Job ID = 5720410 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,290,525 reads read : 26,290,525 reads written : 26,290,525 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289674.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: 00:07:42 26290525 reads; of these: 26290525 (100.00%) were unpaired; of these: 1922316 (7.31%) aligned 0 times 19876553 (75.60%) aligned exactly 1 time 4491656 (17.08%) aligned >1 times 92.69% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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] 6894217 / 24368209 = 0.2829 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 00:37:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.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 00:37:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:37:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:37:12: 1000000 INFO @ Thu, 16 Apr 2020 00:37:19: 2000000 INFO @ Thu, 16 Apr 2020 00:37:26: 3000000 INFO @ Thu, 16 Apr 2020 00:37:33: 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 00:37:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.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 00:37:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:37:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:37:40: 5000000 INFO @ Thu, 16 Apr 2020 00:37:42: 1000000 INFO @ Thu, 16 Apr 2020 00:37:48: 6000000 INFO @ Thu, 16 Apr 2020 00:37:49: 2000000 INFO @ Thu, 16 Apr 2020 00:37:55: 7000000 INFO @ Thu, 16 Apr 2020 00:37:56: 3000000 INFO @ Thu, 16 Apr 2020 00:38:02: 8000000 INFO @ Thu, 16 Apr 2020 00:38:03: 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 00:38:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.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 00:38:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:38:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:38:09: 9000000 INFO @ Thu, 16 Apr 2020 00:38:10: 5000000 INFO @ Thu, 16 Apr 2020 00:38:13: 1000000 INFO @ Thu, 16 Apr 2020 00:38:17: 6000000 INFO @ Thu, 16 Apr 2020 00:38:17: 10000000 INFO @ Thu, 16 Apr 2020 00:38:21: 2000000 INFO @ Thu, 16 Apr 2020 00:38:23: 7000000 INFO @ Thu, 16 Apr 2020 00:38:24: 11000000 INFO @ Thu, 16 Apr 2020 00:38:29: 3000000 INFO @ Thu, 16 Apr 2020 00:38:30: 8000000 INFO @ Thu, 16 Apr 2020 00:38:31: 12000000 INFO @ Thu, 16 Apr 2020 00:38:36: 4000000 INFO @ Thu, 16 Apr 2020 00:38:37: 9000000 INFO @ Thu, 16 Apr 2020 00:38:39: 13000000 INFO @ Thu, 16 Apr 2020 00:38:44: 5000000 INFO @ Thu, 16 Apr 2020 00:38:44: 10000000 INFO @ Thu, 16 Apr 2020 00:38:46: 14000000 INFO @ Thu, 16 Apr 2020 00:38:51: 11000000 INFO @ Thu, 16 Apr 2020 00:38:52: 6000000 INFO @ Thu, 16 Apr 2020 00:38:53: 15000000 INFO @ Thu, 16 Apr 2020 00:38:58: 12000000 INFO @ Thu, 16 Apr 2020 00:38:59: 7000000 INFO @ Thu, 16 Apr 2020 00:39:01: 16000000 INFO @ Thu, 16 Apr 2020 00:39:05: 13000000 INFO @ Thu, 16 Apr 2020 00:39:07: 8000000 INFO @ Thu, 16 Apr 2020 00:39:08: 17000000 INFO @ Thu, 16 Apr 2020 00:39:11: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:39:11: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:39:11: #1 total tags in treatment: 17473992 INFO @ Thu, 16 Apr 2020 00:39:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:39:11: #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 00:39:12: 14000000 INFO @ Thu, 16 Apr 2020 00:39:12: #1 tags after filtering in treatment: 17473992 INFO @ Thu, 16 Apr 2020 00:39:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:39:12: #1 finished! INFO @ Thu, 16 Apr 2020 00:39:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:39:13: #2 number of paired peaks: 4525 INFO @ Thu, 16 Apr 2020 00:39:13: start model_add_line... INFO @ Thu, 16 Apr 2020 00:39:14: start X-correlation... INFO @ Thu, 16 Apr 2020 00:39:14: end of X-cor INFO @ Thu, 16 Apr 2020 00:39:14: #2 finished! INFO @ Thu, 16 Apr 2020 00:39:14: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 00:39:14: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 00:39:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.05_model.r INFO @ Thu, 16 Apr 2020 00:39:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:39:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:39:14: 9000000 INFO @ Thu, 16 Apr 2020 00:39:18: 15000000 INFO @ Thu, 16 Apr 2020 00:39:22: 10000000 INFO @ Thu, 16 Apr 2020 00:39:25: 16000000 INFO @ Thu, 16 Apr 2020 00:39:29: 11000000 INFO @ Thu, 16 Apr 2020 00:39:32: 17000000 INFO @ Thu, 16 Apr 2020 00:39:35: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:39:35: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:39:35: #1 total tags in treatment: 17473992 INFO @ Thu, 16 Apr 2020 00:39:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:39:35: #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 00:39:36: #1 tags after filtering in treatment: 17473992 INFO @ Thu, 16 Apr 2020 00:39:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:39:36: #1 finished! INFO @ Thu, 16 Apr 2020 00:39:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:39:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:39:37: 12000000 INFO @ Thu, 16 Apr 2020 00:39:37: #2 number of paired peaks: 4525 INFO @ Thu, 16 Apr 2020 00:39:37: start model_add_line... INFO @ Thu, 16 Apr 2020 00:39:37: start X-correlation... INFO @ Thu, 16 Apr 2020 00:39:37: end of X-cor INFO @ Thu, 16 Apr 2020 00:39:37: #2 finished! INFO @ Thu, 16 Apr 2020 00:39:37: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 00:39:37: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 00:39:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.10_model.r INFO @ Thu, 16 Apr 2020 00:39:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:39:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:39:43: 13000000 INFO @ Thu, 16 Apr 2020 00:39:50: 14000000 INFO @ Thu, 16 Apr 2020 00:39:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:39:57: 15000000 INFO @ Thu, 16 Apr 2020 00:40:04: 16000000 INFO @ Thu, 16 Apr 2020 00:40:11: 17000000 INFO @ Thu, 16 Apr 2020 00:40:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:40:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:40:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.05_summits.bed INFO @ Thu, 16 Apr 2020 00:40:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (16906 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:40:14: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:40:14: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:40:14: #1 total tags in treatment: 17473992 INFO @ Thu, 16 Apr 2020 00:40:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:14: #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 00:40:14: #1 tags after filtering in treatment: 17473992 INFO @ Thu, 16 Apr 2020 00:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:14: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:16: #2 number of paired peaks: 4525 INFO @ Thu, 16 Apr 2020 00:40:16: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:16: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:16: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:16: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:16: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 00:40:16: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 00:40:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.20_model.r INFO @ Thu, 16 Apr 2020 00:40:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:40:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:40:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:40:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:40:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.10_summits.bed INFO @ Thu, 16 Apr 2020 00:40:37: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (13261 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:40:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:41:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592397/SRX2592397.20_summits.bed INFO @ Thu, 16 Apr 2020 00:41:17: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8543 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。