Job ID = 6497413 SRX = SRX494825 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:13:15 prefetch.2.10.7: 1) Downloading 'SRR1198357'... 2020-06-25T22:13:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:14:58 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:14:59 prefetch.2.10.7: 'SRR1198357' is valid 2020-06-25T22:14:59 prefetch.2.10.7: 1) 'SRR1198357' was downloaded successfully Read 14341533 spots for SRR1198357/SRR1198357.sra Written 14341533 spots for SRR1198357/SRR1198357.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: 00:01:28 14341533 reads; of these: 14341533 (100.00%) were unpaired; of these: 8865289 (61.82%) aligned 0 times 4485245 (31.27%) aligned exactly 1 time 990999 (6.91%) aligned >1 times 38.18% overall alignment rate Time searching: 00:01:28 Overall time: 00:01:28 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_rmdupse_core] 552337 / 5476244 = 0.1009 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 @ Fri, 26 Jun 2020 07:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.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 @ Fri, 26 Jun 2020 07:19:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:19:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:19:13: 1000000 INFO @ Fri, 26 Jun 2020 07:19:19: 2000000 INFO @ Fri, 26 Jun 2020 07:19:25: 3000000 INFO @ Fri, 26 Jun 2020 07:19:30: 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 @ Fri, 26 Jun 2020 07:19:36: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:19:36: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:19:36: #1 total tags in treatment: 4923907 INFO @ Fri, 26 Jun 2020 07:19:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:19:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:19:36: #1 tags after filtering in treatment: 4923907 INFO @ Fri, 26 Jun 2020 07:19:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:19:36: #1 finished! INFO @ Fri, 26 Jun 2020 07:19:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:19:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:19:36: #2 number of paired peaks: 474 WARNING @ Fri, 26 Jun 2020 07:19:36: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Fri, 26 Jun 2020 07:19:36: start model_add_line... INFO @ Fri, 26 Jun 2020 07:19:36: start X-correlation... INFO @ Fri, 26 Jun 2020 07:19:36: end of X-cor INFO @ Fri, 26 Jun 2020 07:19:36: #2 finished! INFO @ Fri, 26 Jun 2020 07:19:36: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 07:19:36: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 26 Jun 2020 07:19:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.05_model.r INFO @ Fri, 26 Jun 2020 07:19:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:19:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.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 @ Fri, 26 Jun 2020 07:19:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:19:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:19:44: 1000000 INFO @ Fri, 26 Jun 2020 07:19:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:19:51: 2000000 INFO @ Fri, 26 Jun 2020 07:19:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:19:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:19:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.05_summits.bed INFO @ Fri, 26 Jun 2020 07:19:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1047 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:19:58: 3000000 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 @ Fri, 26 Jun 2020 07:20:05: 4000000 INFO @ Fri, 26 Jun 2020 07:20:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.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 @ Fri, 26 Jun 2020 07:20:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:20:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:20:12: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:20:12: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:20:12: #1 total tags in treatment: 4923907 INFO @ Fri, 26 Jun 2020 07:20:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:20:12: #1 tags after filtering in treatment: 4923907 INFO @ Fri, 26 Jun 2020 07:20:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:20:12: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:13: #2 number of paired peaks: 474 WARNING @ Fri, 26 Jun 2020 07:20:13: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Fri, 26 Jun 2020 07:20:13: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:13: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:13: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:13: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:13: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 07:20:13: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 26 Jun 2020 07:20:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.10_model.r INFO @ Fri, 26 Jun 2020 07:20:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:20:15: 1000000 INFO @ Fri, 26 Jun 2020 07:20:22: 2000000 INFO @ Fri, 26 Jun 2020 07:20:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:29: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:20:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.10_summits.bed INFO @ Fri, 26 Jun 2020 07:20:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (675 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:20:36: 4000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:20:42: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:20:42: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:20:42: #1 total tags in treatment: 4923907 INFO @ Fri, 26 Jun 2020 07:20:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:20:42: #1 tags after filtering in treatment: 4923907 INFO @ Fri, 26 Jun 2020 07:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:20:42: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:43: #2 number of paired peaks: 474 WARNING @ Fri, 26 Jun 2020 07:20:43: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Fri, 26 Jun 2020 07:20:43: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:43: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:43: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:43: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:43: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 07:20:43: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 26 Jun 2020 07:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.20_model.r INFO @ Fri, 26 Jun 2020 07:20:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:20:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494825/SRX494825.20_summits.bed INFO @ Fri, 26 Jun 2020 07:21:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (424 records, 4 fields): 287 millis CompletedMACS2peakCalling