Job ID = 6497508 SRX = SRX495098 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:38:54 prefetch.2.10.7: 1) Downloading 'SRR1198630'... 2020-06-25T21:38:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:40:36 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:40:37 prefetch.2.10.7: 'SRR1198630' is valid 2020-06-25T21:40:37 prefetch.2.10.7: 1) 'SRR1198630' was downloaded successfully Read 13681119 spots for SRR1198630/SRR1198630.sra Written 13681119 spots for SRR1198630/SRR1198630.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:53 13681119 reads; of these: 13681119 (100.00%) were unpaired; of these: 4006489 (29.28%) aligned 0 times 7379847 (53.94%) aligned exactly 1 time 2294783 (16.77%) aligned >1 times 70.72% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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] 2007180 / 9674630 = 0.2075 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 06:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.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 06:47:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:47:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:47:40: 1000000 INFO @ Fri, 26 Jun 2020 06:47:48: 2000000 INFO @ Fri, 26 Jun 2020 06:47:55: 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 @ Fri, 26 Jun 2020 06:48:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.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 06:48:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:48:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:48:03: 4000000 INFO @ Fri, 26 Jun 2020 06:48:10: 1000000 INFO @ Fri, 26 Jun 2020 06:48:11: 5000000 INFO @ Fri, 26 Jun 2020 06:48:18: 2000000 INFO @ Fri, 26 Jun 2020 06:48:19: 6000000 INFO @ Fri, 26 Jun 2020 06:48:26: 3000000 INFO @ Fri, 26 Jun 2020 06:48:27: 7000000 BedGraph に変換中... INFO @ Fri, 26 Jun 2020 06:48:32: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:48:32: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:48:32: #1 total tags in treatment: 7667450 INFO @ Fri, 26 Jun 2020 06:48:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:48:32: #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 06:48:32: #1 tags after filtering in treatment: 7667450 INFO @ Fri, 26 Jun 2020 06:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:48:32: #1 finished! INFO @ Fri, 26 Jun 2020 06:48:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:48:33: #2 number of paired peaks: 775 WARNING @ Fri, 26 Jun 2020 06:48:33: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Fri, 26 Jun 2020 06:48:33: start model_add_line... INFO @ Fri, 26 Jun 2020 06:48:33: start X-correlation... INFO @ Fri, 26 Jun 2020 06:48:33: end of X-cor INFO @ Fri, 26 Jun 2020 06:48:33: #2 finished! INFO @ Fri, 26 Jun 2020 06:48:33: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 06:48:33: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 06:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.05_model.r INFO @ Fri, 26 Jun 2020 06:48:34: 4000000 INFO @ Fri, 26 Jun 2020 06:48:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:48:40: #3 Pre-compute pvalue-qvalue table... 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 06:48:41: 5000000 INFO @ Fri, 26 Jun 2020 06:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.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 06:48:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:48:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:48:49: 6000000 INFO @ Fri, 26 Jun 2020 06:48:51: 1000000 INFO @ Fri, 26 Jun 2020 06:48:58: 7000000 INFO @ Fri, 26 Jun 2020 06:48:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:48:59: 2000000 INFO @ Fri, 26 Jun 2020 06:49:03: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:49:03: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:49:03: #1 total tags in treatment: 7667450 INFO @ Fri, 26 Jun 2020 06:49:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:49:03: #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 06:49:03: #1 tags after filtering in treatment: 7667450 INFO @ Fri, 26 Jun 2020 06:49:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:49:03: #1 finished! INFO @ Fri, 26 Jun 2020 06:49:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:49:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:49:04: #2 number of paired peaks: 775 WARNING @ Fri, 26 Jun 2020 06:49:04: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Fri, 26 Jun 2020 06:49:04: start model_add_line... INFO @ Fri, 26 Jun 2020 06:49:04: start X-correlation... INFO @ Fri, 26 Jun 2020 06:49:04: end of X-cor INFO @ Fri, 26 Jun 2020 06:49:04: #2 finished! INFO @ Fri, 26 Jun 2020 06:49:04: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 06:49:04: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 06:49:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.10_model.r INFO @ Fri, 26 Jun 2020 06:49:07: 3000000 INFO @ Fri, 26 Jun 2020 06:49:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:49:14: 4000000 INFO @ Fri, 26 Jun 2020 06:49:22: 5000000 BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 06:49:29: 6000000 INFO @ Fri, 26 Jun 2020 06:49:36: 7000000 INFO @ Fri, 26 Jun 2020 06:49:41: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:49:41: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:49:41: #1 total tags in treatment: 7667450 INFO @ Fri, 26 Jun 2020 06:49:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:49:41: #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 06:49:41: #1 tags after filtering in treatment: 7667450 INFO @ Fri, 26 Jun 2020 06:49:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:49:41: #1 finished! INFO @ Fri, 26 Jun 2020 06:49:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:49:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:49:42: #2 number of paired peaks: 775 WARNING @ Fri, 26 Jun 2020 06:49:42: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Fri, 26 Jun 2020 06:49:42: start model_add_line... INFO @ Fri, 26 Jun 2020 06:49:42: start X-correlation... INFO @ Fri, 26 Jun 2020 06:49:42: end of X-cor INFO @ Fri, 26 Jun 2020 06:49:42: #2 finished! INFO @ Fri, 26 Jun 2020 06:49:42: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 06:49:42: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 06:49:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.20_model.r BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:49:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:49:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:49:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:49:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:49:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:49:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.05_summits.bed INFO @ Fri, 26 Jun 2020 06:49:42: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (14294 records, 4 fields): 638 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:50:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:50:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.20_summits.bed INFO @ Fri, 26 Jun 2020 06:50:11: Done! INFO @ Fri, 26 Jun 2020 06:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.10_peaks.xls pass1 - making usageList (6 chroms): 1 millis INFO @ Fri, 26 Jun 2020 06:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495098/SRX495098.10_summits.bed pass2 - checking and writing primary data (1660 records, 4 fields): 1126 millis INFO @ Fri, 26 Jun 2020 06:50:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5860 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling