Job ID = 6366722 SRX = SRX2228875 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:22:16 prefetch.2.10.7: 1) Downloading 'SRR4380331'... 2020-06-15T23:22:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:33 prefetch.2.10.7: 'SRR4380331' is valid 2020-06-15T23:23:33 prefetch.2.10.7: 1) 'SRR4380331' was downloaded successfully Read 11043257 spots for SRR4380331/SRR4380331.sra Written 11043257 spots for SRR4380331/SRR4380331.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: 00:02:23 11043257 reads; of these: 11043257 (100.00%) were unpaired; of these: 1476427 (13.37%) aligned 0 times 7819007 (70.80%) aligned exactly 1 time 1747823 (15.83%) aligned >1 times 86.63% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 1697146 / 9566830 = 0.1774 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 08:29:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.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 08:29:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:33: 1000000 INFO @ Tue, 16 Jun 2020 08:29:39: 2000000 INFO @ Tue, 16 Jun 2020 08:29:46: 3000000 INFO @ Tue, 16 Jun 2020 08:29:52: 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 @ Tue, 16 Jun 2020 08:29:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.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 08:29:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:59: 5000000 INFO @ Tue, 16 Jun 2020 08:30:04: 1000000 INFO @ Tue, 16 Jun 2020 08:30:06: 6000000 INFO @ Tue, 16 Jun 2020 08:30:11: 2000000 INFO @ Tue, 16 Jun 2020 08:30:12: 7000000 INFO @ Tue, 16 Jun 2020 08:30:18: 3000000 INFO @ Tue, 16 Jun 2020 08:30:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:30:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:30:18: #1 total tags in treatment: 7869684 INFO @ Tue, 16 Jun 2020 08:30:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:18: #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 08:30:18: #1 tags after filtering in treatment: 7869684 INFO @ Tue, 16 Jun 2020 08:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:19: #2 number of paired peaks: 373 WARNING @ Tue, 16 Jun 2020 08:30:19: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:19: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:30:19: #2 alternative fragment length(s) may be 2,51 bps INFO @ Tue, 16 Jun 2020 08:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.05_model.r WARNING @ Tue, 16 Jun 2020 08:30:19: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:19: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Tue, 16 Jun 2020 08:30:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:30:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:25: 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 @ Tue, 16 Jun 2020 08:30:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.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 08:30:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:32: 5000000 INFO @ Tue, 16 Jun 2020 08:30:34: 1000000 INFO @ Tue, 16 Jun 2020 08:30:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:38: 6000000 INFO @ Tue, 16 Jun 2020 08:30:40: 2000000 INFO @ Tue, 16 Jun 2020 08:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.05_summits.bed INFO @ Tue, 16 Jun 2020 08:30:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (638 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:30:45: 7000000 INFO @ Tue, 16 Jun 2020 08:30:47: 3000000 INFO @ Tue, 16 Jun 2020 08:30:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:30:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:30:51: #1 total tags in treatment: 7869684 INFO @ Tue, 16 Jun 2020 08:30:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:51: #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 08:30:51: #1 tags after filtering in treatment: 7869684 INFO @ Tue, 16 Jun 2020 08:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:52: #2 number of paired peaks: 373 WARNING @ Tue, 16 Jun 2020 08:30:52: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:52: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:30:52: #2 alternative fragment length(s) may be 2,51 bps INFO @ Tue, 16 Jun 2020 08:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.10_model.r WARNING @ Tue, 16 Jun 2020 08:30:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:52: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Tue, 16 Jun 2020 08:30:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:30:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:54: 4000000 INFO @ Tue, 16 Jun 2020 08:31:00: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:07: 6000000 INFO @ Tue, 16 Jun 2020 08:31:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:13: 7000000 INFO @ Tue, 16 Jun 2020 08:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:31:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:31:19: #1 total tags in treatment: 7869684 INFO @ Tue, 16 Jun 2020 08:31:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:19: #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 08:31:19: #1 tags after filtering in treatment: 7869684 INFO @ Tue, 16 Jun 2020 08:31:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:20: #2 number of paired peaks: 373 WARNING @ Tue, 16 Jun 2020 08:31:20: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:20: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:31:20: #2 alternative fragment length(s) may be 2,51 bps INFO @ Tue, 16 Jun 2020 08:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.20_model.r WARNING @ Tue, 16 Jun 2020 08:31:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:20: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Tue, 16 Jun 2020 08:31:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:31:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:31:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228875/SRX2228875.20_summits.bed INFO @ Tue, 16 Jun 2020 08:31:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (176 records, 4 fields): 1 millis CompletedMACS2peakCalling