Job ID = 5720666 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,812,484 reads read : 8,812,484 reads written : 8,812,484 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289762.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:40 8812484 reads; of these: 8812484 (100.00%) were unpaired; of these: 4141284 (46.99%) aligned 0 times 3819027 (43.34%) aligned exactly 1 time 852173 (9.67%) aligned >1 times 53.01% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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_rmdupse_core] 441410 / 4671200 = 0.0945 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 00:52:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.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 00:52:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:52:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:52:57: 1000000 INFO @ Thu, 16 Apr 2020 00:53:03: 2000000 INFO @ Thu, 16 Apr 2020 00:53:08: 3000000 INFO @ Thu, 16 Apr 2020 00:53:14: 4000000 INFO @ Thu, 16 Apr 2020 00:53:15: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:53:15: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:53:15: #1 total tags in treatment: 4229790 INFO @ Thu, 16 Apr 2020 00:53:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:53:15: #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 00:53:15: #1 tags after filtering in treatment: 4229790 INFO @ Thu, 16 Apr 2020 00:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:53:15: #1 finished! INFO @ Thu, 16 Apr 2020 00:53:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:53:16: #2 number of paired peaks: 3451 INFO @ Thu, 16 Apr 2020 00:53:16: start model_add_line... INFO @ Thu, 16 Apr 2020 00:53:16: start X-correlation... INFO @ Thu, 16 Apr 2020 00:53:16: end of X-cor INFO @ Thu, 16 Apr 2020 00:53:16: #2 finished! INFO @ Thu, 16 Apr 2020 00:53:16: #2 predicted fragment length is 141 bps INFO @ Thu, 16 Apr 2020 00:53:16: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 16 Apr 2020 00:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.05_model.r INFO @ Thu, 16 Apr 2020 00:53:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:53:16: #3 Pre-compute pvalue-qvalue table... 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 00:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.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 00:53:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:53:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:53:27: 1000000 INFO @ Thu, 16 Apr 2020 00:53:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:53:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:53:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.05_summits.bed INFO @ Thu, 16 Apr 2020 00:53:32: Done! INFO @ Thu, 16 Apr 2020 00:53:33: 2000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6688 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:53:39: 3000000 INFO @ Thu, 16 Apr 2020 00:53:44: 4000000 INFO @ Thu, 16 Apr 2020 00:53:45: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:53:45: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:53:45: #1 total tags in treatment: 4229790 INFO @ Thu, 16 Apr 2020 00:53:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:53:45: #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 00:53:45: #1 tags after filtering in treatment: 4229790 INFO @ Thu, 16 Apr 2020 00:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:53:45: #1 finished! INFO @ Thu, 16 Apr 2020 00:53:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:53:46: #2 number of paired peaks: 3451 INFO @ Thu, 16 Apr 2020 00:53:46: start model_add_line... INFO @ Thu, 16 Apr 2020 00:53:46: start X-correlation... INFO @ Thu, 16 Apr 2020 00:53:46: end of X-cor INFO @ Thu, 16 Apr 2020 00:53:46: #2 finished! INFO @ Thu, 16 Apr 2020 00:53:46: #2 predicted fragment length is 141 bps INFO @ Thu, 16 Apr 2020 00:53:46: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 16 Apr 2020 00:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.10_model.r INFO @ Thu, 16 Apr 2020 00:53:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:53:46: #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 00:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.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 00:53:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:53:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:53:57: 1000000 INFO @ Thu, 16 Apr 2020 00:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.10_summits.bed INFO @ Thu, 16 Apr 2020 00:54:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3713 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:54:03: 2000000 INFO @ Thu, 16 Apr 2020 00:54:09: 3000000 INFO @ Thu, 16 Apr 2020 00:54:14: 4000000 INFO @ Thu, 16 Apr 2020 00:54:16: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:54:16: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:54:16: #1 total tags in treatment: 4229790 INFO @ Thu, 16 Apr 2020 00:54:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:54:16: #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 00:54:16: #1 tags after filtering in treatment: 4229790 INFO @ Thu, 16 Apr 2020 00:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:54:16: #1 finished! INFO @ Thu, 16 Apr 2020 00:54:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:54:16: #2 number of paired peaks: 3451 INFO @ Thu, 16 Apr 2020 00:54:16: start model_add_line... INFO @ Thu, 16 Apr 2020 00:54:16: start X-correlation... INFO @ Thu, 16 Apr 2020 00:54:16: end of X-cor INFO @ Thu, 16 Apr 2020 00:54:16: #2 finished! INFO @ Thu, 16 Apr 2020 00:54:16: #2 predicted fragment length is 141 bps INFO @ Thu, 16 Apr 2020 00:54:16: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 16 Apr 2020 00:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.20_model.r INFO @ Thu, 16 Apr 2020 00:54:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:54:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:54:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:54:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:54:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592485/SRX2592485.20_summits.bed INFO @ Thu, 16 Apr 2020 00:54:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1653 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。