Job ID = 10165882 SRX = SRX8832066 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:04:22 20583358 reads; of these: 20583358 (100.00%) were unpaired; of these: 932684 (4.53%) aligned 0 times 16902259 (82.12%) aligned exactly 1 time 2748415 (13.35%) aligned >1 times 95.47% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4426090 / 19650674 = 0.2252 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, 08 Oct 2020 20:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 08 Oct 2020 20:15:25: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:15:25: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:15:32: 1000000 INFO @ Thu, 08 Oct 2020 20:15:39: 2000000 INFO @ Thu, 08 Oct 2020 20:15:46: 3000000 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, 08 Oct 2020 20:15:53: 4000000 INFO @ Thu, 08 Oct 2020 20:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 08 Oct 2020 20:15:54: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:15:54: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:15:59: 5000000 INFO @ Thu, 08 Oct 2020 20:16:00: 1000000 INFO @ Thu, 08 Oct 2020 20:16:05: 6000000 INFO @ Thu, 08 Oct 2020 20:16:06: 2000000 INFO @ Thu, 08 Oct 2020 20:16:11: 7000000 INFO @ Thu, 08 Oct 2020 20:16:12: 3000000 INFO @ Thu, 08 Oct 2020 20:16:17: 8000000 INFO @ Thu, 08 Oct 2020 20:16:18: 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, 08 Oct 2020 20:16:23: 9000000 INFO @ Thu, 08 Oct 2020 20:16:24: 5000000 INFO @ Thu, 08 Oct 2020 20:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 08 Oct 2020 20:16:24: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:16:24: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:16:29: 10000000 INFO @ Thu, 08 Oct 2020 20:16:29: 6000000 INFO @ Thu, 08 Oct 2020 20:16:30: 1000000 INFO @ Thu, 08 Oct 2020 20:16:35: 7000000 INFO @ Thu, 08 Oct 2020 20:16:35: 11000000 INFO @ Thu, 08 Oct 2020 20:16:36: 2000000 INFO @ Thu, 08 Oct 2020 20:16:41: 8000000 INFO @ Thu, 08 Oct 2020 20:16:42: 3000000 INFO @ Thu, 08 Oct 2020 20:16:42: 12000000 INFO @ Thu, 08 Oct 2020 20:16:47: 9000000 INFO @ Thu, 08 Oct 2020 20:16:48: 4000000 INFO @ Thu, 08 Oct 2020 20:16:50: 13000000 INFO @ Thu, 08 Oct 2020 20:16:53: 10000000 INFO @ Thu, 08 Oct 2020 20:16:54: 5000000 INFO @ Thu, 08 Oct 2020 20:16:56: 14000000 INFO @ Thu, 08 Oct 2020 20:16:59: 11000000 INFO @ Thu, 08 Oct 2020 20:17:00: 6000000 INFO @ Thu, 08 Oct 2020 20:17:03: 15000000 INFO @ Thu, 08 Oct 2020 20:17:04: 12000000 INFO @ Thu, 08 Oct 2020 20:17:05: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:17:05: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:17:05: #1 total tags in treatment: 15224584 INFO @ Thu, 08 Oct 2020 20:17:05: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:17:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:17:05: #1 tags after filtering in treatment: 15224584 INFO @ Thu, 08 Oct 2020 20:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:17:05: #1 finished! INFO @ Thu, 08 Oct 2020 20:17:05: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:17:06: #2 number of paired peaks: 907 WARNING @ Thu, 08 Oct 2020 20:17:06: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Thu, 08 Oct 2020 20:17:06: start model_add_line... INFO @ Thu, 08 Oct 2020 20:17:06: start X-correlation... INFO @ Thu, 08 Oct 2020 20:17:06: end of X-cor INFO @ Thu, 08 Oct 2020 20:17:06: #2 finished! INFO @ Thu, 08 Oct 2020 20:17:06: #2 predicted fragment length is 178 bps INFO @ Thu, 08 Oct 2020 20:17:06: #2 alternative fragment length(s) may be 4,178 bps INFO @ Thu, 08 Oct 2020 20:17:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.05_model.r INFO @ Thu, 08 Oct 2020 20:17:06: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:17:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:17:06: 7000000 INFO @ Thu, 08 Oct 2020 20:17:10: 13000000 INFO @ Thu, 08 Oct 2020 20:17:12: 8000000 INFO @ Thu, 08 Oct 2020 20:17:16: 14000000 INFO @ Thu, 08 Oct 2020 20:17:18: 9000000 INFO @ Thu, 08 Oct 2020 20:17:22: 15000000 INFO @ Thu, 08 Oct 2020 20:17:23: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:17:23: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:17:23: #1 total tags in treatment: 15224584 INFO @ Thu, 08 Oct 2020 20:17:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:17:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:17:23: #1 tags after filtering in treatment: 15224584 INFO @ Thu, 08 Oct 2020 20:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:17:23: #1 finished! INFO @ Thu, 08 Oct 2020 20:17:23: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:17:24: 10000000 INFO @ Thu, 08 Oct 2020 20:17:24: #2 number of paired peaks: 907 WARNING @ Thu, 08 Oct 2020 20:17:24: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Thu, 08 Oct 2020 20:17:24: start model_add_line... INFO @ Thu, 08 Oct 2020 20:17:24: start X-correlation... INFO @ Thu, 08 Oct 2020 20:17:24: end of X-cor INFO @ Thu, 08 Oct 2020 20:17:24: #2 finished! INFO @ Thu, 08 Oct 2020 20:17:24: #2 predicted fragment length is 178 bps INFO @ Thu, 08 Oct 2020 20:17:24: #2 alternative fragment length(s) may be 4,178 bps INFO @ Thu, 08 Oct 2020 20:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.10_model.r INFO @ Thu, 08 Oct 2020 20:17:24: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:17:29: 11000000 INFO @ Thu, 08 Oct 2020 20:17:35: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:17:41: 13000000 INFO @ Thu, 08 Oct 2020 20:17:42: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:17:46: 14000000 INFO @ Thu, 08 Oct 2020 20:17:52: 15000000 INFO @ Thu, 08 Oct 2020 20:17:53: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:17:53: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:17:53: #1 total tags in treatment: 15224584 INFO @ Thu, 08 Oct 2020 20:17:53: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:17:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:17:53: #1 tags after filtering in treatment: 15224584 INFO @ Thu, 08 Oct 2020 20:17:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:17:53: #1 finished! INFO @ Thu, 08 Oct 2020 20:17:53: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:17:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:17:54: #2 number of paired peaks: 907 WARNING @ Thu, 08 Oct 2020 20:17:54: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Thu, 08 Oct 2020 20:17:54: start model_add_line... INFO @ Thu, 08 Oct 2020 20:17:54: start X-correlation... INFO @ Thu, 08 Oct 2020 20:17:54: end of X-cor INFO @ Thu, 08 Oct 2020 20:17:54: #2 finished! INFO @ Thu, 08 Oct 2020 20:17:54: #2 predicted fragment length is 178 bps INFO @ Thu, 08 Oct 2020 20:17:54: #2 alternative fragment length(s) may be 4,178 bps INFO @ Thu, 08 Oct 2020 20:17:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.20_model.r INFO @ Thu, 08 Oct 2020 20:17:54: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:17:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:17:59: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.05_summits.bed INFO @ Thu, 08 Oct 2020 20:18:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8899 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:18:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:18:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:18:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.10_summits.bed INFO @ Thu, 08 Oct 2020 20:18:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6662 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:18:30: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:18:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:18:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:18:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832066/SRX8832066.20_summits.bed INFO @ Thu, 08 Oct 2020 20:18:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3873 records, 4 fields): 5 millis CompletedMACS2peakCalling