Job ID = 5720414 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,336,850 reads read : 22,336,850 reads written : 22,336,850 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289676.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: 00:06:46 22336850 reads; of these: 22336850 (100.00%) were unpaired; of these: 1618826 (7.25%) aligned 0 times 16628714 (74.45%) aligned exactly 1 time 4089310 (18.31%) aligned >1 times 92.75% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 7536603 / 20718024 = 0.3638 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 00:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.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 00:35:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:35:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:35:32: 1000000 INFO @ Thu, 16 Apr 2020 00:35:38: 2000000 INFO @ Thu, 16 Apr 2020 00:35:44: 3000000 INFO @ Thu, 16 Apr 2020 00:35:50: 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 00:35:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.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 00:35:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:35:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:35:56: 5000000 INFO @ Thu, 16 Apr 2020 00:36:02: 1000000 INFO @ Thu, 16 Apr 2020 00:36:03: 6000000 INFO @ Thu, 16 Apr 2020 00:36:09: 2000000 INFO @ Thu, 16 Apr 2020 00:36:09: 7000000 INFO @ Thu, 16 Apr 2020 00:36:15: 8000000 INFO @ Thu, 16 Apr 2020 00:36:15: 3000000 INFO @ Thu, 16 Apr 2020 00:36:22: 4000000 INFO @ Thu, 16 Apr 2020 00:36:22: 9000000 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 00:36:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.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 00:36:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:36:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:36:28: 5000000 INFO @ Thu, 16 Apr 2020 00:36:28: 10000000 INFO @ Thu, 16 Apr 2020 00:36:33: 1000000 INFO @ Thu, 16 Apr 2020 00:36:34: 6000000 INFO @ Thu, 16 Apr 2020 00:36:34: 11000000 INFO @ Thu, 16 Apr 2020 00:36:39: 2000000 INFO @ Thu, 16 Apr 2020 00:36:40: 7000000 INFO @ Thu, 16 Apr 2020 00:36:41: 12000000 INFO @ Thu, 16 Apr 2020 00:36:46: 3000000 INFO @ Thu, 16 Apr 2020 00:36:47: 8000000 INFO @ Thu, 16 Apr 2020 00:36:47: 13000000 INFO @ Thu, 16 Apr 2020 00:36:48: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:36:48: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:36:48: #1 total tags in treatment: 13181421 INFO @ Thu, 16 Apr 2020 00:36:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:36:48: #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 00:36:48: #1 tags after filtering in treatment: 13181421 INFO @ Thu, 16 Apr 2020 00:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:36:48: #1 finished! INFO @ Thu, 16 Apr 2020 00:36:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:36:50: #2 number of paired peaks: 1564 INFO @ Thu, 16 Apr 2020 00:36:50: start model_add_line... INFO @ Thu, 16 Apr 2020 00:36:50: start X-correlation... INFO @ Thu, 16 Apr 2020 00:36:50: end of X-cor INFO @ Thu, 16 Apr 2020 00:36:50: #2 finished! INFO @ Thu, 16 Apr 2020 00:36:50: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 00:36:50: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 00:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.05_model.r INFO @ Thu, 16 Apr 2020 00:36:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:36:52: 4000000 INFO @ Thu, 16 Apr 2020 00:36:53: 9000000 INFO @ Thu, 16 Apr 2020 00:36:58: 5000000 INFO @ Thu, 16 Apr 2020 00:36:59: 10000000 INFO @ Thu, 16 Apr 2020 00:37:04: 6000000 INFO @ Thu, 16 Apr 2020 00:37:06: 11000000 INFO @ Thu, 16 Apr 2020 00:37:11: 7000000 INFO @ Thu, 16 Apr 2020 00:37:12: 12000000 INFO @ Thu, 16 Apr 2020 00:37:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:37:17: 8000000 INFO @ Thu, 16 Apr 2020 00:37:18: 13000000 INFO @ Thu, 16 Apr 2020 00:37:19: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:37:19: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:37:19: #1 total tags in treatment: 13181421 INFO @ Thu, 16 Apr 2020 00:37:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:37:19: #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 00:37:19: #1 tags after filtering in treatment: 13181421 INFO @ Thu, 16 Apr 2020 00:37:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:37:19: #1 finished! INFO @ Thu, 16 Apr 2020 00:37:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:37:21: #2 number of paired peaks: 1564 INFO @ Thu, 16 Apr 2020 00:37:21: start model_add_line... INFO @ Thu, 16 Apr 2020 00:37:21: start X-correlation... INFO @ Thu, 16 Apr 2020 00:37:21: end of X-cor INFO @ Thu, 16 Apr 2020 00:37:21: #2 finished! INFO @ Thu, 16 Apr 2020 00:37:21: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 00:37:21: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 00:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.10_model.r INFO @ Thu, 16 Apr 2020 00:37:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:37:23: 9000000 INFO @ Thu, 16 Apr 2020 00:37:29: 10000000 INFO @ Thu, 16 Apr 2020 00:37:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:37:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:37:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.05_summits.bed INFO @ Thu, 16 Apr 2020 00:37:31: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (21336 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:37:35: 11000000 INFO @ Thu, 16 Apr 2020 00:37:42: 12000000 INFO @ Thu, 16 Apr 2020 00:37:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:37:50: 13000000 INFO @ Thu, 16 Apr 2020 00:37:52: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:37:52: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:37:52: #1 total tags in treatment: 13181421 INFO @ Thu, 16 Apr 2020 00:37:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:37:52: #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 00:37:52: #1 tags after filtering in treatment: 13181421 INFO @ Thu, 16 Apr 2020 00:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:37:52: #1 finished! INFO @ Thu, 16 Apr 2020 00:37:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:37:53: #2 number of paired peaks: 1564 INFO @ Thu, 16 Apr 2020 00:37:53: start model_add_line... INFO @ Thu, 16 Apr 2020 00:37:53: start X-correlation... INFO @ Thu, 16 Apr 2020 00:37:53: end of X-cor INFO @ Thu, 16 Apr 2020 00:37:53: #2 finished! INFO @ Thu, 16 Apr 2020 00:37:53: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 00:37:53: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 00:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.20_model.r INFO @ Thu, 16 Apr 2020 00:37:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:37:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:38:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:38:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:38:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.10_summits.bed INFO @ Thu, 16 Apr 2020 00:38:02: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (17825 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:38:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:38:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:38:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:38:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592399/SRX2592399.20_summits.bed INFO @ Thu, 16 Apr 2020 00:38:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (11898 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。