Job ID = 5720703 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,652,212 reads read : 13,652,212 reads written : 13,652,212 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: 00:02:49 13652212 reads; of these: 13652212 (100.00%) were unpaired; of these: 266035 (1.95%) aligned 0 times 12442562 (91.14%) aligned exactly 1 time 943615 (6.91%) aligned >1 times 98.05% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 1905334 / 13386177 = 0.1423 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 01:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.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 01:10:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:10:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:10:09: 1000000 INFO @ Thu, 16 Apr 2020 01:10:13: 2000000 INFO @ Thu, 16 Apr 2020 01:10:18: 3000000 INFO @ Thu, 16 Apr 2020 01:10:22: 4000000 INFO @ Thu, 16 Apr 2020 01:10:27: 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 01:10:32: 6000000 INFO @ Thu, 16 Apr 2020 01:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.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 01:10:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:10:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:10:36: 7000000 INFO @ Thu, 16 Apr 2020 01:10:39: 1000000 INFO @ Thu, 16 Apr 2020 01:10:41: 8000000 INFO @ Thu, 16 Apr 2020 01:10:45: 2000000 INFO @ Thu, 16 Apr 2020 01:10:46: 9000000 INFO @ Thu, 16 Apr 2020 01:10:50: 3000000 INFO @ Thu, 16 Apr 2020 01:10:50: 10000000 INFO @ Thu, 16 Apr 2020 01:10:55: 11000000 INFO @ Thu, 16 Apr 2020 01:10:55: 4000000 INFO @ Thu, 16 Apr 2020 01:10:58: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:10:58: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:10:58: #1 total tags in treatment: 11480843 INFO @ Thu, 16 Apr 2020 01:10:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:10:58: #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 01:10:58: #1 tags after filtering in treatment: 11480843 INFO @ Thu, 16 Apr 2020 01:10:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:10:58: #1 finished! INFO @ Thu, 16 Apr 2020 01:10:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:10:59: #2 number of paired peaks: 10360 INFO @ Thu, 16 Apr 2020 01:10:59: start model_add_line... INFO @ Thu, 16 Apr 2020 01:10:59: start X-correlation... INFO @ Thu, 16 Apr 2020 01:10:59: end of X-cor INFO @ Thu, 16 Apr 2020 01:10:59: #2 finished! INFO @ Thu, 16 Apr 2020 01:10:59: #2 predicted fragment length is 149 bps INFO @ Thu, 16 Apr 2020 01:10:59: #2 alternative fragment length(s) may be 3,149 bps INFO @ Thu, 16 Apr 2020 01:10:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.05_model.r INFO @ Thu, 16 Apr 2020 01:11:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:00: #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 01:11:01: 5000000 INFO @ Thu, 16 Apr 2020 01:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.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 01:11:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:11:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:11:06: 6000000 INFO @ Thu, 16 Apr 2020 01:11:09: 1000000 INFO @ Thu, 16 Apr 2020 01:11:11: 7000000 INFO @ Thu, 16 Apr 2020 01:11:13: 2000000 INFO @ Thu, 16 Apr 2020 01:11:16: 8000000 INFO @ Thu, 16 Apr 2020 01:11:18: 3000000 INFO @ Thu, 16 Apr 2020 01:11:22: 9000000 INFO @ Thu, 16 Apr 2020 01:11:23: 4000000 INFO @ Thu, 16 Apr 2020 01:11:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:11:27: 10000000 INFO @ Thu, 16 Apr 2020 01:11:27: 5000000 INFO @ Thu, 16 Apr 2020 01:11:32: 6000000 INFO @ Thu, 16 Apr 2020 01:11:32: 11000000 INFO @ Thu, 16 Apr 2020 01:11:35: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:11:35: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:11:35: #1 total tags in treatment: 11480843 INFO @ Thu, 16 Apr 2020 01:11:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:11:35: #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 01:11:35: #1 tags after filtering in treatment: 11480843 INFO @ Thu, 16 Apr 2020 01:11:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:11:35: #1 finished! INFO @ Thu, 16 Apr 2020 01:11:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:11:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:11:36: #2 number of paired peaks: 10360 INFO @ Thu, 16 Apr 2020 01:11:36: start model_add_line... INFO @ Thu, 16 Apr 2020 01:11:37: start X-correlation... INFO @ Thu, 16 Apr 2020 01:11:37: end of X-cor INFO @ Thu, 16 Apr 2020 01:11:37: #2 finished! INFO @ Thu, 16 Apr 2020 01:11:37: #2 predicted fragment length is 149 bps INFO @ Thu, 16 Apr 2020 01:11:37: #2 alternative fragment length(s) may be 3,149 bps INFO @ Thu, 16 Apr 2020 01:11:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.10_model.r INFO @ Thu, 16 Apr 2020 01:11:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:11:37: 7000000 INFO @ Thu, 16 Apr 2020 01:11:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:11:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:11:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.05_summits.bed INFO @ Thu, 16 Apr 2020 01:11:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9308 records, 4 fields): 9 millis INFO @ Thu, 16 Apr 2020 01:11:42: 8000000 CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:11:48: 9000000 INFO @ Thu, 16 Apr 2020 01:11:53: 10000000 INFO @ Thu, 16 Apr 2020 01:11:57: 11000000 INFO @ Thu, 16 Apr 2020 01:11:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:12:00: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:12:00: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:12:00: #1 total tags in treatment: 11480843 INFO @ Thu, 16 Apr 2020 01:12:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:12:00: #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 01:12:00: #1 tags after filtering in treatment: 11480843 INFO @ Thu, 16 Apr 2020 01:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:12:00: #1 finished! INFO @ Thu, 16 Apr 2020 01:12:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:12:02: #2 number of paired peaks: 10360 INFO @ Thu, 16 Apr 2020 01:12:02: start model_add_line... INFO @ Thu, 16 Apr 2020 01:12:02: start X-correlation... INFO @ Thu, 16 Apr 2020 01:12:02: end of X-cor INFO @ Thu, 16 Apr 2020 01:12:02: #2 finished! INFO @ Thu, 16 Apr 2020 01:12:02: #2 predicted fragment length is 149 bps INFO @ Thu, 16 Apr 2020 01:12:02: #2 alternative fragment length(s) may be 3,149 bps INFO @ Thu, 16 Apr 2020 01:12:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.20_model.r INFO @ Thu, 16 Apr 2020 01:12:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:12:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:12:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:12:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.10_summits.bed INFO @ Thu, 16 Apr 2020 01:12:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5553 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:12:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158167/SRX4158167.20_summits.bed INFO @ Thu, 16 Apr 2020 01:12:41: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1759 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。