Job ID = 6507820 SRX = SRX494825 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:53:05 prefetch.2.10.7: 1) Downloading 'SRR1198357'... 2020-06-26T12:53:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:54:12 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:54:12 prefetch.2.10.7: 'SRR1198357' is valid 2020-06-26T12:54:12 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: 00:01:33 14341533 reads; of these: 14341533 (100.00%) were unpaired; of these: 8864940 (61.81%) aligned 0 times 4485537 (31.28%) aligned exactly 1 time 991056 (6.91%) aligned >1 times 38.19% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 552356 / 5476593 = 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 21:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:58:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:58:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:59:02: 1000000 INFO @ Fri, 26 Jun 2020 21:59:11: 2000000 INFO @ Fri, 26 Jun 2020 21:59:20: 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 21:59:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:59:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:59:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:59:29: 4000000 INFO @ Fri, 26 Jun 2020 21:59:33: 1000000 INFO @ Fri, 26 Jun 2020 21:59:37: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 21:59:37: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 21:59:37: #1 total tags in treatment: 4924237 INFO @ Fri, 26 Jun 2020 21:59:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:59:37: #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 21:59:37: #1 tags after filtering in treatment: 4924237 INFO @ Fri, 26 Jun 2020 21:59:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:59:37: #1 finished! INFO @ Fri, 26 Jun 2020 21:59:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:59:37: #2 number of paired peaks: 474 WARNING @ Fri, 26 Jun 2020 21:59:37: 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 21:59:37: start model_add_line... INFO @ Fri, 26 Jun 2020 21:59:37: start X-correlation... INFO @ Fri, 26 Jun 2020 21:59:37: end of X-cor INFO @ Fri, 26 Jun 2020 21:59:37: #2 finished! INFO @ Fri, 26 Jun 2020 21:59:37: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 21:59:37: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 26 Jun 2020 21:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.05_model.r INFO @ Fri, 26 Jun 2020 21:59:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 21:59:42: 2000000 INFO @ Fri, 26 Jun 2020 21:59:48: #3 Call peaks for each chromosome... 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 21:59:51: 3000000 INFO @ Fri, 26 Jun 2020 21:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:59:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:59:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:59:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.05_peaks.xls INFO @ Fri, 26 Jun 2020 21:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 21:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.05_summits.bed INFO @ Fri, 26 Jun 2020 21:59:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1047 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:00:00: 4000000 INFO @ Fri, 26 Jun 2020 22:00:02: 1000000 INFO @ Fri, 26 Jun 2020 22:00:08: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:00:08: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:00:08: #1 total tags in treatment: 4924237 INFO @ Fri, 26 Jun 2020 22:00:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:00:08: #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 22:00:09: #1 tags after filtering in treatment: 4924237 INFO @ Fri, 26 Jun 2020 22:00:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:00:09: #1 finished! INFO @ Fri, 26 Jun 2020 22:00:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:00:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:00:09: #2 number of paired peaks: 474 WARNING @ Fri, 26 Jun 2020 22:00:09: 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 22:00:09: start model_add_line... INFO @ Fri, 26 Jun 2020 22:00:09: start X-correlation... INFO @ Fri, 26 Jun 2020 22:00:09: end of X-cor INFO @ Fri, 26 Jun 2020 22:00:09: #2 finished! INFO @ Fri, 26 Jun 2020 22:00:09: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 22:00:09: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 26 Jun 2020 22:00:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.10_model.r INFO @ Fri, 26 Jun 2020 22:00:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:00:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:00:11: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:00:20: 3000000 INFO @ Fri, 26 Jun 2020 22:00:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.10_summits.bed INFO @ Fri, 26 Jun 2020 22:00:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (675 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:00:29: 4000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:00:37: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:00:37: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:00:37: #1 total tags in treatment: 4924237 INFO @ Fri, 26 Jun 2020 22:00:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:00:37: #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 22:00:37: #1 tags after filtering in treatment: 4924237 INFO @ Fri, 26 Jun 2020 22:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:00:37: #1 finished! INFO @ Fri, 26 Jun 2020 22:00:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:00:37: #2 number of paired peaks: 474 WARNING @ Fri, 26 Jun 2020 22:00:37: 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 22:00:37: start model_add_line... INFO @ Fri, 26 Jun 2020 22:00:37: start X-correlation... INFO @ Fri, 26 Jun 2020 22:00:37: end of X-cor INFO @ Fri, 26 Jun 2020 22:00:37: #2 finished! INFO @ Fri, 26 Jun 2020 22:00:37: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 22:00:37: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 26 Jun 2020 22:00:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.20_model.r INFO @ Fri, 26 Jun 2020 22:00:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:00:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:00:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:00:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:00:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:00:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494825/SRX494825.20_summits.bed INFO @ Fri, 26 Jun 2020 22:00:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 3 millis CompletedMACS2peakCalling