Job ID = 5720427 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,377,851 reads read : 11,377,851 reads written : 11,377,851 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289681.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: 00:03:03 11377851 reads; of these: 11377851 (100.00%) were unpaired; of these: 3256550 (28.62%) aligned 0 times 6388471 (56.15%) aligned exactly 1 time 1732830 (15.23%) aligned >1 times 71.38% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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] 673367 / 8121301 = 0.0829 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 00:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.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 00:30:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:30:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:30:11: 1000000 INFO @ Thu, 16 Apr 2020 00:30:17: 2000000 INFO @ Thu, 16 Apr 2020 00:30:22: 3000000 INFO @ Thu, 16 Apr 2020 00:30:28: 4000000 INFO @ Thu, 16 Apr 2020 00:30:33: 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 00:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.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 00:30:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:30:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:30:39: 6000000 INFO @ Thu, 16 Apr 2020 00:30:41: 1000000 INFO @ Thu, 16 Apr 2020 00:30:45: 7000000 INFO @ Thu, 16 Apr 2020 00:30:47: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:30:47: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:30:47: #1 total tags in treatment: 7447934 INFO @ Thu, 16 Apr 2020 00:30:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:30:47: #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 00:30:47: #1 tags after filtering in treatment: 7447934 INFO @ Thu, 16 Apr 2020 00:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:30:47: #1 finished! INFO @ Thu, 16 Apr 2020 00:30:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:30:48: 2000000 INFO @ Thu, 16 Apr 2020 00:30:48: #2 number of paired peaks: 318 WARNING @ Thu, 16 Apr 2020 00:30:48: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Thu, 16 Apr 2020 00:30:48: start model_add_line... INFO @ Thu, 16 Apr 2020 00:30:48: start X-correlation... INFO @ Thu, 16 Apr 2020 00:30:48: end of X-cor INFO @ Thu, 16 Apr 2020 00:30:48: #2 finished! INFO @ Thu, 16 Apr 2020 00:30:48: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:30:48: #2 alternative fragment length(s) may be 55 bps INFO @ Thu, 16 Apr 2020 00:30:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.05_model.r WARNING @ Thu, 16 Apr 2020 00:30:48: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:30:48: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Thu, 16 Apr 2020 00:30:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:30:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:30:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:30:53: 3000000 INFO @ Thu, 16 Apr 2020 00:30:59: 4000000 INFO @ Thu, 16 Apr 2020 00:31:03: #3 Call peaks for each chromosome... 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 00:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.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 00:31:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:31:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:31:05: 5000000 INFO @ Thu, 16 Apr 2020 00:31:11: 1000000 INFO @ Thu, 16 Apr 2020 00:31:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:31:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:31:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.05_summits.bed INFO @ Thu, 16 Apr 2020 00:31:11: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1639 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:31:12: 6000000 INFO @ Thu, 16 Apr 2020 00:31:18: 2000000 INFO @ Thu, 16 Apr 2020 00:31:18: 7000000 INFO @ Thu, 16 Apr 2020 00:31:21: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:31:21: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:31:21: #1 total tags in treatment: 7447934 INFO @ Thu, 16 Apr 2020 00:31:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:31:21: #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 00:31:21: #1 tags after filtering in treatment: 7447934 INFO @ Thu, 16 Apr 2020 00:31:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:31:21: #1 finished! INFO @ Thu, 16 Apr 2020 00:31:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:31:22: #2 number of paired peaks: 318 WARNING @ Thu, 16 Apr 2020 00:31:22: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Thu, 16 Apr 2020 00:31:22: start model_add_line... INFO @ Thu, 16 Apr 2020 00:31:22: start X-correlation... INFO @ Thu, 16 Apr 2020 00:31:22: end of X-cor INFO @ Thu, 16 Apr 2020 00:31:22: #2 finished! INFO @ Thu, 16 Apr 2020 00:31:22: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:31:22: #2 alternative fragment length(s) may be 55 bps INFO @ Thu, 16 Apr 2020 00:31:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.10_model.r WARNING @ Thu, 16 Apr 2020 00:31:22: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:31:22: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Thu, 16 Apr 2020 00:31:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:31:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:31:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:31:24: 3000000 INFO @ Thu, 16 Apr 2020 00:31:30: 4000000 INFO @ Thu, 16 Apr 2020 00:31:36: 5000000 INFO @ Thu, 16 Apr 2020 00:31:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:31:41: 6000000 INFO @ Thu, 16 Apr 2020 00:31:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:31:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:31:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.10_summits.bed INFO @ Thu, 16 Apr 2020 00:31:45: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (916 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:31:46: 7000000 INFO @ Thu, 16 Apr 2020 00:31:49: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:31:49: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:31:49: #1 total tags in treatment: 7447934 INFO @ Thu, 16 Apr 2020 00:31:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:31:49: #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 00:31:49: #1 tags after filtering in treatment: 7447934 INFO @ Thu, 16 Apr 2020 00:31:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:31:49: #1 finished! INFO @ Thu, 16 Apr 2020 00:31:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:31:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:31:49: #2 number of paired peaks: 318 WARNING @ Thu, 16 Apr 2020 00:31:49: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Thu, 16 Apr 2020 00:31:49: start model_add_line... INFO @ Thu, 16 Apr 2020 00:31:49: start X-correlation... INFO @ Thu, 16 Apr 2020 00:31:49: end of X-cor INFO @ Thu, 16 Apr 2020 00:31:49: #2 finished! INFO @ Thu, 16 Apr 2020 00:31:49: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:31:49: #2 alternative fragment length(s) may be 55 bps INFO @ Thu, 16 Apr 2020 00:31:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.20_model.r WARNING @ Thu, 16 Apr 2020 00:31:50: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:31:50: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Thu, 16 Apr 2020 00:31:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:31:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:32:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592404/SRX2592404.20_summits.bed INFO @ Thu, 16 Apr 2020 00:32:13: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (604 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。