Job ID = 6456595 SRX = SRX3663164 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:56:01 prefetch.2.10.7: 1) Downloading 'SRR6686974'... 2020-06-21T10:56:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:59:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:59:10 prefetch.2.10.7: 1) 'SRR6686974' was downloaded successfully Read 21147260 spots for SRR6686974/SRR6686974.sra Written 21147260 spots for SRR6686974/SRR6686974.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: 00:04:44 21147260 reads; of these: 21147260 (100.00%) were unpaired; of these: 2528479 (11.96%) aligned 0 times 15707964 (74.28%) aligned exactly 1 time 2910817 (13.76%) aligned >1 times 88.04% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2188305 / 18618781 = 0.1175 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 @ Sun, 21 Jun 2020 20:10:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:10:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:06: 1000000 INFO @ Sun, 21 Jun 2020 20:10:12: 2000000 INFO @ Sun, 21 Jun 2020 20:10:18: 3000000 INFO @ Sun, 21 Jun 2020 20:10:24: 4000000 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 @ Sun, 21 Jun 2020 20:10:30: 5000000 INFO @ Sun, 21 Jun 2020 20:10:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:10:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:36: 6000000 INFO @ Sun, 21 Jun 2020 20:10:37: 1000000 INFO @ Sun, 21 Jun 2020 20:10:43: 7000000 INFO @ Sun, 21 Jun 2020 20:10:44: 2000000 INFO @ Sun, 21 Jun 2020 20:10:50: 8000000 INFO @ Sun, 21 Jun 2020 20:10:51: 3000000 INFO @ Sun, 21 Jun 2020 20:10:57: 9000000 INFO @ Sun, 21 Jun 2020 20:10:58: 4000000 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 @ Sun, 21 Jun 2020 20:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:11:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:04: 10000000 INFO @ Sun, 21 Jun 2020 20:11:04: 5000000 INFO @ Sun, 21 Jun 2020 20:11:07: 1000000 INFO @ Sun, 21 Jun 2020 20:11:11: 11000000 INFO @ Sun, 21 Jun 2020 20:11:11: 6000000 INFO @ Sun, 21 Jun 2020 20:11:14: 2000000 INFO @ Sun, 21 Jun 2020 20:11:18: 12000000 INFO @ Sun, 21 Jun 2020 20:11:18: 7000000 INFO @ Sun, 21 Jun 2020 20:11:21: 3000000 INFO @ Sun, 21 Jun 2020 20:11:24: 13000000 INFO @ Sun, 21 Jun 2020 20:11:25: 8000000 INFO @ Sun, 21 Jun 2020 20:11:28: 4000000 INFO @ Sun, 21 Jun 2020 20:11:31: 9000000 INFO @ Sun, 21 Jun 2020 20:11:31: 14000000 INFO @ Sun, 21 Jun 2020 20:11:34: 5000000 INFO @ Sun, 21 Jun 2020 20:11:38: 10000000 INFO @ Sun, 21 Jun 2020 20:11:38: 15000000 INFO @ Sun, 21 Jun 2020 20:11:41: 6000000 INFO @ Sun, 21 Jun 2020 20:11:45: 11000000 INFO @ Sun, 21 Jun 2020 20:11:45: 16000000 INFO @ Sun, 21 Jun 2020 20:11:48: 7000000 INFO @ Sun, 21 Jun 2020 20:11:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:11:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:11:48: #1 total tags in treatment: 16430476 INFO @ Sun, 21 Jun 2020 20:11:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:11:48: #1 tags after filtering in treatment: 16430364 INFO @ Sun, 21 Jun 2020 20:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:49: #2 number of paired peaks: 241 WARNING @ Sun, 21 Jun 2020 20:11:49: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Sun, 21 Jun 2020 20:11:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:50: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:50: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:50: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:11:50: #2 alternative fragment length(s) may be 2,51,111,524,598 bps INFO @ Sun, 21 Jun 2020 20:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.05_model.r WARNING @ Sun, 21 Jun 2020 20:11:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:11:50: #2 You may need to consider one of the other alternative d(s): 2,51,111,524,598 WARNING @ Sun, 21 Jun 2020 20:11:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:11:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:11:51: 12000000 INFO @ Sun, 21 Jun 2020 20:11:54: 8000000 INFO @ Sun, 21 Jun 2020 20:11:58: 13000000 INFO @ Sun, 21 Jun 2020 20:12:01: 9000000 INFO @ Sun, 21 Jun 2020 20:12:05: 14000000 INFO @ Sun, 21 Jun 2020 20:12:07: 10000000 INFO @ Sun, 21 Jun 2020 20:12:12: 15000000 INFO @ Sun, 21 Jun 2020 20:12:14: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:12:18: 16000000 INFO @ Sun, 21 Jun 2020 20:12:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:21: 12000000 INFO @ Sun, 21 Jun 2020 20:12:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:12:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:12:21: #1 total tags in treatment: 16430476 INFO @ Sun, 21 Jun 2020 20:12:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:12:22: #1 tags after filtering in treatment: 16430364 INFO @ Sun, 21 Jun 2020 20:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:23: #2 number of paired peaks: 241 WARNING @ Sun, 21 Jun 2020 20:12:23: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Sun, 21 Jun 2020 20:12:23: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:23: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:23: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:23: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:23: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:12:23: #2 alternative fragment length(s) may be 2,51,111,524,598 bps INFO @ Sun, 21 Jun 2020 20:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.10_model.r WARNING @ Sun, 21 Jun 2020 20:12:23: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:12:23: #2 You may need to consider one of the other alternative d(s): 2,51,111,524,598 WARNING @ Sun, 21 Jun 2020 20:12:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:12:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:27: 13000000 INFO @ Sun, 21 Jun 2020 20:12:33: 14000000 INFO @ Sun, 21 Jun 2020 20:12:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.05_summits.bed INFO @ Sun, 21 Jun 2020 20:12:35: Done! pass1 - making usageList (222 chroms): 1 millis pass2 - checking and writing primary data (597 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:12:39: 15000000 INFO @ Sun, 21 Jun 2020 20:12:45: 16000000 INFO @ Sun, 21 Jun 2020 20:12:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:12:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:12:47: #1 total tags in treatment: 16430476 INFO @ Sun, 21 Jun 2020 20:12:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:12:48: #1 tags after filtering in treatment: 16430364 INFO @ Sun, 21 Jun 2020 20:12:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:49: #2 number of paired peaks: 241 WARNING @ Sun, 21 Jun 2020 20:12:49: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Sun, 21 Jun 2020 20:12:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:49: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:12:49: #2 alternative fragment length(s) may be 2,51,111,524,598 bps INFO @ Sun, 21 Jun 2020 20:12:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.20_model.r WARNING @ Sun, 21 Jun 2020 20:12:49: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:12:49: #2 You may need to consider one of the other alternative d(s): 2,51,111,524,598 WARNING @ Sun, 21 Jun 2020 20:12:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:12:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:12:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.10_summits.bed INFO @ Sun, 21 Jun 2020 20:13:07: Done! pass1 - making usageList (122 chroms): 1 millis pass2 - checking and writing primary data (333 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:13:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:13:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:13:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:13:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3663164/SRX3663164.20_summits.bed INFO @ Sun, 21 Jun 2020 20:13:33: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 3 millis CompletedMACS2peakCalling