Job ID = 6507893 SRX = SRX494978 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:21:49 prefetch.2.10.7: 1) Downloading 'SRR1198510'... 2020-06-26T13:21:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:23:00 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:23:00 prefetch.2.10.7: 'SRR1198510' is valid 2020-06-26T13:23:00 prefetch.2.10.7: 1) 'SRR1198510' was downloaded successfully Read 16137366 spots for SRR1198510/SRR1198510.sra Written 16137366 spots for SRR1198510/SRR1198510.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: 00:02:18 16137366 reads; of these: 16137366 (100.00%) were unpaired; of these: 921385 (5.71%) aligned 0 times 12433879 (77.05%) aligned exactly 1 time 2782102 (17.24%) aligned >1 times 94.29% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 1283713 / 15215981 = 0.0844 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 22:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.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 22:29:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:31: 1000000 INFO @ Fri, 26 Jun 2020 22:29:36: 2000000 INFO @ Fri, 26 Jun 2020 22:29:41: 3000000 INFO @ Fri, 26 Jun 2020 22:29:46: 4000000 INFO @ Fri, 26 Jun 2020 22:29:51: 5000000 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 22:29:55: 6000000 INFO @ Fri, 26 Jun 2020 22:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.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 22:29:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:30:01: 7000000 INFO @ Fri, 26 Jun 2020 22:30:01: 1000000 INFO @ Fri, 26 Jun 2020 22:30:06: 8000000 INFO @ Fri, 26 Jun 2020 22:30:07: 2000000 INFO @ Fri, 26 Jun 2020 22:30:12: 9000000 INFO @ Fri, 26 Jun 2020 22:30:12: 3000000 INFO @ Fri, 26 Jun 2020 22:30:17: 10000000 INFO @ Fri, 26 Jun 2020 22:30:17: 4000000 INFO @ Fri, 26 Jun 2020 22:30:22: 11000000 INFO @ Fri, 26 Jun 2020 22:30:23: 5000000 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 22:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.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 22:30:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:30:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:30:27: 12000000 INFO @ Fri, 26 Jun 2020 22:30:28: 6000000 INFO @ Fri, 26 Jun 2020 22:30:32: 1000000 INFO @ Fri, 26 Jun 2020 22:30:33: 13000000 INFO @ Fri, 26 Jun 2020 22:30:34: 7000000 INFO @ Fri, 26 Jun 2020 22:30:37: 2000000 INFO @ Fri, 26 Jun 2020 22:30:38: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 22:30:38: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 22:30:38: #1 total tags in treatment: 13932268 INFO @ Fri, 26 Jun 2020 22:30:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:30:38: #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 22:30:38: #1 tags after filtering in treatment: 13932268 INFO @ Fri, 26 Jun 2020 22:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:30:38: #1 finished! INFO @ Fri, 26 Jun 2020 22:30:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:30:39: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 22:30:39: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 22:30:39: start model_add_line... INFO @ Fri, 26 Jun 2020 22:30:39: start X-correlation... INFO @ Fri, 26 Jun 2020 22:30:39: end of X-cor INFO @ Fri, 26 Jun 2020 22:30:39: #2 finished! INFO @ Fri, 26 Jun 2020 22:30:39: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 22:30:39: #2 alternative fragment length(s) may be 2,26,572 bps INFO @ Fri, 26 Jun 2020 22:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.05_model.r WARNING @ Fri, 26 Jun 2020 22:30:39: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:30:39: #2 You may need to consider one of the other alternative d(s): 2,26,572 WARNING @ Fri, 26 Jun 2020 22:30:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:30:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:30:39: 8000000 INFO @ Fri, 26 Jun 2020 22:30:43: 3000000 INFO @ Fri, 26 Jun 2020 22:30:45: 9000000 INFO @ Fri, 26 Jun 2020 22:30:49: 4000000 INFO @ Fri, 26 Jun 2020 22:30:50: 10000000 INFO @ Fri, 26 Jun 2020 22:30:54: 5000000 INFO @ Fri, 26 Jun 2020 22:30:55: 11000000 INFO @ Fri, 26 Jun 2020 22:31:00: 6000000 INFO @ Fri, 26 Jun 2020 22:31:00: 12000000 INFO @ Fri, 26 Jun 2020 22:31:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:31:05: 7000000 INFO @ Fri, 26 Jun 2020 22:31:06: 13000000 INFO @ Fri, 26 Jun 2020 22:31:10: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 22:31:10: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 22:31:10: #1 total tags in treatment: 13932268 INFO @ Fri, 26 Jun 2020 22:31:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:31:10: #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 22:31:11: 8000000 INFO @ Fri, 26 Jun 2020 22:31:11: #1 tags after filtering in treatment: 13932268 INFO @ Fri, 26 Jun 2020 22:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:31:11: #1 finished! INFO @ Fri, 26 Jun 2020 22:31:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:31:12: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 22:31:12: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 22:31:12: start model_add_line... INFO @ Fri, 26 Jun 2020 22:31:12: start X-correlation... INFO @ Fri, 26 Jun 2020 22:31:12: end of X-cor INFO @ Fri, 26 Jun 2020 22:31:12: #2 finished! INFO @ Fri, 26 Jun 2020 22:31:12: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 22:31:12: #2 alternative fragment length(s) may be 2,26,572 bps INFO @ Fri, 26 Jun 2020 22:31:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.10_model.r WARNING @ Fri, 26 Jun 2020 22:31:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:31:12: #2 You may need to consider one of the other alternative d(s): 2,26,572 WARNING @ Fri, 26 Jun 2020 22:31:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:31:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:31:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.05_summits.bed INFO @ Fri, 26 Jun 2020 22:31:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:31:16: 9000000 INFO @ Fri, 26 Jun 2020 22:31:21: 10000000 INFO @ Fri, 26 Jun 2020 22:31:26: 11000000 INFO @ Fri, 26 Jun 2020 22:31:31: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:31:36: 13000000 INFO @ Fri, 26 Jun 2020 22:31:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:31:41: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 22:31:41: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 22:31:41: #1 total tags in treatment: 13932268 INFO @ Fri, 26 Jun 2020 22:31:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:31:41: #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 22:31:41: #1 tags after filtering in treatment: 13932268 INFO @ Fri, 26 Jun 2020 22:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:31:41: #1 finished! INFO @ Fri, 26 Jun 2020 22:31:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:31:42: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 22:31:42: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 22:31:42: start model_add_line... INFO @ Fri, 26 Jun 2020 22:31:42: start X-correlation... INFO @ Fri, 26 Jun 2020 22:31:42: end of X-cor INFO @ Fri, 26 Jun 2020 22:31:42: #2 finished! INFO @ Fri, 26 Jun 2020 22:31:42: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 22:31:42: #2 alternative fragment length(s) may be 2,26,572 bps INFO @ Fri, 26 Jun 2020 22:31:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.20_model.r WARNING @ Fri, 26 Jun 2020 22:31:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:31:42: #2 You may need to consider one of the other alternative d(s): 2,26,572 WARNING @ Fri, 26 Jun 2020 22:31:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:31:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:31:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:31:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:31:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.10_summits.bed INFO @ Fri, 26 Jun 2020 22:31:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:32:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494978/SRX494978.20_summits.bed INFO @ Fri, 26 Jun 2020 22:32:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling