Job ID = 5720650 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,532,108 reads read : 17,532,108 reads written : 17,532,108 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289747.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: 00:04:28 17532108 reads; of these: 17532108 (100.00%) were unpaired; of these: 1621966 (9.25%) aligned 0 times 13046419 (74.41%) aligned exactly 1 time 2863723 (16.33%) aligned >1 times 90.75% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 5645162 / 15910142 = 0.3548 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 00:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.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 00:55:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:14: 1000000 INFO @ Thu, 16 Apr 2020 00:55:19: 2000000 INFO @ Thu, 16 Apr 2020 00:55:25: 3000000 INFO @ Thu, 16 Apr 2020 00:55:30: 4000000 INFO @ Thu, 16 Apr 2020 00:55:36: 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 00:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.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 00:55:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:41: 6000000 INFO @ Thu, 16 Apr 2020 00:55:43: 1000000 INFO @ Thu, 16 Apr 2020 00:55:46: 7000000 INFO @ Thu, 16 Apr 2020 00:55:48: 2000000 INFO @ Thu, 16 Apr 2020 00:55:51: 8000000 INFO @ Thu, 16 Apr 2020 00:55:53: 3000000 INFO @ Thu, 16 Apr 2020 00:55:57: 9000000 INFO @ Thu, 16 Apr 2020 00:55:58: 4000000 INFO @ Thu, 16 Apr 2020 00:56:03: 5000000 INFO @ Thu, 16 Apr 2020 00:56:03: 10000000 INFO @ Thu, 16 Apr 2020 00:56:04: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:04: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:04: #1 total tags in treatment: 10264980 INFO @ Thu, 16 Apr 2020 00:56:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:04: #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 00:56:04: #1 tags after filtering in treatment: 10264980 INFO @ Thu, 16 Apr 2020 00:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:04: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:06: #2 number of paired peaks: 8431 INFO @ Thu, 16 Apr 2020 00:56:06: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:06: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:06: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:06: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:06: #2 predicted fragment length is 202 bps INFO @ Thu, 16 Apr 2020 00:56:06: #2 alternative fragment length(s) may be 202 bps INFO @ Thu, 16 Apr 2020 00:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.05_model.r INFO @ Thu, 16 Apr 2020 00:56:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:06: #3 Pre-compute pvalue-qvalue table... 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 00:56:07: 6000000 INFO @ Thu, 16 Apr 2020 00:56:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.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 00:56:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:56:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:56:12: 7000000 INFO @ Thu, 16 Apr 2020 00:56:13: 1000000 INFO @ Thu, 16 Apr 2020 00:56:17: 8000000 INFO @ Thu, 16 Apr 2020 00:56:18: 2000000 INFO @ Thu, 16 Apr 2020 00:56:21: 9000000 INFO @ Thu, 16 Apr 2020 00:56:23: 3000000 INFO @ Thu, 16 Apr 2020 00:56:26: 10000000 INFO @ Thu, 16 Apr 2020 00:56:27: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:27: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:27: #1 total tags in treatment: 10264980 INFO @ Thu, 16 Apr 2020 00:56:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:27: #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 00:56:27: #1 tags after filtering in treatment: 10264980 INFO @ Thu, 16 Apr 2020 00:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:27: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:28: 4000000 INFO @ Thu, 16 Apr 2020 00:56:29: #2 number of paired peaks: 8431 INFO @ Thu, 16 Apr 2020 00:56:29: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:29: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:29: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:29: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:29: #2 predicted fragment length is 202 bps INFO @ Thu, 16 Apr 2020 00:56:29: #2 alternative fragment length(s) may be 202 bps INFO @ Thu, 16 Apr 2020 00:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.10_model.r INFO @ Thu, 16 Apr 2020 00:56:29: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:32: 5000000 INFO @ Thu, 16 Apr 2020 00:56:37: 6000000 INFO @ Thu, 16 Apr 2020 00:56:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:42: 7000000 INFO @ Thu, 16 Apr 2020 00:56:46: 8000000 INFO @ Thu, 16 Apr 2020 00:56:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.05_summits.bed INFO @ Thu, 16 Apr 2020 00:56:51: Done! INFO @ Thu, 16 Apr 2020 00:56:51: 9000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (10001 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:56:56: 10000000 INFO @ Thu, 16 Apr 2020 00:56:57: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:57: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:57: #1 total tags in treatment: 10264980 INFO @ Thu, 16 Apr 2020 00:56:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:57: #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 00:56:57: #1 tags after filtering in treatment: 10264980 INFO @ Thu, 16 Apr 2020 00:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:57: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:58: #2 number of paired peaks: 8431 INFO @ Thu, 16 Apr 2020 00:56:58: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:58: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:58: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:58: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:58: #2 predicted fragment length is 202 bps INFO @ Thu, 16 Apr 2020 00:56:58: #2 alternative fragment length(s) may be 202 bps INFO @ Thu, 16 Apr 2020 00:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.20_model.r INFO @ Thu, 16 Apr 2020 00:56:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:57:02: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.10_summits.bed INFO @ Thu, 16 Apr 2020 00:57:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8264 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:57:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592470/SRX2592470.20_summits.bed INFO @ Thu, 16 Apr 2020 00:57:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6372 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。