Job ID = 6528249 SRX = SRX495191 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:51:29 prefetch.2.10.7: 1) Downloading 'SRR1198696'... 2020-06-29T14:51:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:53:34 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:53:35 prefetch.2.10.7: 'SRR1198696' is valid 2020-06-29T14:53:35 prefetch.2.10.7: 1) 'SRR1198696' was downloaded successfully Read 17312339 spots for SRR1198696/SRR1198696.sra Written 17312339 spots for SRR1198696/SRR1198696.sra 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: 00:03:11 17312339 reads; of these: 17312339 (100.00%) were unpaired; of these: 4597892 (26.56%) aligned 0 times 11646742 (67.27%) aligned exactly 1 time 1067705 (6.17%) aligned >1 times 73.44% overall alignment rate Time searching: 00:03:11 Overall time: 00:03:11 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] 2592418 / 12714447 = 0.2039 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 @ Tue, 30 Jun 2020 00:04:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.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 @ Tue, 30 Jun 2020 00:04:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:04:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:05:04: 1000000 INFO @ Tue, 30 Jun 2020 00:05:09: 2000000 INFO @ Tue, 30 Jun 2020 00:05:14: 3000000 INFO @ Tue, 30 Jun 2020 00:05:18: 4000000 INFO @ Tue, 30 Jun 2020 00:05:23: 5000000 INFO @ Tue, 30 Jun 2020 00:05:28: 6000000 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 @ Tue, 30 Jun 2020 00:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.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 @ Tue, 30 Jun 2020 00:05:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:05:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:05:32: 7000000 INFO @ Tue, 30 Jun 2020 00:05:34: 1000000 INFO @ Tue, 30 Jun 2020 00:05:37: 8000000 INFO @ Tue, 30 Jun 2020 00:05:39: 2000000 INFO @ Tue, 30 Jun 2020 00:05:42: 9000000 INFO @ Tue, 30 Jun 2020 00:05:44: 3000000 INFO @ Tue, 30 Jun 2020 00:05:47: 10000000 INFO @ Tue, 30 Jun 2020 00:05:47: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 00:05:47: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 00:05:47: #1 total tags in treatment: 10122029 INFO @ Tue, 30 Jun 2020 00:05:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:05:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:05:47: #1 tags after filtering in treatment: 10122029 INFO @ Tue, 30 Jun 2020 00:05:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:05:47: #1 finished! INFO @ Tue, 30 Jun 2020 00:05:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:05:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:05:48: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 00:05:48: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 00:05:48: start model_add_line... INFO @ Tue, 30 Jun 2020 00:05:48: start X-correlation... INFO @ Tue, 30 Jun 2020 00:05:48: end of X-cor INFO @ Tue, 30 Jun 2020 00:05:48: #2 finished! INFO @ Tue, 30 Jun 2020 00:05:48: #2 predicted fragment length is 9 bps INFO @ Tue, 30 Jun 2020 00:05:48: #2 alternative fragment length(s) may be 9,67,120,167,233,292,523,561,587 bps INFO @ Tue, 30 Jun 2020 00:05:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.05_model.r WARNING @ Tue, 30 Jun 2020 00:05:48: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:05:48: #2 You may need to consider one of the other alternative d(s): 9,67,120,167,233,292,523,561,587 WARNING @ Tue, 30 Jun 2020 00:05:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:05:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:05:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:05:48: 4000000 INFO @ Tue, 30 Jun 2020 00:05:53: 5000000 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 @ Tue, 30 Jun 2020 00:05:58: 6000000 INFO @ Tue, 30 Jun 2020 00:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.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 @ Tue, 30 Jun 2020 00:06:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:06:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:06:03: 7000000 INFO @ Tue, 30 Jun 2020 00:06:05: 1000000 INFO @ Tue, 30 Jun 2020 00:06:07: 8000000 INFO @ Tue, 30 Jun 2020 00:06:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:06:09: 2000000 INFO @ Tue, 30 Jun 2020 00:06:12: 9000000 INFO @ Tue, 30 Jun 2020 00:06:14: 3000000 INFO @ Tue, 30 Jun 2020 00:06:17: 10000000 INFO @ Tue, 30 Jun 2020 00:06:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.05_summits.bed INFO @ Tue, 30 Jun 2020 00:06:17: Done! INFO @ Tue, 30 Jun 2020 00:06:18: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 00:06:18: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 00:06:18: #1 total tags in treatment: 10122029 INFO @ Tue, 30 Jun 2020 00:06:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:06:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:06:18: #1 tags after filtering in treatment: 10122029 INFO @ Tue, 30 Jun 2020 00:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:06:18: #1 finished! INFO @ Tue, 30 Jun 2020 00:06:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:06:18: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 00:06:18: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 00:06:18: start model_add_line... INFO @ Tue, 30 Jun 2020 00:06:18: start X-correlation... INFO @ Tue, 30 Jun 2020 00:06:18: end of X-cor INFO @ Tue, 30 Jun 2020 00:06:18: #2 finished! INFO @ Tue, 30 Jun 2020 00:06:18: #2 predicted fragment length is 9 bps INFO @ Tue, 30 Jun 2020 00:06:18: #2 alternative fragment length(s) may be 9,67,120,167,233,292,523,561,587 bps INFO @ Tue, 30 Jun 2020 00:06:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.10_model.r WARNING @ Tue, 30 Jun 2020 00:06:18: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:06:18: #2 You may need to consider one of the other alternative d(s): 9,67,120,167,233,292,523,561,587 WARNING @ Tue, 30 Jun 2020 00:06:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:06:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:06:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:06:19: 4000000 INFO @ Tue, 30 Jun 2020 00:06:24: 5000000 INFO @ Tue, 30 Jun 2020 00:06:29: 6000000 INFO @ Tue, 30 Jun 2020 00:06:33: 7000000 INFO @ Tue, 30 Jun 2020 00:06:38: 8000000 INFO @ Tue, 30 Jun 2020 00:06:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:06:43: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:06:48: 10000000 INFO @ Tue, 30 Jun 2020 00:06:48: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 00:06:48: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 00:06:48: #1 total tags in treatment: 10122029 INFO @ Tue, 30 Jun 2020 00:06:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:06:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:06:48: #1 tags after filtering in treatment: 10122029 INFO @ Tue, 30 Jun 2020 00:06:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:06:48: #1 finished! INFO @ Tue, 30 Jun 2020 00:06:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.10_summits.bed INFO @ Tue, 30 Jun 2020 00:06:48: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:06:49: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 00:06:49: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 00:06:49: start model_add_line... INFO @ Tue, 30 Jun 2020 00:06:49: start X-correlation... INFO @ Tue, 30 Jun 2020 00:06:49: end of X-cor INFO @ Tue, 30 Jun 2020 00:06:49: #2 finished! INFO @ Tue, 30 Jun 2020 00:06:49: #2 predicted fragment length is 9 bps INFO @ Tue, 30 Jun 2020 00:06:49: #2 alternative fragment length(s) may be 9,67,120,167,233,292,523,561,587 bps INFO @ Tue, 30 Jun 2020 00:06:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.20_model.r WARNING @ Tue, 30 Jun 2020 00:06:49: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:06:49: #2 You may need to consider one of the other alternative d(s): 9,67,120,167,233,292,523,561,587 WARNING @ Tue, 30 Jun 2020 00:06:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:06:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:06:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:07:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495191/SRX495191.20_summits.bed INFO @ Tue, 30 Jun 2020 00:07:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling