Job ID = 6497500 SRX = SRX495021 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:40:20 prefetch.2.10.7: 1) Downloading 'SRR1198553'... 2020-06-25T22:40:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:41:54 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:41:55 prefetch.2.10.7: 'SRR1198553' is valid 2020-06-25T22:41:55 prefetch.2.10.7: 1) 'SRR1198553' was downloaded successfully Read 18854814 spots for SRR1198553/SRR1198553.sra Written 18854814 spots for SRR1198553/SRR1198553.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: 00:03:50 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289134 (1.53%) aligned 0 times 14953707 (79.31%) aligned exactly 1 time 3611973 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 3521540 / 18565680 = 0.1897 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 07:50:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.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 07:50:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:50:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:51:01: 1000000 INFO @ Fri, 26 Jun 2020 07:51:06: 2000000 INFO @ Fri, 26 Jun 2020 07:51:12: 3000000 INFO @ Fri, 26 Jun 2020 07:51:17: 4000000 INFO @ Fri, 26 Jun 2020 07:51:22: 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 07:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.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 07:51:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:51:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:51:28: 6000000 INFO @ Fri, 26 Jun 2020 07:51:31: 1000000 INFO @ Fri, 26 Jun 2020 07:51:34: 7000000 INFO @ Fri, 26 Jun 2020 07:51:37: 2000000 INFO @ Fri, 26 Jun 2020 07:51:39: 8000000 INFO @ Fri, 26 Jun 2020 07:51:42: 3000000 INFO @ Fri, 26 Jun 2020 07:51:45: 9000000 INFO @ Fri, 26 Jun 2020 07:51:48: 4000000 INFO @ Fri, 26 Jun 2020 07:51:50: 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 @ Fri, 26 Jun 2020 07:51:54: 5000000 INFO @ Fri, 26 Jun 2020 07:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.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 07:51:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:51:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:51:56: 11000000 INFO @ Fri, 26 Jun 2020 07:51:59: 6000000 INFO @ Fri, 26 Jun 2020 07:52:01: 1000000 INFO @ Fri, 26 Jun 2020 07:52:02: 12000000 INFO @ Fri, 26 Jun 2020 07:52:05: 7000000 INFO @ Fri, 26 Jun 2020 07:52:07: 2000000 INFO @ Fri, 26 Jun 2020 07:52:07: 13000000 INFO @ Fri, 26 Jun 2020 07:52:11: 8000000 INFO @ Fri, 26 Jun 2020 07:52:12: 3000000 INFO @ Fri, 26 Jun 2020 07:52:13: 14000000 INFO @ Fri, 26 Jun 2020 07:52:16: 9000000 INFO @ Fri, 26 Jun 2020 07:52:18: 4000000 INFO @ Fri, 26 Jun 2020 07:52:19: 15000000 INFO @ Fri, 26 Jun 2020 07:52:19: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:52:19: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:52:19: #1 total tags in treatment: 15044140 INFO @ Fri, 26 Jun 2020 07:52:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:52:19: #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 07:52:19: #1 tags after filtering in treatment: 15044140 INFO @ Fri, 26 Jun 2020 07:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:52:19: #1 finished! INFO @ Fri, 26 Jun 2020 07:52:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:52:20: #2 number of paired peaks: 439 WARNING @ Fri, 26 Jun 2020 07:52:20: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Fri, 26 Jun 2020 07:52:20: start model_add_line... INFO @ Fri, 26 Jun 2020 07:52:20: start X-correlation... INFO @ Fri, 26 Jun 2020 07:52:20: end of X-cor INFO @ Fri, 26 Jun 2020 07:52:20: #2 finished! INFO @ Fri, 26 Jun 2020 07:52:20: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 07:52:20: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 07:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.05_model.r WARNING @ Fri, 26 Jun 2020 07:52:21: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:52:21: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 07:52:21: #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 07:52:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:52:22: 10000000 INFO @ Fri, 26 Jun 2020 07:52:24: 5000000 INFO @ Fri, 26 Jun 2020 07:52:28: 11000000 INFO @ Fri, 26 Jun 2020 07:52:30: 6000000 INFO @ Fri, 26 Jun 2020 07:52:33: 12000000 INFO @ Fri, 26 Jun 2020 07:52:35: 7000000 INFO @ Fri, 26 Jun 2020 07:52:39: 13000000 INFO @ Fri, 26 Jun 2020 07:52:41: 8000000 INFO @ Fri, 26 Jun 2020 07:52:45: 14000000 INFO @ Fri, 26 Jun 2020 07:52:47: 9000000 INFO @ Fri, 26 Jun 2020 07:52:50: 15000000 INFO @ Fri, 26 Jun 2020 07:52:51: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:52:51: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:52:51: #1 total tags in treatment: 15044140 INFO @ Fri, 26 Jun 2020 07:52:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:52:51: #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 07:52:51: #1 tags after filtering in treatment: 15044140 INFO @ Fri, 26 Jun 2020 07:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:52:51: #1 finished! INFO @ Fri, 26 Jun 2020 07:52:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:52:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:52:52: #2 number of paired peaks: 439 WARNING @ Fri, 26 Jun 2020 07:52:52: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Fri, 26 Jun 2020 07:52:52: start model_add_line... INFO @ Fri, 26 Jun 2020 07:52:52: start X-correlation... INFO @ Fri, 26 Jun 2020 07:52:52: end of X-cor INFO @ Fri, 26 Jun 2020 07:52:52: #2 finished! INFO @ Fri, 26 Jun 2020 07:52:52: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 07:52:52: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 07:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.10_model.r WARNING @ Fri, 26 Jun 2020 07:52:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:52:52: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 07:52:52: #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 07:52:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:52:52: 10000000 INFO @ Fri, 26 Jun 2020 07:52:58: 11000000 INFO @ Fri, 26 Jun 2020 07:53:03: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.05_summits.bed INFO @ Fri, 26 Jun 2020 07:53:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4185 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:53:09: 13000000 INFO @ Fri, 26 Jun 2020 07:53:14: 14000000 INFO @ Fri, 26 Jun 2020 07:53:20: 15000000 INFO @ Fri, 26 Jun 2020 07:53:20: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:53:20: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:53:20: #1 total tags in treatment: 15044140 INFO @ Fri, 26 Jun 2020 07:53:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:53:20: #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 07:53:20: #1 tags after filtering in treatment: 15044140 INFO @ Fri, 26 Jun 2020 07:53:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:53:20: #1 finished! INFO @ Fri, 26 Jun 2020 07:53:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:53:21: #2 number of paired peaks: 439 WARNING @ Fri, 26 Jun 2020 07:53:21: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Fri, 26 Jun 2020 07:53:21: start model_add_line... INFO @ Fri, 26 Jun 2020 07:53:22: start X-correlation... INFO @ Fri, 26 Jun 2020 07:53:22: end of X-cor INFO @ Fri, 26 Jun 2020 07:53:22: #2 finished! INFO @ Fri, 26 Jun 2020 07:53:22: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 07:53:22: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 07:53:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.20_model.r WARNING @ Fri, 26 Jun 2020 07:53:22: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:53:22: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 07:53:22: #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 07:53:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:53:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:53:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.10_summits.bed INFO @ Fri, 26 Jun 2020 07:53:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1024 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:53:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:54:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:54:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:54:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495021/SRX495021.20_summits.bed INFO @ Fri, 26 Jun 2020 07:54:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 37 millis CompletedMACS2peakCalling