Job ID = 6507969 SRX = SRX514569 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:03:12 prefetch.2.10.7: 1) Downloading 'SRR1230857'... 2020-06-26T14:03:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:05:35 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:05:35 prefetch.2.10.7: 1) 'SRR1230857' was downloaded successfully Read 22858982 spots for SRR1230857/SRR1230857.sra Written 22858982 spots for SRR1230857/SRR1230857.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: 00:05:12 22858982 reads; of these: 22858982 (100.00%) were unpaired; of these: 654321 (2.86%) aligned 0 times 18698534 (81.80%) aligned exactly 1 time 3506127 (15.34%) aligned >1 times 97.14% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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 12 files... [bam_rmdupse_core] 8948116 / 22204661 = 0.4030 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 23:16:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.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 23:16:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:16:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:16:38: 1000000 INFO @ Fri, 26 Jun 2020 23:16:43: 2000000 INFO @ Fri, 26 Jun 2020 23:16:47: 3000000 INFO @ Fri, 26 Jun 2020 23:16:52: 4000000 INFO @ Fri, 26 Jun 2020 23:16:56: 5000000 INFO @ Fri, 26 Jun 2020 23:17:01: 6000000 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 23:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.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 23:17:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:17:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:17:05: 7000000 INFO @ Fri, 26 Jun 2020 23:17:09: 1000000 INFO @ Fri, 26 Jun 2020 23:17:10: 8000000 INFO @ Fri, 26 Jun 2020 23:17:14: 2000000 INFO @ Fri, 26 Jun 2020 23:17:14: 9000000 INFO @ Fri, 26 Jun 2020 23:17:19: 3000000 INFO @ Fri, 26 Jun 2020 23:17:19: 10000000 INFO @ Fri, 26 Jun 2020 23:17:24: 11000000 INFO @ Fri, 26 Jun 2020 23:17:24: 4000000 INFO @ Fri, 26 Jun 2020 23:17:28: 12000000 INFO @ Fri, 26 Jun 2020 23:17:29: 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 23:17:33: 13000000 INFO @ Fri, 26 Jun 2020 23:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.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 23:17:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:17:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:17:34: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:17:34: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:17:34: #1 total tags in treatment: 13256545 INFO @ Fri, 26 Jun 2020 23:17:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:17:34: #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 23:17:34: #1 tags after filtering in treatment: 13256545 INFO @ Fri, 26 Jun 2020 23:17:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:17:34: #1 finished! INFO @ Fri, 26 Jun 2020 23:17:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:17:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:17:35: 6000000 INFO @ Fri, 26 Jun 2020 23:17:35: #2 number of paired peaks: 327 WARNING @ Fri, 26 Jun 2020 23:17:35: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Fri, 26 Jun 2020 23:17:35: start model_add_line... INFO @ Fri, 26 Jun 2020 23:17:35: start X-correlation... INFO @ Fri, 26 Jun 2020 23:17:35: end of X-cor INFO @ Fri, 26 Jun 2020 23:17:35: #2 finished! INFO @ Fri, 26 Jun 2020 23:17:35: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 23:17:35: #2 alternative fragment length(s) may be 2,50,541,575 bps INFO @ Fri, 26 Jun 2020 23:17:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.05_model.r WARNING @ Fri, 26 Jun 2020 23:17:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:17:35: #2 You may need to consider one of the other alternative d(s): 2,50,541,575 WARNING @ Fri, 26 Jun 2020 23:17:35: #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 23:17:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:17:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:17:38: 1000000 INFO @ Fri, 26 Jun 2020 23:17:40: 7000000 INFO @ Fri, 26 Jun 2020 23:17:43: 2000000 INFO @ Fri, 26 Jun 2020 23:17:46: 8000000 INFO @ Fri, 26 Jun 2020 23:17:47: 3000000 INFO @ Fri, 26 Jun 2020 23:17:52: 9000000 INFO @ Fri, 26 Jun 2020 23:17:52: 4000000 INFO @ Fri, 26 Jun 2020 23:17:57: 5000000 INFO @ Fri, 26 Jun 2020 23:17:58: 10000000 INFO @ Fri, 26 Jun 2020 23:18:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:18:02: 6000000 INFO @ Fri, 26 Jun 2020 23:18:03: 11000000 INFO @ Fri, 26 Jun 2020 23:18:06: 7000000 INFO @ Fri, 26 Jun 2020 23:18:09: 12000000 INFO @ Fri, 26 Jun 2020 23:18:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:18:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:18:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.05_summits.bed INFO @ Fri, 26 Jun 2020 23:18:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (749 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:18:11: 8000000 INFO @ Fri, 26 Jun 2020 23:18:14: 13000000 INFO @ Fri, 26 Jun 2020 23:18:16: 9000000 INFO @ Fri, 26 Jun 2020 23:18:16: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:18:16: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:18:16: #1 total tags in treatment: 13256545 INFO @ Fri, 26 Jun 2020 23:18:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:18:16: #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 23:18:16: #1 tags after filtering in treatment: 13256545 INFO @ Fri, 26 Jun 2020 23:18:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:18:16: #1 finished! INFO @ Fri, 26 Jun 2020 23:18:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:18:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:18:17: #2 number of paired peaks: 327 WARNING @ Fri, 26 Jun 2020 23:18:17: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Fri, 26 Jun 2020 23:18:17: start model_add_line... INFO @ Fri, 26 Jun 2020 23:18:17: start X-correlation... INFO @ Fri, 26 Jun 2020 23:18:17: end of X-cor INFO @ Fri, 26 Jun 2020 23:18:17: #2 finished! INFO @ Fri, 26 Jun 2020 23:18:17: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 23:18:17: #2 alternative fragment length(s) may be 2,50,541,575 bps INFO @ Fri, 26 Jun 2020 23:18:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.10_model.r WARNING @ Fri, 26 Jun 2020 23:18:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:18:17: #2 You may need to consider one of the other alternative d(s): 2,50,541,575 WARNING @ Fri, 26 Jun 2020 23:18:17: #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 23:18:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:18:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:18:20: 10000000 INFO @ Fri, 26 Jun 2020 23:18:25: 11000000 INFO @ Fri, 26 Jun 2020 23:18:30: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:18:34: 13000000 INFO @ Fri, 26 Jun 2020 23:18:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:18:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:18:36: #1 total tags in treatment: 13256545 INFO @ Fri, 26 Jun 2020 23:18:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:18:36: #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 23:18:36: #1 tags after filtering in treatment: 13256545 INFO @ Fri, 26 Jun 2020 23:18:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:18:36: #1 finished! INFO @ Fri, 26 Jun 2020 23:18:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:18:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:18:37: #2 number of paired peaks: 327 WARNING @ Fri, 26 Jun 2020 23:18:37: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Fri, 26 Jun 2020 23:18:37: start model_add_line... INFO @ Fri, 26 Jun 2020 23:18:37: start X-correlation... INFO @ Fri, 26 Jun 2020 23:18:37: end of X-cor INFO @ Fri, 26 Jun 2020 23:18:37: #2 finished! INFO @ Fri, 26 Jun 2020 23:18:37: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 23:18:37: #2 alternative fragment length(s) may be 2,50,541,575 bps INFO @ Fri, 26 Jun 2020 23:18:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.20_model.r WARNING @ Fri, 26 Jun 2020 23:18:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:18:37: #2 You may need to consider one of the other alternative d(s): 2,50,541,575 WARNING @ Fri, 26 Jun 2020 23:18:37: #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 23:18:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:18:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.10_summits.bed INFO @ Fri, 26 Jun 2020 23:18:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (473 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:19:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:19:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:19:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:19:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX514569/SRX514569.20_summits.bed INFO @ Fri, 26 Jun 2020 23:19:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 1 millis CompletedMACS2peakCalling