Job ID = 6366202 SRX = SRX076077 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:42:22 prefetch.2.10.7: 1) Downloading 'SRR275567'... 2020-06-15T22:42:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:31 prefetch.2.10.7: 'SRR275567' is valid 2020-06-15T22:43:31 prefetch.2.10.7: 1) 'SRR275567' was downloaded successfully Read 16917825 spots for SRR275567/SRR275567.sra Written 16917825 spots for SRR275567/SRR275567.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: 00:02:53 16917825 reads; of these: 16917825 (100.00%) were unpaired; of these: 264902 (1.57%) aligned 0 times 13671674 (80.81%) aligned exactly 1 time 2981249 (17.62%) aligned >1 times 98.43% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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 8 files... [bam_rmdupse_core] 2382397 / 16652923 = 0.1431 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 07:50:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.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 07:50:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:41: 1000000 INFO @ Tue, 16 Jun 2020 07:50:46: 2000000 INFO @ Tue, 16 Jun 2020 07:50:52: 3000000 INFO @ Tue, 16 Jun 2020 07:50:57: 4000000 INFO @ Tue, 16 Jun 2020 07:51:02: 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 @ Tue, 16 Jun 2020 07:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.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 07:51:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:08: 6000000 INFO @ Tue, 16 Jun 2020 07:51:11: 1000000 INFO @ Tue, 16 Jun 2020 07:51:14: 7000000 INFO @ Tue, 16 Jun 2020 07:51:17: 2000000 INFO @ Tue, 16 Jun 2020 07:51:20: 8000000 INFO @ Tue, 16 Jun 2020 07:51:22: 3000000 INFO @ Tue, 16 Jun 2020 07:51:25: 9000000 INFO @ Tue, 16 Jun 2020 07:51:28: 4000000 INFO @ Tue, 16 Jun 2020 07:51:31: 10000000 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 07:51:34: 5000000 INFO @ Tue, 16 Jun 2020 07:51:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.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 07:51:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:37: 11000000 INFO @ Tue, 16 Jun 2020 07:51:39: 6000000 INFO @ Tue, 16 Jun 2020 07:51:41: 1000000 INFO @ Tue, 16 Jun 2020 07:51:43: 12000000 INFO @ Tue, 16 Jun 2020 07:51:45: 7000000 INFO @ Tue, 16 Jun 2020 07:51:47: 2000000 INFO @ Tue, 16 Jun 2020 07:51:49: 13000000 INFO @ Tue, 16 Jun 2020 07:51:51: 8000000 INFO @ Tue, 16 Jun 2020 07:51:53: 3000000 INFO @ Tue, 16 Jun 2020 07:51:55: 14000000 INFO @ Tue, 16 Jun 2020 07:51:56: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:51:56: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:51:56: #1 total tags in treatment: 14270526 INFO @ Tue, 16 Jun 2020 07:51:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:56: #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 07:51:56: #1 tags after filtering in treatment: 14270526 INFO @ Tue, 16 Jun 2020 07:51:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:56: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:57: 9000000 INFO @ Tue, 16 Jun 2020 07:51:57: #2 number of paired peaks: 273 WARNING @ Tue, 16 Jun 2020 07:51:57: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:57: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:57: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:57: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:57: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:57: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:51:57: #2 alternative fragment length(s) may be 2,34,577 bps INFO @ Tue, 16 Jun 2020 07:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.05_model.r WARNING @ Tue, 16 Jun 2020 07:51:57: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:57: #2 You may need to consider one of the other alternative d(s): 2,34,577 WARNING @ Tue, 16 Jun 2020 07:51:57: #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 07:51:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:51:59: 4000000 INFO @ Tue, 16 Jun 2020 07:52:02: 10000000 INFO @ Tue, 16 Jun 2020 07:52:05: 5000000 INFO @ Tue, 16 Jun 2020 07:52:08: 11000000 INFO @ Tue, 16 Jun 2020 07:52:11: 6000000 INFO @ Tue, 16 Jun 2020 07:52:14: 12000000 INFO @ Tue, 16 Jun 2020 07:52:17: 7000000 INFO @ Tue, 16 Jun 2020 07:52:19: 13000000 INFO @ Tue, 16 Jun 2020 07:52:22: 8000000 INFO @ Tue, 16 Jun 2020 07:52:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:25: 14000000 INFO @ Tue, 16 Jun 2020 07:52:27: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:52:27: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:52:27: #1 total tags in treatment: 14270526 INFO @ Tue, 16 Jun 2020 07:52:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:27: #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 07:52:27: #1 tags after filtering in treatment: 14270526 INFO @ Tue, 16 Jun 2020 07:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:27: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:28: #2 number of paired peaks: 273 WARNING @ Tue, 16 Jun 2020 07:52:28: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:28: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:28: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:52:28: #2 alternative fragment length(s) may be 2,34,577 bps INFO @ Tue, 16 Jun 2020 07:52:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.10_model.r WARNING @ Tue, 16 Jun 2020 07:52:28: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:28: #2 You may need to consider one of the other alternative d(s): 2,34,577 WARNING @ Tue, 16 Jun 2020 07:52:28: #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 07:52:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:28: 9000000 INFO @ Tue, 16 Jun 2020 07:52:34: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.05_summits.bed INFO @ Tue, 16 Jun 2020 07:52:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (619 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:52:40: 11000000 INFO @ Tue, 16 Jun 2020 07:52:46: 12000000 INFO @ Tue, 16 Jun 2020 07:52:52: 13000000 INFO @ Tue, 16 Jun 2020 07:52:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:57: 14000000 INFO @ Tue, 16 Jun 2020 07:52:59: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:52:59: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:52:59: #1 total tags in treatment: 14270526 INFO @ Tue, 16 Jun 2020 07:52:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:59: #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 07:52:59: #1 tags after filtering in treatment: 14270526 INFO @ Tue, 16 Jun 2020 07:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:59: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:00: #2 number of paired peaks: 273 WARNING @ Tue, 16 Jun 2020 07:53:00: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:00: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:53:00: #2 alternative fragment length(s) may be 2,34,577 bps INFO @ Tue, 16 Jun 2020 07:53:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.20_model.r WARNING @ Tue, 16 Jun 2020 07:53:00: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:00: #2 You may need to consider one of the other alternative d(s): 2,34,577 WARNING @ Tue, 16 Jun 2020 07:53:00: #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 07:53:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:08: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX076077/SRX076077.20_summits.bed INFO @ Tue, 16 Jun 2020 07:53:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (85 records, 4 fields): 1 millis CompletedMACS2peakCalling