Job ID = 5720687 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,211,150 reads read : 15,211,150 reads written : 15,211,150 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289779.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: 00:03:13 15211150 reads; of these: 15211150 (100.00%) were unpaired; of these: 4987878 (32.79%) aligned 0 times 9021498 (59.31%) aligned exactly 1 time 1201774 (7.90%) aligned >1 times 67.21% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 1781816 / 10223272 = 0.1743 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 01:00:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.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 01:00:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:27: 1000000 INFO @ Thu, 16 Apr 2020 01:00:32: 2000000 INFO @ Thu, 16 Apr 2020 01:00:37: 3000000 INFO @ Thu, 16 Apr 2020 01:00:43: 4000000 INFO @ Thu, 16 Apr 2020 01:00:48: 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 01:00:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.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 01:00:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:53: 6000000 INFO @ Thu, 16 Apr 2020 01:00:57: 1000000 INFO @ Thu, 16 Apr 2020 01:00:58: 7000000 INFO @ Thu, 16 Apr 2020 01:01:02: 2000000 INFO @ Thu, 16 Apr 2020 01:01:04: 8000000 INFO @ Thu, 16 Apr 2020 01:01:06: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:01:06: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:01:06: #1 total tags in treatment: 8441456 INFO @ Thu, 16 Apr 2020 01:01:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:06: #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 01:01:06: #1 tags after filtering in treatment: 8441456 INFO @ Thu, 16 Apr 2020 01:01:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:06: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:07: #2 number of paired peaks: 9059 INFO @ Thu, 16 Apr 2020 01:01:07: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:07: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:07: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:07: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:07: #2 predicted fragment length is 211 bps INFO @ Thu, 16 Apr 2020 01:01:07: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 16 Apr 2020 01:01:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.05_model.r INFO @ Thu, 16 Apr 2020 01:01:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:01:07: 3000000 INFO @ Thu, 16 Apr 2020 01:01:13: 4000000 INFO @ Thu, 16 Apr 2020 01:01:18: 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 01:01:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.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 01:01:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:23: 6000000 INFO @ Thu, 16 Apr 2020 01:01:28: 1000000 INFO @ Thu, 16 Apr 2020 01:01:29: 7000000 INFO @ Thu, 16 Apr 2020 01:01:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:01:35: 8000000 INFO @ Thu, 16 Apr 2020 01:01:35: 2000000 INFO @ Thu, 16 Apr 2020 01:01:37: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:01:37: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:01:37: #1 total tags in treatment: 8441456 INFO @ Thu, 16 Apr 2020 01:01:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:37: #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 01:01:37: #1 tags after filtering in treatment: 8441456 INFO @ Thu, 16 Apr 2020 01:01:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:37: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:38: #2 number of paired peaks: 9059 INFO @ Thu, 16 Apr 2020 01:01:38: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:39: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:39: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:39: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:39: #2 predicted fragment length is 211 bps INFO @ Thu, 16 Apr 2020 01:01:39: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 16 Apr 2020 01:01:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.10_model.r INFO @ Thu, 16 Apr 2020 01:01:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:01:41: 3000000 INFO @ Thu, 16 Apr 2020 01:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:01:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:01:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.05_summits.bed INFO @ Thu, 16 Apr 2020 01:01:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (10466 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:01:48: 4000000 INFO @ Thu, 16 Apr 2020 01:01:54: 5000000 INFO @ Thu, 16 Apr 2020 01:02:00: 6000000 INFO @ Thu, 16 Apr 2020 01:02:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:07: 7000000 INFO @ Thu, 16 Apr 2020 01:02:13: 8000000 INFO @ Thu, 16 Apr 2020 01:02:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.10_summits.bed INFO @ Thu, 16 Apr 2020 01:02:14: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8208 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:02:15: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:02:15: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:02:15: #1 total tags in treatment: 8441456 INFO @ Thu, 16 Apr 2020 01:02:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:15: #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 01:02:16: #1 tags after filtering in treatment: 8441456 INFO @ Thu, 16 Apr 2020 01:02:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:16: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:17: #2 number of paired peaks: 9059 INFO @ Thu, 16 Apr 2020 01:02:17: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:17: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:17: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:17: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:17: #2 predicted fragment length is 211 bps INFO @ Thu, 16 Apr 2020 01:02:17: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 16 Apr 2020 01:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.20_model.r INFO @ Thu, 16 Apr 2020 01:02:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:02:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:02:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592502/SRX2592502.20_summits.bed INFO @ Thu, 16 Apr 2020 01:02:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5969 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。