Job ID = 6366536 SRX = SRX1769991 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:43:22 prefetch.2.10.7: 1) Downloading 'SRR3535770'... 2020-06-15T22:43:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:45:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:45:23 prefetch.2.10.7: 1) 'SRR3535770' was downloaded successfully Read 22271448 spots for SRR3535770/SRR3535770.sra Written 22271448 spots for SRR3535770/SRR3535770.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: 00:04:05 22271448 reads; of these: 22271448 (100.00%) were unpaired; of these: 8706381 (39.09%) aligned 0 times 9226984 (41.43%) aligned exactly 1 time 4338083 (19.48%) aligned >1 times 60.91% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 5601861 / 13565067 = 0.4130 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, 16 Jun 2020 07:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.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 @ Tue, 16 Jun 2020 07:53:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:45: 1000000 INFO @ Tue, 16 Jun 2020 07:53:49: 2000000 INFO @ Tue, 16 Jun 2020 07:53:54: 3000000 INFO @ Tue, 16 Jun 2020 07:53:59: 4000000 INFO @ Tue, 16 Jun 2020 07:54:03: 5000000 INFO @ Tue, 16 Jun 2020 07:54:08: 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, 16 Jun 2020 07:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.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 @ Tue, 16 Jun 2020 07:54:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:12: 7000000 INFO @ Tue, 16 Jun 2020 07:54:15: 1000000 INFO @ Tue, 16 Jun 2020 07:54:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:54:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:54:17: #1 total tags in treatment: 7963206 INFO @ Tue, 16 Jun 2020 07:54:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:54:17: #1 tags after filtering in treatment: 7963206 INFO @ Tue, 16 Jun 2020 07:54:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:17: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:18: #2 number of paired peaks: 915 WARNING @ Tue, 16 Jun 2020 07:54:18: Fewer paired peaks (915) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 915 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:18: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:18: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:18: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:18: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:18: #2 predicted fragment length is 217 bps INFO @ Tue, 16 Jun 2020 07:54:18: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 16 Jun 2020 07:54:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.05_model.r INFO @ Tue, 16 Jun 2020 07:54:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:54:19: 2000000 INFO @ Tue, 16 Jun 2020 07:54:24: 3000000 INFO @ Tue, 16 Jun 2020 07:54:29: 4000000 INFO @ Tue, 16 Jun 2020 07:54:33: 5000000 INFO @ Tue, 16 Jun 2020 07:54:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:38: 6000000 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, 16 Jun 2020 07:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.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 @ Tue, 16 Jun 2020 07:54:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:43: 7000000 INFO @ Tue, 16 Jun 2020 07:54:45: 1000000 INFO @ Tue, 16 Jun 2020 07:54:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.05_summits.bed INFO @ Tue, 16 Jun 2020 07:54:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1179 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:54:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:54:47: #1 total tags in treatment: 7963206 INFO @ Tue, 16 Jun 2020 07:54:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:54:47: #1 tags after filtering in treatment: 7963206 INFO @ Tue, 16 Jun 2020 07:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:47: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:48: #2 number of paired peaks: 915 WARNING @ Tue, 16 Jun 2020 07:54:48: Fewer paired peaks (915) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 915 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:48: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:48: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:48: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:48: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:48: #2 predicted fragment length is 217 bps INFO @ Tue, 16 Jun 2020 07:54:48: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 16 Jun 2020 07:54:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.10_model.r INFO @ Tue, 16 Jun 2020 07:54:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:54:49: 2000000 INFO @ Tue, 16 Jun 2020 07:54:54: 3000000 INFO @ Tue, 16 Jun 2020 07:54:59: 4000000 INFO @ Tue, 16 Jun 2020 07:55:03: 5000000 INFO @ Tue, 16 Jun 2020 07:55:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:08: 6000000 INFO @ Tue, 16 Jun 2020 07:55:13: 7000000 INFO @ Tue, 16 Jun 2020 07:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.10_summits.bed INFO @ Tue, 16 Jun 2020 07:55:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (871 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:55:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:55:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:55:17: #1 total tags in treatment: 7963206 INFO @ Tue, 16 Jun 2020 07:55:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:55:17: #1 tags after filtering in treatment: 7963206 INFO @ Tue, 16 Jun 2020 07:55:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:17: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:18: #2 number of paired peaks: 915 WARNING @ Tue, 16 Jun 2020 07:55:18: Fewer paired peaks (915) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 915 pairs to build model! INFO @ Tue, 16 Jun 2020 07:55:18: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:18: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:18: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:18: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:18: #2 predicted fragment length is 217 bps INFO @ Tue, 16 Jun 2020 07:55:18: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 16 Jun 2020 07:55:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.20_model.r INFO @ Tue, 16 Jun 2020 07:55:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:55:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769991/SRX1769991.20_summits.bed INFO @ Tue, 16 Jun 2020 07:55:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 1 millis CompletedMACS2peakCalling