Job ID = 5720904 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,826,584 reads read : 20,826,584 reads written : 20,826,584 rm: cannot remove ‘[DSE]RR*’: 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: 00:08:02 20826584 reads; of these: 20826584 (100.00%) were unpaired; of these: 2190531 (10.52%) aligned 0 times 12833386 (61.62%) aligned exactly 1 time 5802667 (27.86%) aligned >1 times 89.48% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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] 12564428 / 18636053 = 0.6742 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 03:22:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.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 03:22:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:22:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:22:28: 1000000 INFO @ Thu, 16 Apr 2020 03:22:34: 2000000 INFO @ Thu, 16 Apr 2020 03:22:40: 3000000 INFO @ Thu, 16 Apr 2020 03:22:46: 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 03:22:51: 5000000 INFO @ Thu, 16 Apr 2020 03:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.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 03:22:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:22:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:22:57: 6000000 INFO @ Thu, 16 Apr 2020 03:22:58: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:22:58: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:22:58: #1 total tags in treatment: 6071625 INFO @ Thu, 16 Apr 2020 03:22:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:22:58: #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 03:22:58: #1 tags after filtering in treatment: 6071625 INFO @ Thu, 16 Apr 2020 03:22:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:22:58: #1 finished! INFO @ Thu, 16 Apr 2020 03:22:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:22:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:22:58: #2 number of paired peaks: 924 WARNING @ Thu, 16 Apr 2020 03:22:58: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Thu, 16 Apr 2020 03:22:58: start model_add_line... INFO @ Thu, 16 Apr 2020 03:22:59: start X-correlation... INFO @ Thu, 16 Apr 2020 03:22:59: end of X-cor INFO @ Thu, 16 Apr 2020 03:22:59: #2 finished! INFO @ Thu, 16 Apr 2020 03:22:59: #2 predicted fragment length is 77 bps INFO @ Thu, 16 Apr 2020 03:22:59: #2 alternative fragment length(s) may be 77 bps INFO @ Thu, 16 Apr 2020 03:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.05_model.r WARNING @ Thu, 16 Apr 2020 03:22:59: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:22:59: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Thu, 16 Apr 2020 03:22:59: #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 03:22:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:22:59: 1000000 INFO @ Thu, 16 Apr 2020 03:23:05: 2000000 INFO @ Thu, 16 Apr 2020 03:23:11: 3000000 INFO @ Thu, 16 Apr 2020 03:23:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:23:16: 4000000 INFO @ Thu, 16 Apr 2020 03:23:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:23:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:23:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.05_summits.bed INFO @ Thu, 16 Apr 2020 03:23:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4523 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 03:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.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 03:23:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:23:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:23:23: 5000000 INFO @ Thu, 16 Apr 2020 03:23:28: 1000000 INFO @ Thu, 16 Apr 2020 03:23:29: 6000000 INFO @ Thu, 16 Apr 2020 03:23:29: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:23:29: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:23:29: #1 total tags in treatment: 6071625 INFO @ Thu, 16 Apr 2020 03:23:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:23:29: #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 03:23:30: #1 tags after filtering in treatment: 6071625 INFO @ Thu, 16 Apr 2020 03:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:23:30: #1 finished! INFO @ Thu, 16 Apr 2020 03:23:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:23:30: #2 number of paired peaks: 924 WARNING @ Thu, 16 Apr 2020 03:23:30: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Thu, 16 Apr 2020 03:23:30: start model_add_line... INFO @ Thu, 16 Apr 2020 03:23:30: start X-correlation... INFO @ Thu, 16 Apr 2020 03:23:30: end of X-cor INFO @ Thu, 16 Apr 2020 03:23:30: #2 finished! INFO @ Thu, 16 Apr 2020 03:23:30: #2 predicted fragment length is 77 bps INFO @ Thu, 16 Apr 2020 03:23:30: #2 alternative fragment length(s) may be 77 bps INFO @ Thu, 16 Apr 2020 03:23:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.10_model.r WARNING @ Thu, 16 Apr 2020 03:23:30: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:23:30: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Thu, 16 Apr 2020 03:23:30: #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 03:23:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:23:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:23:35: 2000000 INFO @ Thu, 16 Apr 2020 03:23:41: 3000000 INFO @ Thu, 16 Apr 2020 03:23:43: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:23:47: 4000000 INFO @ Thu, 16 Apr 2020 03:23:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.10_summits.bed INFO @ Thu, 16 Apr 2020 03:23:50: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1493 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:23:53: 5000000 INFO @ Thu, 16 Apr 2020 03:23:58: 6000000 INFO @ Thu, 16 Apr 2020 03:23:59: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:23:59: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:23:59: #1 total tags in treatment: 6071625 INFO @ Thu, 16 Apr 2020 03:23:59: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:23:59: #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 03:23:59: #1 tags after filtering in treatment: 6071625 INFO @ Thu, 16 Apr 2020 03:23:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:23:59: #1 finished! INFO @ Thu, 16 Apr 2020 03:23:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:23:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:23:59: #2 number of paired peaks: 924 WARNING @ Thu, 16 Apr 2020 03:23:59: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Thu, 16 Apr 2020 03:23:59: start model_add_line... INFO @ Thu, 16 Apr 2020 03:23:59: start X-correlation... INFO @ Thu, 16 Apr 2020 03:23:59: end of X-cor INFO @ Thu, 16 Apr 2020 03:23:59: #2 finished! INFO @ Thu, 16 Apr 2020 03:23:59: #2 predicted fragment length is 77 bps INFO @ Thu, 16 Apr 2020 03:23:59: #2 alternative fragment length(s) may be 77 bps INFO @ Thu, 16 Apr 2020 03:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.20_model.r WARNING @ Thu, 16 Apr 2020 03:23:59: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:23:59: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Thu, 16 Apr 2020 03:23:59: #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 03:23:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:24:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:24:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:24:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:24:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775931/SRX5775931.20_summits.bed INFO @ Thu, 16 Apr 2020 03:24:20: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。