Job ID = 5720392 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,285,434 reads read : 19,285,434 reads written : 19,285,434 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289664.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: 00:03:19 19285434 reads; of these: 19285434 (100.00%) were unpaired; of these: 12447111 (64.54%) aligned 0 times 5407093 (28.04%) aligned exactly 1 time 1431230 (7.42%) aligned >1 times 35.46% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 3852813 / 6838323 = 0.5634 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 00:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.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 00:22:29: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:22:29: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:22:33: 1000000 INFO @ Thu, 16 Apr 2020 00:22:38: 2000000 INFO @ Thu, 16 Apr 2020 00:22:43: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:22:43: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:22:43: #1 total tags in treatment: 2985510 INFO @ Thu, 16 Apr 2020 00:22:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:22:43: #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 00:22:43: #1 tags after filtering in treatment: 2985510 INFO @ Thu, 16 Apr 2020 00:22:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:22:43: #1 finished! INFO @ Thu, 16 Apr 2020 00:22:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:22:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:22:44: #2 number of paired peaks: 205 WARNING @ Thu, 16 Apr 2020 00:22:44: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Thu, 16 Apr 2020 00:22:44: start model_add_line... INFO @ Thu, 16 Apr 2020 00:22:44: start X-correlation... INFO @ Thu, 16 Apr 2020 00:22:44: end of X-cor INFO @ Thu, 16 Apr 2020 00:22:44: #2 finished! INFO @ Thu, 16 Apr 2020 00:22:44: #2 predicted fragment length is 268 bps INFO @ Thu, 16 Apr 2020 00:22:44: #2 alternative fragment length(s) may be 66,268 bps INFO @ Thu, 16 Apr 2020 00:22:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.05_model.r INFO @ Thu, 16 Apr 2020 00:22:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:22:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:22:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.05_summits.bed INFO @ Thu, 16 Apr 2020 00:22:55: Done! 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 00:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.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 00:22:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:22:59: #1 read treatment tags... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11127 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:23:03: 1000000 INFO @ Thu, 16 Apr 2020 00:23:08: 2000000 INFO @ Thu, 16 Apr 2020 00:23:13: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:23:13: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:23:13: #1 total tags in treatment: 2985510 INFO @ Thu, 16 Apr 2020 00:23:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:23:13: #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 00:23:13: #1 tags after filtering in treatment: 2985510 INFO @ Thu, 16 Apr 2020 00:23:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:23:13: #1 finished! INFO @ Thu, 16 Apr 2020 00:23:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:23:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:23:14: #2 number of paired peaks: 205 WARNING @ Thu, 16 Apr 2020 00:23:14: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Thu, 16 Apr 2020 00:23:14: start model_add_line... INFO @ Thu, 16 Apr 2020 00:23:14: start X-correlation... INFO @ Thu, 16 Apr 2020 00:23:14: end of X-cor INFO @ Thu, 16 Apr 2020 00:23:14: #2 finished! INFO @ Thu, 16 Apr 2020 00:23:14: #2 predicted fragment length is 268 bps INFO @ Thu, 16 Apr 2020 00:23:14: #2 alternative fragment length(s) may be 66,268 bps INFO @ Thu, 16 Apr 2020 00:23:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.10_model.r INFO @ Thu, 16 Apr 2020 00:23:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:23:21: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:23:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:23:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:23:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.10_summits.bed INFO @ Thu, 16 Apr 2020 00:23:25: Done! 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 00:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.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 00:23:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:23:28: #1 read treatment tags... pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8770 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:23:33: 1000000 INFO @ Thu, 16 Apr 2020 00:23:38: 2000000 INFO @ Thu, 16 Apr 2020 00:23:42: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:23:42: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:23:42: #1 total tags in treatment: 2985510 INFO @ Thu, 16 Apr 2020 00:23:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:23:42: #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 00:23:42: #1 tags after filtering in treatment: 2985510 INFO @ Thu, 16 Apr 2020 00:23:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:23:42: #1 finished! INFO @ Thu, 16 Apr 2020 00:23:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:23:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:23:43: #2 number of paired peaks: 205 WARNING @ Thu, 16 Apr 2020 00:23:43: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Thu, 16 Apr 2020 00:23:43: start model_add_line... INFO @ Thu, 16 Apr 2020 00:23:43: start X-correlation... INFO @ Thu, 16 Apr 2020 00:23:43: end of X-cor INFO @ Thu, 16 Apr 2020 00:23:43: #2 finished! INFO @ Thu, 16 Apr 2020 00:23:43: #2 predicted fragment length is 268 bps INFO @ Thu, 16 Apr 2020 00:23:43: #2 alternative fragment length(s) may be 66,268 bps INFO @ Thu, 16 Apr 2020 00:23:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.20_model.r INFO @ Thu, 16 Apr 2020 00:23:43: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:23:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:23:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592387/SRX2592387.20_summits.bed INFO @ Thu, 16 Apr 2020 00:23:54: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5950 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。