr 2020 01:02:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:01: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:02: #2 number of paired peaks: 7408 INFO @ Thu, 16 Apr 2020 01:02:02: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:02: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:02: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:02: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:02: #2 predicted fragment length is 204 bps INFO @ Thu, 16 Apr 2020 01:02:02: #2 alternative fragment length(s) may be 204 bps INFO @ Thu, 16 Apr 2020 01:02:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.20_model.r INFO @ Thu, 16 Apr 2020 01:02:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:02:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.10_summits.bed INFO @ Thu, 16 Apr 2020 01:02:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8726 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:02:34: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592491/SRX2592491.20_summits.bed INFO @ Thu, 16 Apr 2020 01:02:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6241 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。