Job ID = 5720760 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,882,157 reads read : 25,764,314 reads written : 12,882,157 reads 0-length : 12,882,157 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: 00:05:23 12882157 reads; of these: 12882157 (100.00%) were unpaired; of these: 528114 (4.10%) aligned 0 times 9191067 (71.35%) aligned exactly 1 time 3162976 (24.55%) aligned >1 times 95.90% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 960551 / 12354043 = 0.0778 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 01:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.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 01:28:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:28:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:28:58: 1000000 INFO @ Thu, 16 Apr 2020 01:29:04: 2000000 INFO @ Thu, 16 Apr 2020 01:29:10: 3000000 INFO @ Thu, 16 Apr 2020 01:29:15: 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 01:29:21: 5000000 INFO @ Thu, 16 Apr 2020 01:29:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.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 01:29:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:29:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:29:26: 6000000 INFO @ Thu, 16 Apr 2020 01:29:29: 1000000 INFO @ Thu, 16 Apr 2020 01:29:32: 7000000 INFO @ Thu, 16 Apr 2020 01:29:35: 2000000 INFO @ Thu, 16 Apr 2020 01:29:38: 8000000 INFO @ Thu, 16 Apr 2020 01:29:41: 3000000 INFO @ Thu, 16 Apr 2020 01:29:45: 9000000 INFO @ Thu, 16 Apr 2020 01:29:47: 4000000 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 01:29:51: 10000000 INFO @ Thu, 16 Apr 2020 01:29:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.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 01:29:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:29:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:29:54: 5000000 INFO @ Thu, 16 Apr 2020 01:29:57: 11000000 INFO @ Thu, 16 Apr 2020 01:30:00: 1000000 INFO @ Thu, 16 Apr 2020 01:30:00: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:30:00: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:30:00: #1 total tags in treatment: 11393492 INFO @ Thu, 16 Apr 2020 01:30:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:30:00: #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 01:30:00: 6000000 INFO @ Thu, 16 Apr 2020 01:30:00: #1 tags after filtering in treatment: 11393492 INFO @ Thu, 16 Apr 2020 01:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:30:00: #1 finished! INFO @ Thu, 16 Apr 2020 01:30:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:30:01: #2 number of paired peaks: 676 WARNING @ Thu, 16 Apr 2020 01:30:01: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Thu, 16 Apr 2020 01:30:01: start model_add_line... INFO @ Thu, 16 Apr 2020 01:30:01: start X-correlation... INFO @ Thu, 16 Apr 2020 01:30:01: end of X-cor INFO @ Thu, 16 Apr 2020 01:30:01: #2 finished! INFO @ Thu, 16 Apr 2020 01:30:01: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 01:30:01: #2 alternative fragment length(s) may be 84 bps INFO @ Thu, 16 Apr 2020 01:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.05_model.r WARNING @ Thu, 16 Apr 2020 01:30:01: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:30:01: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Thu, 16 Apr 2020 01:30:01: #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 01:30:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:30:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:30:06: 7000000 INFO @ Thu, 16 Apr 2020 01:30:06: 2000000 INFO @ Thu, 16 Apr 2020 01:30:12: 8000000 INFO @ Thu, 16 Apr 2020 01:30:12: 3000000 INFO @ Thu, 16 Apr 2020 01:30:18: 9000000 INFO @ Thu, 16 Apr 2020 01:30:18: 4000000 INFO @ Thu, 16 Apr 2020 01:30:24: 10000000 INFO @ Thu, 16 Apr 2020 01:30:24: 5000000 INFO @ Thu, 16 Apr 2020 01:30:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:30:30: 11000000 INFO @ Thu, 16 Apr 2020 01:30:31: 6000000 INFO @ Thu, 16 Apr 2020 01:30:33: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:30:33: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:30:33: #1 total tags in treatment: 11393492 INFO @ Thu, 16 Apr 2020 01:30:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:30:33: #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 01:30:33: #1 tags after filtering in treatment: 11393492 INFO @ Thu, 16 Apr 2020 01:30:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:30:33: #1 finished! INFO @ Thu, 16 Apr 2020 01:30:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:30:34: #2 number of paired peaks: 676 WARNING @ Thu, 16 Apr 2020 01:30:34: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Thu, 16 Apr 2020 01:30:34: start model_add_line... INFO @ Thu, 16 Apr 2020 01:30:34: start X-correlation... INFO @ Thu, 16 Apr 2020 01:30:34: end of X-cor INFO @ Thu, 16 Apr 2020 01:30:34: #2 finished! INFO @ Thu, 16 Apr 2020 01:30:34: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 01:30:34: #2 alternative fragment length(s) may be 84 bps INFO @ Thu, 16 Apr 2020 01:30:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.10_model.r WARNING @ Thu, 16 Apr 2020 01:30:34: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:30:34: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Thu, 16 Apr 2020 01:30:34: #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 01:30:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:30:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:30:37: 7000000 INFO @ Thu, 16 Apr 2020 01:30:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:30:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:30:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.05_summits.bed INFO @ Thu, 16 Apr 2020 01:30:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3999 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:30:42: 8000000 INFO @ Thu, 16 Apr 2020 01:30:48: 9000000 INFO @ Thu, 16 Apr 2020 01:30:54: 10000000 INFO @ Thu, 16 Apr 2020 01:30:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:31:00: 11000000 INFO @ Thu, 16 Apr 2020 01:31:02: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:31:02: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:31:02: #1 total tags in treatment: 11393492 INFO @ Thu, 16 Apr 2020 01:31:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:31:02: #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 01:31:02: #1 tags after filtering in treatment: 11393492 INFO @ Thu, 16 Apr 2020 01:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:31:02: #1 finished! INFO @ Thu, 16 Apr 2020 01:31:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:31:03: #2 number of paired peaks: 676 WARNING @ Thu, 16 Apr 2020 01:31:03: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Thu, 16 Apr 2020 01:31:03: start model_add_line... INFO @ Thu, 16 Apr 2020 01:31:03: start X-correlation... INFO @ Thu, 16 Apr 2020 01:31:03: end of X-cor INFO @ Thu, 16 Apr 2020 01:31:03: #2 finished! INFO @ Thu, 16 Apr 2020 01:31:03: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 01:31:03: #2 alternative fragment length(s) may be 84 bps INFO @ Thu, 16 Apr 2020 01:31:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.20_model.r WARNING @ Thu, 16 Apr 2020 01:31:03: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:31:03: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Thu, 16 Apr 2020 01:31:03: #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 01:31:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:31:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:31:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.10_summits.bed INFO @ Thu, 16 Apr 2020 01:31:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1806 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:31:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:31:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226997/SRX5226997.20_summits.bed INFO @ Thu, 16 Apr 2020 01:31:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (705 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。