Job ID = 5720689 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,093,976 reads read : 19,093,976 reads written : 19,093,976 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR6967847.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: 00:04:58 19093976 reads; of these: 19093976 (100.00%) were unpaired; of these: 2493289 (13.06%) aligned 0 times 13444929 (70.41%) aligned exactly 1 time 3155758 (16.53%) aligned >1 times 86.94% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 3237062 / 16600687 = 0.1950 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 01:04:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.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 01:04:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:04:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:04:24: 1000000 INFO @ Thu, 16 Apr 2020 01:04:29: 2000000 INFO @ Thu, 16 Apr 2020 01:04:35: 3000000 INFO @ Thu, 16 Apr 2020 01:04:40: 4000000 INFO @ Thu, 16 Apr 2020 01:04:45: 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 01:04:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.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 01:04:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:04:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:04:51: 6000000 INFO @ Thu, 16 Apr 2020 01:04:53: 1000000 INFO @ Thu, 16 Apr 2020 01:04:56: 7000000 INFO @ Thu, 16 Apr 2020 01:04:59: 2000000 INFO @ Thu, 16 Apr 2020 01:05:02: 8000000 INFO @ Thu, 16 Apr 2020 01:05:04: 3000000 INFO @ Thu, 16 Apr 2020 01:05:07: 9000000 INFO @ Thu, 16 Apr 2020 01:05:10: 4000000 INFO @ Thu, 16 Apr 2020 01:05:13: 10000000 INFO @ Thu, 16 Apr 2020 01:05:15: 5000000 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 01:05:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.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 01:05:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:05:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:05:19: 11000000 INFO @ Thu, 16 Apr 2020 01:05:21: 6000000 INFO @ Thu, 16 Apr 2020 01:05:24: 1000000 INFO @ Thu, 16 Apr 2020 01:05:24: 12000000 INFO @ Thu, 16 Apr 2020 01:05:26: 7000000 INFO @ Thu, 16 Apr 2020 01:05:29: 2000000 INFO @ Thu, 16 Apr 2020 01:05:30: 13000000 INFO @ Thu, 16 Apr 2020 01:05:32: 8000000 INFO @ Thu, 16 Apr 2020 01:05:32: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:05:32: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:05:32: #1 total tags in treatment: 13363625 INFO @ Thu, 16 Apr 2020 01:05:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:05:32: #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 01:05:33: #1 tags after filtering in treatment: 13363625 INFO @ Thu, 16 Apr 2020 01:05:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:05:33: #1 finished! INFO @ Thu, 16 Apr 2020 01:05:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:05:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:05:33: #2 number of paired peaks: 1105 INFO @ Thu, 16 Apr 2020 01:05:33: start model_add_line... INFO @ Thu, 16 Apr 2020 01:05:34: start X-correlation... INFO @ Thu, 16 Apr 2020 01:05:34: end of X-cor INFO @ Thu, 16 Apr 2020 01:05:34: #2 finished! INFO @ Thu, 16 Apr 2020 01:05:34: #2 predicted fragment length is 157 bps INFO @ Thu, 16 Apr 2020 01:05:34: #2 alternative fragment length(s) may be 157 bps INFO @ Thu, 16 Apr 2020 01:05:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.05_model.r INFO @ Thu, 16 Apr 2020 01:05:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:05:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:05:35: 3000000 INFO @ Thu, 16 Apr 2020 01:05:38: 9000000 INFO @ Thu, 16 Apr 2020 01:05:40: 4000000 INFO @ Thu, 16 Apr 2020 01:05:43: 10000000 INFO @ Thu, 16 Apr 2020 01:05:46: 5000000 INFO @ Thu, 16 Apr 2020 01:05:49: 11000000 INFO @ Thu, 16 Apr 2020 01:05:51: 6000000 INFO @ Thu, 16 Apr 2020 01:05:55: 12000000 INFO @ Thu, 16 Apr 2020 01:05:57: 7000000 INFO @ Thu, 16 Apr 2020 01:06:00: 13000000 INFO @ Thu, 16 Apr 2020 01:06:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:06:02: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:06:02: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:06:02: #1 total tags in treatment: 13363625 INFO @ Thu, 16 Apr 2020 01:06:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:06:02: #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 01:06:03: 8000000 INFO @ Thu, 16 Apr 2020 01:06:03: #1 tags after filtering in treatment: 13363625 INFO @ Thu, 16 Apr 2020 01:06:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:06:03: #1 finished! INFO @ Thu, 16 Apr 2020 01:06:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:06:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:06:04: #2 number of paired peaks: 1105 INFO @ Thu, 16 Apr 2020 01:06:04: start model_add_line... INFO @ Thu, 16 Apr 2020 01:06:04: start X-correlation... INFO @ Thu, 16 Apr 2020 01:06:04: end of X-cor INFO @ Thu, 16 Apr 2020 01:06:04: #2 finished! INFO @ Thu, 16 Apr 2020 01:06:04: #2 predicted fragment length is 157 bps INFO @ Thu, 16 Apr 2020 01:06:04: #2 alternative fragment length(s) may be 157 bps INFO @ Thu, 16 Apr 2020 01:06:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.10_model.r INFO @ Thu, 16 Apr 2020 01:06:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:06:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:06:08: 9000000 INFO @ Thu, 16 Apr 2020 01:06:14: 10000000 INFO @ Thu, 16 Apr 2020 01:06:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:06:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:06:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.05_summits.bed INFO @ Thu, 16 Apr 2020 01:06:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8813 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:06:19: 11000000 INFO @ Thu, 16 Apr 2020 01:06:25: 12000000 INFO @ Thu, 16 Apr 2020 01:06:30: 13000000 INFO @ Thu, 16 Apr 2020 01:06:32: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:06:32: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:06:32: #1 total tags in treatment: 13363625 INFO @ Thu, 16 Apr 2020 01:06:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:06:32: #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 01:06:32: #1 tags after filtering in treatment: 13363625 INFO @ Thu, 16 Apr 2020 01:06:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:06:32: #1 finished! INFO @ Thu, 16 Apr 2020 01:06:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:06:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:06:33: #2 number of paired peaks: 1105 INFO @ Thu, 16 Apr 2020 01:06:33: start model_add_line... INFO @ Thu, 16 Apr 2020 01:06:34: start X-correlation... INFO @ Thu, 16 Apr 2020 01:06:34: end of X-cor INFO @ Thu, 16 Apr 2020 01:06:34: #2 finished! INFO @ Thu, 16 Apr 2020 01:06:34: #2 predicted fragment length is 157 bps INFO @ Thu, 16 Apr 2020 01:06:34: #2 alternative fragment length(s) may be 157 bps INFO @ Thu, 16 Apr 2020 01:06:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.20_model.r INFO @ Thu, 16 Apr 2020 01:06:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.10_summits.bed INFO @ Thu, 16 Apr 2020 01:06:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5848 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:07:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3909720/SRX3909720.20_summits.bed INFO @ Thu, 16 Apr 2020 01:07:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3322 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。