Job ID = 6365888 SRX = SRX012296 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:35:06 prefetch.2.10.7: 1) Downloading 'SRR029215'... 2020-06-15T22:35:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:55 prefetch.2.10.7: 1) 'SRR029215' was downloaded successfully Read 8370026 spots for SRR029215/SRR029215.sra Written 8370026 spots for SRR029215/SRR029215.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: 00:01:14 8370026 reads; of these: 8370026 (100.00%) were unpaired; of these: 2457629 (29.36%) aligned 0 times 4923796 (58.83%) aligned exactly 1 time 988601 (11.81%) aligned >1 times 70.64% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 748719 / 5912397 = 0.1266 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 07:51:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.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 07:51:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:28: 1000000 INFO @ Tue, 16 Jun 2020 07:51:33: 2000000 INFO @ Tue, 16 Jun 2020 07:51:38: 3000000 INFO @ Tue, 16 Jun 2020 07:51:43: 4000000 INFO @ Tue, 16 Jun 2020 07:51:48: 5000000 INFO @ Tue, 16 Jun 2020 07:51:49: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:51:49: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:51:49: #1 total tags in treatment: 5163678 INFO @ Tue, 16 Jun 2020 07:51:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:49: #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 07:51:49: #1 tags after filtering in treatment: 5163678 INFO @ Tue, 16 Jun 2020 07:51:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:49: #2 number of paired peaks: 216 WARNING @ Tue, 16 Jun 2020 07:51:49: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:49: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:51:49: #2 alternative fragment length(s) may be 3,14,39,66,414,432,527,548,577,596 bps INFO @ Tue, 16 Jun 2020 07:51:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.05_model.r WARNING @ Tue, 16 Jun 2020 07:51:49: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:49: #2 You may need to consider one of the other alternative d(s): 3,14,39,66,414,432,527,548,577,596 WARNING @ Tue, 16 Jun 2020 07:51:49: #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 07:51:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:49: #3 Pre-compute pvalue-qvalue table... 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 07:51:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.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 07:51:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:58: 1000000 INFO @ Tue, 16 Jun 2020 07:52:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:03: 2000000 INFO @ Tue, 16 Jun 2020 07:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.05_summits.bed INFO @ Tue, 16 Jun 2020 07:52:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:52:08: 3000000 INFO @ Tue, 16 Jun 2020 07:52:13: 4000000 INFO @ Tue, 16 Jun 2020 07:52:18: 5000000 INFO @ Tue, 16 Jun 2020 07:52:18: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:52:18: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:52:18: #1 total tags in treatment: 5163678 INFO @ Tue, 16 Jun 2020 07:52:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:18: #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 07:52:19: #1 tags after filtering in treatment: 5163678 INFO @ Tue, 16 Jun 2020 07:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:19: #2 number of paired peaks: 216 WARNING @ Tue, 16 Jun 2020 07:52:19: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:19: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:52:19: #2 alternative fragment length(s) may be 3,14,39,66,414,432,527,548,577,596 bps INFO @ Tue, 16 Jun 2020 07:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.10_model.r WARNING @ Tue, 16 Jun 2020 07:52:19: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:19: #2 You may need to consider one of the other alternative d(s): 3,14,39,66,414,432,527,548,577,596 WARNING @ Tue, 16 Jun 2020 07:52:19: #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 07:52:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:19: #3 Pre-compute pvalue-qvalue table... 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 07:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.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 07:52:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:28: 1000000 INFO @ Tue, 16 Jun 2020 07:52:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:33: 2000000 INFO @ Tue, 16 Jun 2020 07:52:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.10_summits.bed INFO @ Tue, 16 Jun 2020 07:52:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:52:38: 3000000 INFO @ Tue, 16 Jun 2020 07:52:43: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:52:48: 5000000 INFO @ Tue, 16 Jun 2020 07:52:49: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:52:49: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:52:49: #1 total tags in treatment: 5163678 INFO @ Tue, 16 Jun 2020 07:52:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:49: #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 07:52:49: #1 tags after filtering in treatment: 5163678 INFO @ Tue, 16 Jun 2020 07:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:50: #2 number of paired peaks: 216 WARNING @ Tue, 16 Jun 2020 07:52:50: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:50: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:50: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:50: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:50: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:50: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:52:50: #2 alternative fragment length(s) may be 3,14,39,66,414,432,527,548,577,596 bps INFO @ Tue, 16 Jun 2020 07:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.20_model.r WARNING @ Tue, 16 Jun 2020 07:52:50: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:50: #2 You may need to consider one of the other alternative d(s): 3,14,39,66,414,432,527,548,577,596 WARNING @ Tue, 16 Jun 2020 07:52:50: #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 07:52:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:53:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX012296/SRX012296.20_summits.bed INFO @ Tue, 16 Jun 2020 07:53:06: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling