Job ID = 6367921 SRX = SRX4200530 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:42:03 prefetch.2.10.7: 1) Downloading 'SRR7297996'... 2020-06-15T23:42:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:05 prefetch.2.10.7: 1) 'SRR7297996' was downloaded successfully 2020-06-15T23:48:05 prefetch.2.10.7: 'SRR7297996' has 0 unresolved dependencies Read 24414932 spots for SRR7297996/SRR7297996.sra Written 24414932 spots for SRR7297996/SRR7297996.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: 00:11:26 24414932 reads; of these: 24414932 (100.00%) were unpaired; of these: 1615291 (6.62%) aligned 0 times 18748488 (76.79%) aligned exactly 1 time 4051153 (16.59%) aligned >1 times 93.38% overall alignment rate Time searching: 00:11:26 Overall time: 00:11:26 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] 12533243 / 22799641 = 0.5497 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 09:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.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 09:09:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:08: 1000000 INFO @ Tue, 16 Jun 2020 09:09:15: 2000000 INFO @ Tue, 16 Jun 2020 09:09:21: 3000000 INFO @ Tue, 16 Jun 2020 09:09:28: 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 09:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.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 09:09:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:35: 5000000 INFO @ Tue, 16 Jun 2020 09:09:38: 1000000 INFO @ Tue, 16 Jun 2020 09:09:42: 6000000 INFO @ Tue, 16 Jun 2020 09:09:46: 2000000 INFO @ Tue, 16 Jun 2020 09:09:49: 7000000 INFO @ Tue, 16 Jun 2020 09:09:53: 3000000 INFO @ Tue, 16 Jun 2020 09:09:56: 8000000 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 09:10:00: 4000000 INFO @ Tue, 16 Jun 2020 09:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.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 09:10:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:03: 9000000 INFO @ Tue, 16 Jun 2020 09:10:07: 5000000 INFO @ Tue, 16 Jun 2020 09:10:09: 1000000 INFO @ Tue, 16 Jun 2020 09:10:10: 10000000 INFO @ Tue, 16 Jun 2020 09:10:12: #1 tag size is determined as 100 bps INFO @ Tue, 16 Jun 2020 09:10:12: #1 tag size = 100 INFO @ Tue, 16 Jun 2020 09:10:12: #1 total tags in treatment: 10266398 INFO @ Tue, 16 Jun 2020 09:10:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:12: #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 09:10:12: #1 tags after filtering in treatment: 10266398 INFO @ Tue, 16 Jun 2020 09:10:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:13: #2 number of paired peaks: 180 WARNING @ Tue, 16 Jun 2020 09:10:13: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:13: #2 predicted fragment length is 98 bps INFO @ Tue, 16 Jun 2020 09:10:13: #2 alternative fragment length(s) may be 4,98,528,559 bps INFO @ Tue, 16 Jun 2020 09:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.05_model.r WARNING @ Tue, 16 Jun 2020 09:10:13: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:13: #2 You may need to consider one of the other alternative d(s): 4,98,528,559 WARNING @ Tue, 16 Jun 2020 09:10:13: #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 09:10:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:14: 6000000 INFO @ Tue, 16 Jun 2020 09:10:17: 2000000 INFO @ Tue, 16 Jun 2020 09:10:21: 7000000 INFO @ Tue, 16 Jun 2020 09:10:25: 3000000 INFO @ Tue, 16 Jun 2020 09:10:28: 8000000 INFO @ Tue, 16 Jun 2020 09:10:34: 4000000 INFO @ Tue, 16 Jun 2020 09:10:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:36: 9000000 INFO @ Tue, 16 Jun 2020 09:10:42: 5000000 INFO @ Tue, 16 Jun 2020 09:10:44: 10000000 INFO @ Tue, 16 Jun 2020 09:10:46: #1 tag size is determined as 100 bps INFO @ Tue, 16 Jun 2020 09:10:46: #1 tag size = 100 INFO @ Tue, 16 Jun 2020 09:10:46: #1 total tags in treatment: 10266398 INFO @ Tue, 16 Jun 2020 09:10:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:46: #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 09:10:46: #1 tags after filtering in treatment: 10266398 INFO @ Tue, 16 Jun 2020 09:10:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:46: #2 number of paired peaks: 180 WARNING @ Tue, 16 Jun 2020 09:10:46: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:47: #2 predicted fragment length is 98 bps INFO @ Tue, 16 Jun 2020 09:10:47: #2 alternative fragment length(s) may be 4,98,528,559 bps INFO @ Tue, 16 Jun 2020 09:10:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.10_model.r WARNING @ Tue, 16 Jun 2020 09:10:47: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:47: #2 You may need to consider one of the other alternative d(s): 4,98,528,559 WARNING @ Tue, 16 Jun 2020 09:10:47: #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 09:10:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:50: 6000000 INFO @ Tue, 16 Jun 2020 09:10:57: 7000000 INFO @ Tue, 16 Jun 2020 09:11:05: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:12: 9000000 INFO @ Tue, 16 Jun 2020 09:11:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (251 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:20: 10000000 INFO @ Tue, 16 Jun 2020 09:11:22: #1 tag size is determined as 100 bps INFO @ Tue, 16 Jun 2020 09:11:22: #1 tag size = 100 INFO @ Tue, 16 Jun 2020 09:11:22: #1 total tags in treatment: 10266398 INFO @ Tue, 16 Jun 2020 09:11:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:22: #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 09:11:22: #1 tags after filtering in treatment: 10266398 INFO @ Tue, 16 Jun 2020 09:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:23: #2 number of paired peaks: 180 WARNING @ Tue, 16 Jun 2020 09:11:23: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:23: #2 predicted fragment length is 98 bps INFO @ Tue, 16 Jun 2020 09:11:23: #2 alternative fragment length(s) may be 4,98,528,559 bps INFO @ Tue, 16 Jun 2020 09:11:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.20_model.r WARNING @ Tue, 16 Jun 2020 09:11:23: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:23: #2 You may need to consider one of the other alternative d(s): 4,98,528,559 WARNING @ Tue, 16 Jun 2020 09:11:23: #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 09:11:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200530/SRX4200530.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (112 records, 4 fields): 1 millis CompletedMACS2peakCalling