Job ID = 6367299 SRX = SRX331061 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:19:31 prefetch.2.10.7: 1) Downloading 'SRR947285'... 2020-06-15T23:19:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:20:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:20:13 prefetch.2.10.7: 'SRR947285' is valid 2020-06-15T23:20:13 prefetch.2.10.7: 1) 'SRR947285' was downloaded successfully Read 11881109 spots for SRR947285/SRR947285.sra Written 11881109 spots for SRR947285/SRR947285.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: 00:01:48 11881109 reads; of these: 11881109 (100.00%) were unpaired; of these: 314790 (2.65%) aligned 0 times 9549550 (80.38%) aligned exactly 1 time 2016769 (16.97%) aligned >1 times 97.35% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 1247116 / 11566319 = 0.1078 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 08:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.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 08:25:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:21: 1000000 INFO @ Tue, 16 Jun 2020 08:25:27: 2000000 INFO @ Tue, 16 Jun 2020 08:25:33: 3000000 INFO @ Tue, 16 Jun 2020 08:25:39: 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 08:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.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 08:25:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:45: 5000000 INFO @ Tue, 16 Jun 2020 08:25:51: 1000000 INFO @ Tue, 16 Jun 2020 08:25:51: 6000000 INFO @ Tue, 16 Jun 2020 08:25:58: 2000000 INFO @ Tue, 16 Jun 2020 08:25:58: 7000000 INFO @ Tue, 16 Jun 2020 08:26:05: 3000000 INFO @ Tue, 16 Jun 2020 08:26:05: 8000000 INFO @ Tue, 16 Jun 2020 08:26:11: 4000000 INFO @ Tue, 16 Jun 2020 08:26:12: 9000000 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 08:26:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.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 08:26:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:18: 5000000 INFO @ Tue, 16 Jun 2020 08:26:19: 10000000 INFO @ Tue, 16 Jun 2020 08:26:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:26:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:26:21: #1 total tags in treatment: 10319203 INFO @ Tue, 16 Jun 2020 08:26:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:21: #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 08:26:21: 1000000 INFO @ Tue, 16 Jun 2020 08:26:21: #1 tags after filtering in treatment: 10319203 INFO @ Tue, 16 Jun 2020 08:26:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:22: #2 number of paired peaks: 390 WARNING @ Tue, 16 Jun 2020 08:26:22: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:22: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:26:22: #2 alternative fragment length(s) may be 1,25,536,560,570 bps INFO @ Tue, 16 Jun 2020 08:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.05_model.r WARNING @ Tue, 16 Jun 2020 08:26:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:22: #2 You may need to consider one of the other alternative d(s): 1,25,536,560,570 WARNING @ Tue, 16 Jun 2020 08:26:22: #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 08:26:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:25: 6000000 INFO @ Tue, 16 Jun 2020 08:26:27: 2000000 INFO @ Tue, 16 Jun 2020 08:26:32: 7000000 INFO @ Tue, 16 Jun 2020 08:26:34: 3000000 INFO @ Tue, 16 Jun 2020 08:26:38: 8000000 INFO @ Tue, 16 Jun 2020 08:26:40: 4000000 INFO @ Tue, 16 Jun 2020 08:26:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:45: 9000000 INFO @ Tue, 16 Jun 2020 08:26:46: 5000000 INFO @ Tue, 16 Jun 2020 08:26:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.05_summits.bed INFO @ Tue, 16 Jun 2020 08:26:49: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:52: 10000000 INFO @ Tue, 16 Jun 2020 08:26:53: 6000000 INFO @ Tue, 16 Jun 2020 08:26:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:26:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:26:54: #1 total tags in treatment: 10319203 INFO @ Tue, 16 Jun 2020 08:26:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:54: #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 08:26:54: #1 tags after filtering in treatment: 10319203 INFO @ Tue, 16 Jun 2020 08:26:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:55: #2 number of paired peaks: 390 WARNING @ Tue, 16 Jun 2020 08:26:55: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:55: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:26:55: #2 alternative fragment length(s) may be 1,25,536,560,570 bps INFO @ Tue, 16 Jun 2020 08:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.10_model.r WARNING @ Tue, 16 Jun 2020 08:26:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:55: #2 You may need to consider one of the other alternative d(s): 1,25,536,560,570 WARNING @ Tue, 16 Jun 2020 08:26:55: #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 08:26:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:58: 7000000 INFO @ Tue, 16 Jun 2020 08:27:04: 8000000 INFO @ Tue, 16 Jun 2020 08:27:09: 9000000 INFO @ Tue, 16 Jun 2020 08:27:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:15: 10000000 INFO @ Tue, 16 Jun 2020 08:27:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:17: #1 total tags in treatment: 10319203 INFO @ Tue, 16 Jun 2020 08:27:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:17: #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 08:27:17: #1 tags after filtering in treatment: 10319203 INFO @ Tue, 16 Jun 2020 08:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:18: #2 number of paired peaks: 390 WARNING @ Tue, 16 Jun 2020 08:27:18: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:18: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:27:18: #2 alternative fragment length(s) may be 1,25,536,560,570 bps INFO @ Tue, 16 Jun 2020 08:27:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.20_model.r WARNING @ Tue, 16 Jun 2020 08:27:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:18: #2 You may need to consider one of the other alternative d(s): 1,25,536,560,570 WARNING @ Tue, 16 Jun 2020 08:27:18: #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 08:27:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331061/SRX331061.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:44: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling