Job ID = 5720957 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,923,810 reads read : 29,923,810 reads written : 29,923,810 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:32 29923810 reads; of these: 29923810 (100.00%) were unpaired; of these: 8038105 (26.86%) aligned 0 times 15654815 (52.32%) aligned exactly 1 time 6230890 (20.82%) aligned >1 times 73.14% overall alignment rate Time searching: 00:09:33 Overall time: 00:09:33 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 12 files... [bam_rmdupse_core] 12059249 / 21885705 = 0.5510 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 03:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.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 03:55:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:55:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:55:53: 1000000 INFO @ Thu, 16 Apr 2020 03:56:00: 2000000 INFO @ Thu, 16 Apr 2020 03:56:07: 3000000 INFO @ Thu, 16 Apr 2020 03:56:14: 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 03:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.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 03:56:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:56:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:56:21: 5000000 INFO @ Thu, 16 Apr 2020 03:56:23: 1000000 INFO @ Thu, 16 Apr 2020 03:56:28: 6000000 INFO @ Thu, 16 Apr 2020 03:56:30: 2000000 INFO @ Thu, 16 Apr 2020 03:56:36: 7000000 INFO @ Thu, 16 Apr 2020 03:56:36: 3000000 INFO @ Thu, 16 Apr 2020 03:56:43: 4000000 INFO @ Thu, 16 Apr 2020 03:56:43: 8000000 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 03:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.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 03:56:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:56:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:56:49: 5000000 INFO @ Thu, 16 Apr 2020 03:56:51: 9000000 INFO @ Thu, 16 Apr 2020 03:56:53: 1000000 INFO @ Thu, 16 Apr 2020 03:56:56: 6000000 INFO @ Thu, 16 Apr 2020 03:56:57: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:56:57: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:56:57: #1 total tags in treatment: 9826456 INFO @ Thu, 16 Apr 2020 03:56:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:56:57: #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 03:56:57: #1 tags after filtering in treatment: 9826456 INFO @ Thu, 16 Apr 2020 03:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:56:57: #1 finished! INFO @ Thu, 16 Apr 2020 03:56:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:56:58: #2 number of paired peaks: 152 WARNING @ Thu, 16 Apr 2020 03:56:58: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Thu, 16 Apr 2020 03:56:58: start model_add_line... INFO @ Thu, 16 Apr 2020 03:56:58: start X-correlation... INFO @ Thu, 16 Apr 2020 03:56:58: end of X-cor INFO @ Thu, 16 Apr 2020 03:56:58: #2 finished! INFO @ Thu, 16 Apr 2020 03:56:58: #2 predicted fragment length is 57 bps INFO @ Thu, 16 Apr 2020 03:56:58: #2 alternative fragment length(s) may be 57 bps INFO @ Thu, 16 Apr 2020 03:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.05_model.r WARNING @ Thu, 16 Apr 2020 03:56:58: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:56:58: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Thu, 16 Apr 2020 03:56:58: #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 03:56:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:57:00: 2000000 INFO @ Thu, 16 Apr 2020 03:57:03: 7000000 INFO @ Thu, 16 Apr 2020 03:57:06: 3000000 INFO @ Thu, 16 Apr 2020 03:57:09: 8000000 INFO @ Thu, 16 Apr 2020 03:57:13: 4000000 INFO @ Thu, 16 Apr 2020 03:57:16: 9000000 INFO @ Thu, 16 Apr 2020 03:57:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:57:19: 5000000 INFO @ Thu, 16 Apr 2020 03:57:21: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:57:21: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:57:21: #1 total tags in treatment: 9826456 INFO @ Thu, 16 Apr 2020 03:57:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:57:21: #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 03:57:21: #1 tags after filtering in treatment: 9826456 INFO @ Thu, 16 Apr 2020 03:57:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:57:21: #1 finished! INFO @ Thu, 16 Apr 2020 03:57:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:57:22: #2 number of paired peaks: 152 WARNING @ Thu, 16 Apr 2020 03:57:22: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Thu, 16 Apr 2020 03:57:22: start model_add_line... INFO @ Thu, 16 Apr 2020 03:57:22: start X-correlation... INFO @ Thu, 16 Apr 2020 03:57:22: end of X-cor INFO @ Thu, 16 Apr 2020 03:57:22: #2 finished! INFO @ Thu, 16 Apr 2020 03:57:22: #2 predicted fragment length is 57 bps INFO @ Thu, 16 Apr 2020 03:57:22: #2 alternative fragment length(s) may be 57 bps INFO @ Thu, 16 Apr 2020 03:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.10_model.r WARNING @ Thu, 16 Apr 2020 03:57:22: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:57:22: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Thu, 16 Apr 2020 03:57:22: #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 03:57:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:57:25: 6000000 INFO @ Thu, 16 Apr 2020 03:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.05_summits.bed INFO @ Thu, 16 Apr 2020 03:57:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2190 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:57:31: 7000000 INFO @ Thu, 16 Apr 2020 03:57:36: 8000000 INFO @ Thu, 16 Apr 2020 03:57:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:57:42: 9000000 INFO @ Thu, 16 Apr 2020 03:57:46: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:57:46: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:57:46: #1 total tags in treatment: 9826456 INFO @ Thu, 16 Apr 2020 03:57:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:57:46: #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 03:57:47: #1 tags after filtering in treatment: 9826456 INFO @ Thu, 16 Apr 2020 03:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:57:47: #1 finished! INFO @ Thu, 16 Apr 2020 03:57:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:57:47: #2 number of paired peaks: 152 WARNING @ Thu, 16 Apr 2020 03:57:47: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Thu, 16 Apr 2020 03:57:47: start model_add_line... INFO @ Thu, 16 Apr 2020 03:57:47: start X-correlation... INFO @ Thu, 16 Apr 2020 03:57:47: end of X-cor INFO @ Thu, 16 Apr 2020 03:57:47: #2 finished! INFO @ Thu, 16 Apr 2020 03:57:47: #2 predicted fragment length is 57 bps INFO @ Thu, 16 Apr 2020 03:57:47: #2 alternative fragment length(s) may be 57 bps INFO @ Thu, 16 Apr 2020 03:57:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.20_model.r WARNING @ Thu, 16 Apr 2020 03:57:47: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:57:47: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Thu, 16 Apr 2020 03:57:47: #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 03:57:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:57:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:57:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:57:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:57:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.10_summits.bed INFO @ Thu, 16 Apr 2020 03:57:51: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (935 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:58:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:58:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386751/SRX6386751.20_summits.bed INFO @ Thu, 16 Apr 2020 03:58:16: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。