Job ID = 6527407 SRX = SRX3043413 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:12:30 prefetch.2.10.7: 1) Downloading 'SRR5875897'... 2020-06-29T12:12:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:15:15 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:15:15 prefetch.2.10.7: 1) 'SRR5875897' was downloaded successfully Read 15936085 spots for SRR5875897/SRR5875897.sra Written 15936085 spots for SRR5875897/SRR5875897.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: 00:04:43 15936085 reads; of these: 15936085 (100.00%) were unpaired; of these: 231159 (1.45%) aligned 0 times 13473067 (84.54%) aligned exactly 1 time 2231859 (14.01%) aligned >1 times 98.55% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 1685150 / 15704926 = 0.1073 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 @ Mon, 29 Jun 2020 21:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.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 @ Mon, 29 Jun 2020 21:31:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:31:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:31:17: 1000000 INFO @ Mon, 29 Jun 2020 21:31:24: 2000000 INFO @ Mon, 29 Jun 2020 21:31:30: 3000000 INFO @ Mon, 29 Jun 2020 21:31:36: 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 @ Mon, 29 Jun 2020 21:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.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 @ Mon, 29 Jun 2020 21:31:41: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:31:41: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:31:43: 5000000 INFO @ Mon, 29 Jun 2020 21:31:48: 1000000 INFO @ Mon, 29 Jun 2020 21:31:50: 6000000 INFO @ Mon, 29 Jun 2020 21:31:55: 2000000 INFO @ Mon, 29 Jun 2020 21:31:57: 7000000 INFO @ Mon, 29 Jun 2020 21:32:01: 3000000 INFO @ Mon, 29 Jun 2020 21:32:03: 8000000 INFO @ Mon, 29 Jun 2020 21:32:08: 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 @ Mon, 29 Jun 2020 21:32:10: 9000000 INFO @ Mon, 29 Jun 2020 21:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.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 @ Mon, 29 Jun 2020 21:32:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:32:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:32:15: 5000000 INFO @ Mon, 29 Jun 2020 21:32:18: 10000000 INFO @ Mon, 29 Jun 2020 21:32:18: 1000000 INFO @ Mon, 29 Jun 2020 21:32:22: 6000000 INFO @ Mon, 29 Jun 2020 21:32:26: 11000000 INFO @ Mon, 29 Jun 2020 21:32:26: 2000000 INFO @ Mon, 29 Jun 2020 21:32:30: 7000000 INFO @ Mon, 29 Jun 2020 21:32:33: 3000000 INFO @ Mon, 29 Jun 2020 21:32:33: 12000000 INFO @ Mon, 29 Jun 2020 21:32:37: 8000000 INFO @ Mon, 29 Jun 2020 21:32:40: 4000000 INFO @ Mon, 29 Jun 2020 21:32:41: 13000000 INFO @ Mon, 29 Jun 2020 21:32:44: 9000000 INFO @ Mon, 29 Jun 2020 21:32:48: 5000000 INFO @ Mon, 29 Jun 2020 21:32:48: 14000000 INFO @ Mon, 29 Jun 2020 21:32:49: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:32:49: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:32:49: #1 total tags in treatment: 14019776 INFO @ Mon, 29 Jun 2020 21:32:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:32:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:32:49: #1 tags after filtering in treatment: 14019776 INFO @ Mon, 29 Jun 2020 21:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:32:49: #1 finished! INFO @ Mon, 29 Jun 2020 21:32:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:32:50: #2 number of paired peaks: 133 WARNING @ Mon, 29 Jun 2020 21:32:50: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Mon, 29 Jun 2020 21:32:50: start model_add_line... INFO @ Mon, 29 Jun 2020 21:32:50: start X-correlation... INFO @ Mon, 29 Jun 2020 21:32:50: end of X-cor INFO @ Mon, 29 Jun 2020 21:32:50: #2 finished! INFO @ Mon, 29 Jun 2020 21:32:50: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:32:50: #2 alternative fragment length(s) may be 1,33,54,494 bps INFO @ Mon, 29 Jun 2020 21:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.05_model.r WARNING @ Mon, 29 Jun 2020 21:32:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:32:50: #2 You may need to consider one of the other alternative d(s): 1,33,54,494 WARNING @ Mon, 29 Jun 2020 21:32:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:32:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:32:51: 10000000 INFO @ Mon, 29 Jun 2020 21:32:54: 6000000 INFO @ Mon, 29 Jun 2020 21:32:58: 11000000 INFO @ Mon, 29 Jun 2020 21:33:01: 7000000 INFO @ Mon, 29 Jun 2020 21:33:05: 12000000 INFO @ Mon, 29 Jun 2020 21:33:08: 8000000 INFO @ Mon, 29 Jun 2020 21:33:11: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:33:12: 13000000 INFO @ Mon, 29 Jun 2020 21:33:15: 9000000 INFO @ Mon, 29 Jun 2020 21:33:18: 14000000 INFO @ Mon, 29 Jun 2020 21:33:19: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:33:19: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:33:19: #1 total tags in treatment: 14019776 INFO @ Mon, 29 Jun 2020 21:33:19: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:33:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:33:19: #1 tags after filtering in treatment: 14019776 INFO @ Mon, 29 Jun 2020 21:33:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:33:19: #1 finished! INFO @ Mon, 29 Jun 2020 21:33:19: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:33:20: #2 number of paired peaks: 133 WARNING @ Mon, 29 Jun 2020 21:33:20: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Mon, 29 Jun 2020 21:33:20: start model_add_line... INFO @ Mon, 29 Jun 2020 21:33:20: start X-correlation... INFO @ Mon, 29 Jun 2020 21:33:20: end of X-cor INFO @ Mon, 29 Jun 2020 21:33:20: #2 finished! INFO @ Mon, 29 Jun 2020 21:33:20: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:33:20: #2 alternative fragment length(s) may be 1,33,54,494 bps INFO @ Mon, 29 Jun 2020 21:33:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.10_model.r WARNING @ Mon, 29 Jun 2020 21:33:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:33:20: #2 You may need to consider one of the other alternative d(s): 1,33,54,494 WARNING @ Mon, 29 Jun 2020 21:33:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:33:20: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:33:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:33:21: 10000000 INFO @ Mon, 29 Jun 2020 21:33:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:33:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:33:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.05_summits.bed INFO @ Mon, 29 Jun 2020 21:33:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:33:28: 11000000 INFO @ Mon, 29 Jun 2020 21:33:34: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:33:41: 13000000 INFO @ Mon, 29 Jun 2020 21:33:41: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:33:49: 14000000 INFO @ Mon, 29 Jun 2020 21:33:49: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:33:49: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:33:49: #1 total tags in treatment: 14019776 INFO @ Mon, 29 Jun 2020 21:33:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:33:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:33:49: #1 tags after filtering in treatment: 14019776 INFO @ Mon, 29 Jun 2020 21:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:33:49: #1 finished! INFO @ Mon, 29 Jun 2020 21:33:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:33:50: #2 number of paired peaks: 133 WARNING @ Mon, 29 Jun 2020 21:33:50: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Mon, 29 Jun 2020 21:33:50: start model_add_line... INFO @ Mon, 29 Jun 2020 21:33:50: start X-correlation... INFO @ Mon, 29 Jun 2020 21:33:50: end of X-cor INFO @ Mon, 29 Jun 2020 21:33:50: #2 finished! INFO @ Mon, 29 Jun 2020 21:33:50: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:33:50: #2 alternative fragment length(s) may be 1,33,54,494 bps INFO @ Mon, 29 Jun 2020 21:33:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.20_model.r WARNING @ Mon, 29 Jun 2020 21:33:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:33:50: #2 You may need to consider one of the other alternative d(s): 1,33,54,494 WARNING @ Mon, 29 Jun 2020 21:33:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:33:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:33:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.10_summits.bed INFO @ Mon, 29 Jun 2020 21:33:52: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:34:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:34:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:34:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:34:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3043413/SRX3043413.20_summits.bed INFO @ Mon, 29 Jun 2020 21:34:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling