Job ID = 5721205 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,131,564 reads read : 24,131,564 reads written : 24,131,564 rm: cannot remove ‘[DSE]RR*’: 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: 00:08:04 24131564 reads; of these: 24131564 (100.00%) were unpaired; of these: 1346029 (5.58%) aligned 0 times 15861489 (65.73%) aligned exactly 1 time 6924046 (28.69%) aligned >1 times 94.42% overall alignment rate Time searching: 00:08:04 Overall time: 00:08:04 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] 3727785 / 22785535 = 0.1636 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 06:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.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 06:06:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:06:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:06:20: 1000000 INFO @ Thu, 16 Apr 2020 06:06:26: 2000000 INFO @ Thu, 16 Apr 2020 06:06:32: 3000000 INFO @ Thu, 16 Apr 2020 06:06:38: 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 @ Thu, 16 Apr 2020 06:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.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 06:06:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:06:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:06:44: 5000000 INFO @ Thu, 16 Apr 2020 06:06:50: 1000000 INFO @ Thu, 16 Apr 2020 06:06:51: 6000000 INFO @ Thu, 16 Apr 2020 06:06:56: 2000000 INFO @ Thu, 16 Apr 2020 06:06:57: 7000000 INFO @ Thu, 16 Apr 2020 06:07:02: 3000000 INFO @ Thu, 16 Apr 2020 06:07:04: 8000000 INFO @ Thu, 16 Apr 2020 06:07:09: 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 @ Thu, 16 Apr 2020 06:07:10: 9000000 INFO @ Thu, 16 Apr 2020 06:07:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.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 06:07:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:07:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:07:15: 5000000 INFO @ Thu, 16 Apr 2020 06:07:17: 10000000 INFO @ Thu, 16 Apr 2020 06:07:20: 1000000 INFO @ Thu, 16 Apr 2020 06:07:22: 6000000 INFO @ Thu, 16 Apr 2020 06:07:23: 11000000 INFO @ Thu, 16 Apr 2020 06:07:26: 2000000 INFO @ Thu, 16 Apr 2020 06:07:29: 7000000 INFO @ Thu, 16 Apr 2020 06:07:30: 12000000 INFO @ Thu, 16 Apr 2020 06:07:33: 3000000 INFO @ Thu, 16 Apr 2020 06:07:35: 8000000 INFO @ Thu, 16 Apr 2020 06:07:37: 13000000 INFO @ Thu, 16 Apr 2020 06:07:40: 4000000 INFO @ Thu, 16 Apr 2020 06:07:42: 9000000 INFO @ Thu, 16 Apr 2020 06:07:43: 14000000 INFO @ Thu, 16 Apr 2020 06:07:46: 5000000 INFO @ Thu, 16 Apr 2020 06:07:48: 10000000 INFO @ Thu, 16 Apr 2020 06:07:50: 15000000 INFO @ Thu, 16 Apr 2020 06:07:53: 6000000 INFO @ Thu, 16 Apr 2020 06:07:55: 11000000 INFO @ Thu, 16 Apr 2020 06:07:56: 16000000 INFO @ Thu, 16 Apr 2020 06:07:59: 7000000 INFO @ Thu, 16 Apr 2020 06:08:01: 12000000 INFO @ Thu, 16 Apr 2020 06:08:03: 17000000 INFO @ Thu, 16 Apr 2020 06:08:06: 8000000 INFO @ Thu, 16 Apr 2020 06:08:08: 13000000 INFO @ Thu, 16 Apr 2020 06:08:09: 18000000 INFO @ Thu, 16 Apr 2020 06:08:13: 9000000 INFO @ Thu, 16 Apr 2020 06:08:15: 14000000 INFO @ Thu, 16 Apr 2020 06:08:16: 19000000 INFO @ Thu, 16 Apr 2020 06:08:16: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:08:16: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:08:16: #1 total tags in treatment: 19057750 INFO @ Thu, 16 Apr 2020 06:08:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:08:16: #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 06:08:16: #1 tags after filtering in treatment: 19057750 INFO @ Thu, 16 Apr 2020 06:08:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:08:16: #1 finished! INFO @ Thu, 16 Apr 2020 06:08:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:08:18: #2 number of paired peaks: 607 WARNING @ Thu, 16 Apr 2020 06:08:18: Fewer paired peaks (607) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 607 pairs to build model! INFO @ Thu, 16 Apr 2020 06:08:18: start model_add_line... INFO @ Thu, 16 Apr 2020 06:08:18: start X-correlation... INFO @ Thu, 16 Apr 2020 06:08:18: end of X-cor INFO @ Thu, 16 Apr 2020 06:08:18: #2 finished! INFO @ Thu, 16 Apr 2020 06:08:18: #2 predicted fragment length is 126 bps INFO @ Thu, 16 Apr 2020 06:08:18: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 16 Apr 2020 06:08:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.05_model.r INFO @ Thu, 16 Apr 2020 06:08:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:08:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:08:19: 10000000 INFO @ Thu, 16 Apr 2020 06:08:21: 15000000 INFO @ Thu, 16 Apr 2020 06:08:26: 11000000 INFO @ Thu, 16 Apr 2020 06:08:27: 16000000 INFO @ Thu, 16 Apr 2020 06:08:32: 12000000 INFO @ Thu, 16 Apr 2020 06:08:34: 17000000 INFO @ Thu, 16 Apr 2020 06:08:39: 13000000 INFO @ Thu, 16 Apr 2020 06:08:40: 18000000 INFO @ Thu, 16 Apr 2020 06:08:45: 14000000 INFO @ Thu, 16 Apr 2020 06:08:46: 19000000 INFO @ Thu, 16 Apr 2020 06:08:47: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:08:47: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:08:47: #1 total tags in treatment: 19057750 INFO @ Thu, 16 Apr 2020 06:08:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:08:47: #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 06:08:47: #1 tags after filtering in treatment: 19057750 INFO @ Thu, 16 Apr 2020 06:08:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:08:47: #1 finished! INFO @ Thu, 16 Apr 2020 06:08:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:08:48: #2 number of paired peaks: 607 WARNING @ Thu, 16 Apr 2020 06:08:48: Fewer paired peaks (607) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 607 pairs to build model! INFO @ Thu, 16 Apr 2020 06:08:48: start model_add_line... INFO @ Thu, 16 Apr 2020 06:08:48: start X-correlation... INFO @ Thu, 16 Apr 2020 06:08:48: end of X-cor INFO @ Thu, 16 Apr 2020 06:08:48: #2 finished! INFO @ Thu, 16 Apr 2020 06:08:48: #2 predicted fragment length is 126 bps INFO @ Thu, 16 Apr 2020 06:08:48: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 16 Apr 2020 06:08:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.10_model.r INFO @ Thu, 16 Apr 2020 06:08:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:08:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:08:52: 15000000 INFO @ Thu, 16 Apr 2020 06:08:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:08:58: 16000000 INFO @ Thu, 16 Apr 2020 06:09:04: 17000000 INFO @ Thu, 16 Apr 2020 06:09:10: 18000000 INFO @ Thu, 16 Apr 2020 06:09:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:09:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:09:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.05_summits.bed INFO @ Thu, 16 Apr 2020 06:09:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6041 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:09:16: 19000000 INFO @ Thu, 16 Apr 2020 06:09:17: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:09:17: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:09:17: #1 total tags in treatment: 19057750 INFO @ Thu, 16 Apr 2020 06:09:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:09:17: #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 06:09:17: #1 tags after filtering in treatment: 19057750 INFO @ Thu, 16 Apr 2020 06:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:09:17: #1 finished! INFO @ Thu, 16 Apr 2020 06:09:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:09:18: #2 number of paired peaks: 607 WARNING @ Thu, 16 Apr 2020 06:09:18: Fewer paired peaks (607) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 607 pairs to build model! INFO @ Thu, 16 Apr 2020 06:09:18: start model_add_line... INFO @ Thu, 16 Apr 2020 06:09:18: start X-correlation... INFO @ Thu, 16 Apr 2020 06:09:18: end of X-cor INFO @ Thu, 16 Apr 2020 06:09:18: #2 finished! INFO @ Thu, 16 Apr 2020 06:09:18: #2 predicted fragment length is 126 bps INFO @ Thu, 16 Apr 2020 06:09:18: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 16 Apr 2020 06:09:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.20_model.r INFO @ Thu, 16 Apr 2020 06:09:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:09:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:09:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:09:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:09:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:09:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.10_summits.bed INFO @ Thu, 16 Apr 2020 06:09:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3986 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:09:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827671/SRX6827671.20_summits.bed INFO @ Thu, 16 Apr 2020 06:10:14: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2356 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。