Job ID = 7108179 SRX = SRX7960938 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10059618 spots for SRR11359443/SRR11359443.sra Written 10059618 spots for SRR11359443/SRR11359443.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: 00:04:14 10059618 reads; of these: 10059618 (100.00%) were unpaired; of these: 542887 (5.40%) aligned 0 times 7311165 (72.68%) aligned exactly 1 time 2205566 (21.92%) aligned >1 times 94.60% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5138570 / 9516731 = 0.5400 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 @ Wed, 22 Jul 2020 13:38:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Jul 2020 13:38:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:38:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:38:52: 1000000 INFO @ Wed, 22 Jul 2020 13:39:00: 2000000 INFO @ Wed, 22 Jul 2020 13:39:07: 3000000 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 @ Wed, 22 Jul 2020 13:39:14: 4000000 INFO @ Wed, 22 Jul 2020 13:39:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Jul 2020 13:39:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:39:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:39:17: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:39:17: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:39:17: #1 total tags in treatment: 4378161 INFO @ Wed, 22 Jul 2020 13:39:17: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:39:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:39:17: #1 tags after filtering in treatment: 4378161 INFO @ Wed, 22 Jul 2020 13:39:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:39:17: #1 finished! INFO @ Wed, 22 Jul 2020 13:39:17: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:39:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:39:18: #2 number of paired peaks: 102 WARNING @ Wed, 22 Jul 2020 13:39:18: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Wed, 22 Jul 2020 13:39:18: start model_add_line... INFO @ Wed, 22 Jul 2020 13:39:18: start X-correlation... INFO @ Wed, 22 Jul 2020 13:39:18: end of X-cor INFO @ Wed, 22 Jul 2020 13:39:18: #2 finished! INFO @ Wed, 22 Jul 2020 13:39:18: #2 predicted fragment length is 255 bps INFO @ Wed, 22 Jul 2020 13:39:18: #2 alternative fragment length(s) may be 2,27,60,120,151,167,185,206,233,255,286,309,328,349,368,399,435,469,476,577 bps INFO @ Wed, 22 Jul 2020 13:39:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.05_model.r WARNING @ Wed, 22 Jul 2020 13:39:18: #2 Since the d (255) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:39:18: #2 You may need to consider one of the other alternative d(s): 2,27,60,120,151,167,185,206,233,255,286,309,328,349,368,399,435,469,476,577 WARNING @ Wed, 22 Jul 2020 13:39:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:39:18: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:39:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:39:22: 1000000 INFO @ Wed, 22 Jul 2020 13:39:30: 2000000 INFO @ Wed, 22 Jul 2020 13:39:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:39:38: 3000000 INFO @ Wed, 22 Jul 2020 13:39:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:39:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:39:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.05_summits.bed INFO @ Wed, 22 Jul 2020 13:39:41: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1306 records, 4 fields): 41 millis CompletedMACS2peakCalling 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 @ Wed, 22 Jul 2020 13:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Jul 2020 13:39:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:39:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:39:45: 4000000 INFO @ Wed, 22 Jul 2020 13:39:48: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:39:48: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:39:48: #1 total tags in treatment: 4378161 INFO @ Wed, 22 Jul 2020 13:39:48: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:39:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:39:48: #1 tags after filtering in treatment: 4378161 INFO @ Wed, 22 Jul 2020 13:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:39:48: #1 finished! INFO @ Wed, 22 Jul 2020 13:39:48: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:39:49: #2 number of paired peaks: 102 WARNING @ Wed, 22 Jul 2020 13:39:49: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Wed, 22 Jul 2020 13:39:49: start model_add_line... INFO @ Wed, 22 Jul 2020 13:39:49: start X-correlation... INFO @ Wed, 22 Jul 2020 13:39:49: end of X-cor INFO @ Wed, 22 Jul 2020 13:39:49: #2 finished! INFO @ Wed, 22 Jul 2020 13:39:49: #2 predicted fragment length is 255 bps INFO @ Wed, 22 Jul 2020 13:39:49: #2 alternative fragment length(s) may be 2,27,60,120,151,167,185,206,233,255,286,309,328,349,368,399,435,469,476,577 bps INFO @ Wed, 22 Jul 2020 13:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.10_model.r WARNING @ Wed, 22 Jul 2020 13:39:49: #2 Since the d (255) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:39:49: #2 You may need to consider one of the other alternative d(s): 2,27,60,120,151,167,185,206,233,255,286,309,328,349,368,399,435,469,476,577 WARNING @ Wed, 22 Jul 2020 13:39:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:39:49: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:39:53: 1000000 INFO @ Wed, 22 Jul 2020 13:40:00: 2000000 INFO @ Wed, 22 Jul 2020 13:40:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:40:08: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:40:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:40:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:40:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.10_summits.bed INFO @ Wed, 22 Jul 2020 13:40:11: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1160 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:40:15: 4000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:40:18: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:40:18: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:40:18: #1 total tags in treatment: 4378161 INFO @ Wed, 22 Jul 2020 13:40:18: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:40:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:40:18: #1 tags after filtering in treatment: 4378161 INFO @ Wed, 22 Jul 2020 13:40:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:40:18: #1 finished! INFO @ Wed, 22 Jul 2020 13:40:18: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:40:19: #2 number of paired peaks: 102 WARNING @ Wed, 22 Jul 2020 13:40:19: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Wed, 22 Jul 2020 13:40:19: start model_add_line... INFO @ Wed, 22 Jul 2020 13:40:19: start X-correlation... INFO @ Wed, 22 Jul 2020 13:40:19: end of X-cor INFO @ Wed, 22 Jul 2020 13:40:19: #2 finished! INFO @ Wed, 22 Jul 2020 13:40:19: #2 predicted fragment length is 255 bps INFO @ Wed, 22 Jul 2020 13:40:19: #2 alternative fragment length(s) may be 2,27,60,120,151,167,185,206,233,255,286,309,328,349,368,399,435,469,476,577 bps INFO @ Wed, 22 Jul 2020 13:40:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.20_model.r WARNING @ Wed, 22 Jul 2020 13:40:19: #2 Since the d (255) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:40:19: #2 You may need to consider one of the other alternative d(s): 2,27,60,120,151,167,185,206,233,255,286,309,328,349,368,399,435,469,476,577 WARNING @ Wed, 22 Jul 2020 13:40:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:40:19: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:40:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:40:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:40:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:40:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960938/SRX7960938.20_summits.bed INFO @ Wed, 22 Jul 2020 13:40:41: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (958 records, 4 fields): 3 millis CompletedMACS2peakCalling