Job ID = 14160691 SRX = SRX10399012 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:03:53 12931999 reads; of these: 12931999 (100.00%) were unpaired; of these: 3900439 (30.16%) aligned 0 times 7587368 (58.67%) aligned exactly 1 time 1444192 (11.17%) aligned >1 times 69.84% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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_rmdupse_core] 1477355 / 9031560 = 0.1636 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.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 @ Thu, 09 Dec 2021 03:51:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:51:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:51:48: 1000000 INFO @ Thu, 09 Dec 2021 03:51:54: 2000000 INFO @ Thu, 09 Dec 2021 03:52:01: 3000000 INFO @ Thu, 09 Dec 2021 03:52:07: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:52:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.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 @ Thu, 09 Dec 2021 03:52:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:52:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:52:14: 5000000 INFO @ Thu, 09 Dec 2021 03:52:17: 1000000 INFO @ Thu, 09 Dec 2021 03:52:20: 6000000 INFO @ Thu, 09 Dec 2021 03:52:23: 2000000 INFO @ Thu, 09 Dec 2021 03:52:27: 7000000 INFO @ Thu, 09 Dec 2021 03:52:29: 3000000 INFO @ Thu, 09 Dec 2021 03:52:30: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:52:30: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:52:30: #1 total tags in treatment: 7554205 INFO @ Thu, 09 Dec 2021 03:52:30: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:52:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:52:30: #1 tags after filtering in treatment: 7554205 INFO @ Thu, 09 Dec 2021 03:52:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:52:30: #1 finished! INFO @ Thu, 09 Dec 2021 03:52:30: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:52:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:52:31: #2 number of paired peaks: 604 WARNING @ Thu, 09 Dec 2021 03:52:31: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Thu, 09 Dec 2021 03:52:31: start model_add_line... INFO @ Thu, 09 Dec 2021 03:52:31: start X-correlation... INFO @ Thu, 09 Dec 2021 03:52:31: end of X-cor INFO @ Thu, 09 Dec 2021 03:52:31: #2 finished! INFO @ Thu, 09 Dec 2021 03:52:31: #2 predicted fragment length is 126 bps INFO @ Thu, 09 Dec 2021 03:52:31: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 09 Dec 2021 03:52:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.05_model.r WARNING @ Thu, 09 Dec 2021 03:52:31: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:52:31: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Thu, 09 Dec 2021 03:52:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:52:31: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:52:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:52:35: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:52:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.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 @ Thu, 09 Dec 2021 03:52:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:52:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:52:41: 5000000 INFO @ Thu, 09 Dec 2021 03:52:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:52:47: 6000000 INFO @ Thu, 09 Dec 2021 03:52:48: 1000000 INFO @ Thu, 09 Dec 2021 03:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.05_summits.bed INFO @ Thu, 09 Dec 2021 03:52:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1425 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:52:53: 7000000 INFO @ Thu, 09 Dec 2021 03:52:55: 2000000 INFO @ Thu, 09 Dec 2021 03:52:56: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:52:56: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:52:56: #1 total tags in treatment: 7554205 INFO @ Thu, 09 Dec 2021 03:52:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:52:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:52:56: #1 tags after filtering in treatment: 7554205 INFO @ Thu, 09 Dec 2021 03:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:52:56: #1 finished! INFO @ Thu, 09 Dec 2021 03:52:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:52:57: #2 number of paired peaks: 604 WARNING @ Thu, 09 Dec 2021 03:52:57: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Thu, 09 Dec 2021 03:52:57: start model_add_line... INFO @ Thu, 09 Dec 2021 03:52:57: start X-correlation... INFO @ Thu, 09 Dec 2021 03:52:57: end of X-cor INFO @ Thu, 09 Dec 2021 03:52:57: #2 finished! INFO @ Thu, 09 Dec 2021 03:52:57: #2 predicted fragment length is 126 bps INFO @ Thu, 09 Dec 2021 03:52:57: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 09 Dec 2021 03:52:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.10_model.r WARNING @ Thu, 09 Dec 2021 03:52:57: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:52:57: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Thu, 09 Dec 2021 03:52:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:52:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:53:02: 3000000 INFO @ Thu, 09 Dec 2021 03:53:08: 4000000 INFO @ Thu, 09 Dec 2021 03:53:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:53:15: 5000000 INFO @ Thu, 09 Dec 2021 03:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.10_summits.bed INFO @ Thu, 09 Dec 2021 03:53:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (977 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:53:21: 6000000 INFO @ Thu, 09 Dec 2021 03:53:28: 7000000 INFO @ Thu, 09 Dec 2021 03:53:31: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:53:31: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:53:31: #1 total tags in treatment: 7554205 INFO @ Thu, 09 Dec 2021 03:53:31: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:53:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:53:31: #1 tags after filtering in treatment: 7554205 INFO @ Thu, 09 Dec 2021 03:53:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:53:31: #1 finished! INFO @ Thu, 09 Dec 2021 03:53:31: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:53:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:53:32: #2 number of paired peaks: 604 WARNING @ Thu, 09 Dec 2021 03:53:32: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Thu, 09 Dec 2021 03:53:32: start model_add_line... INFO @ Thu, 09 Dec 2021 03:53:32: start X-correlation... INFO @ Thu, 09 Dec 2021 03:53:32: end of X-cor INFO @ Thu, 09 Dec 2021 03:53:32: #2 finished! INFO @ Thu, 09 Dec 2021 03:53:32: #2 predicted fragment length is 126 bps INFO @ Thu, 09 Dec 2021 03:53:32: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 09 Dec 2021 03:53:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.20_model.r WARNING @ Thu, 09 Dec 2021 03:53:32: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:53:32: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Thu, 09 Dec 2021 03:53:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:53:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:53:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:53:47: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:53:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:53:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:53:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399012/SRX10399012.20_summits.bed INFO @ Thu, 09 Dec 2021 03:53:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (600 records, 4 fields): 2 millis CompletedMACS2peakCalling