Job ID = 6455631 SRX = SRX287943 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:11:21 prefetch.2.10.7: 1) Downloading 'SRR870132'... 2020-06-21T10:11:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:14:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:14:48 prefetch.2.10.7: 1) 'SRR870132' was downloaded successfully Read 16844504 spots for SRR870132/SRR870132.sra Written 16844504 spots for SRR870132/SRR870132.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: 00:07:07 16844504 reads; of these: 16844504 (100.00%) were unpaired; of these: 992520 (5.89%) aligned 0 times 4670206 (27.73%) aligned exactly 1 time 11181778 (66.38%) aligned >1 times 94.11% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 5348286 / 15851984 = 0.3374 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 19:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.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 19:26:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:57: 1000000 INFO @ Sun, 21 Jun 2020 19:27:03: 2000000 INFO @ Sun, 21 Jun 2020 19:27:09: 3000000 INFO @ Sun, 21 Jun 2020 19:27:15: 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 19:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.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 19:27:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:22: 5000000 INFO @ Sun, 21 Jun 2020 19:27:29: 1000000 INFO @ Sun, 21 Jun 2020 19:27:30: 6000000 INFO @ Sun, 21 Jun 2020 19:27:37: 2000000 INFO @ Sun, 21 Jun 2020 19:27:38: 7000000 INFO @ Sun, 21 Jun 2020 19:27:45: 3000000 INFO @ Sun, 21 Jun 2020 19:27:46: 8000000 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 19:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.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 19:27:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:53: 4000000 INFO @ Sun, 21 Jun 2020 19:27:53: 9000000 INFO @ Sun, 21 Jun 2020 19:27:58: 1000000 INFO @ Sun, 21 Jun 2020 19:28:01: 10000000 INFO @ Sun, 21 Jun 2020 19:28:01: 5000000 INFO @ Sun, 21 Jun 2020 19:28:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:05: #1 total tags in treatment: 10503698 INFO @ Sun, 21 Jun 2020 19:28:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:05: #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 19:28:05: 2000000 INFO @ Sun, 21 Jun 2020 19:28:06: #1 tags after filtering in treatment: 10503698 INFO @ Sun, 21 Jun 2020 19:28:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:07: #2 number of paired peaks: 3426 INFO @ Sun, 21 Jun 2020 19:28:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:07: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:28:07: #2 alternative fragment length(s) may be 3,50,598 bps INFO @ Sun, 21 Jun 2020 19:28:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.05_model.r WARNING @ Sun, 21 Jun 2020 19:28:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:07: #2 You may need to consider one of the other alternative d(s): 3,50,598 WARNING @ Sun, 21 Jun 2020 19:28:07: #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 19:28:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:10: 6000000 INFO @ Sun, 21 Jun 2020 19:28:13: 3000000 INFO @ Sun, 21 Jun 2020 19:28:18: 7000000 INFO @ Sun, 21 Jun 2020 19:28:20: 4000000 INFO @ Sun, 21 Jun 2020 19:28:26: 8000000 INFO @ Sun, 21 Jun 2020 19:28:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:28: 5000000 INFO @ Sun, 21 Jun 2020 19:28:34: 9000000 INFO @ Sun, 21 Jun 2020 19:28:35: 6000000 INFO @ Sun, 21 Jun 2020 19:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.05_summits.bed INFO @ Sun, 21 Jun 2020 19:28:36: Done! pass1 - making usageList (1330 chroms): 2 millis pass2 - checking and writing primary data (5157 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:42: 10000000 INFO @ Sun, 21 Jun 2020 19:28:42: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:28:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:46: #1 total tags in treatment: 10503698 INFO @ Sun, 21 Jun 2020 19:28:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:46: #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 19:28:47: #1 tags after filtering in treatment: 10503698 INFO @ Sun, 21 Jun 2020 19:28:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:48: #2 number of paired peaks: 3426 INFO @ Sun, 21 Jun 2020 19:28:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:48: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:28:48: #2 alternative fragment length(s) may be 3,50,598 bps INFO @ Sun, 21 Jun 2020 19:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.10_model.r WARNING @ Sun, 21 Jun 2020 19:28:48: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:48: #2 You may need to consider one of the other alternative d(s): 3,50,598 WARNING @ Sun, 21 Jun 2020 19:28:48: #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 19:28:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:50: 8000000 INFO @ Sun, 21 Jun 2020 19:28:56: 9000000 INFO @ Sun, 21 Jun 2020 19:29:03: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:29:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:06: #1 total tags in treatment: 10503698 INFO @ Sun, 21 Jun 2020 19:29:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:06: #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 19:29:06: #1 tags after filtering in treatment: 10503698 INFO @ Sun, 21 Jun 2020 19:29:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:07: #2 number of paired peaks: 3426 INFO @ Sun, 21 Jun 2020 19:29:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:07: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:29:07: #2 alternative fragment length(s) may be 3,50,598 bps INFO @ Sun, 21 Jun 2020 19:29:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.20_model.r WARNING @ Sun, 21 Jun 2020 19:29:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:29:07: #2 You may need to consider one of the other alternative d(s): 3,50,598 WARNING @ Sun, 21 Jun 2020 19:29:07: #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 19:29:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.10_summits.bed INFO @ Sun, 21 Jun 2020 19:29:18: Done! pass1 - making usageList (1045 chroms): 2 millis pass2 - checking and writing primary data (3466 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:29:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287943/SRX287943.20_summits.bed INFO @ Sun, 21 Jun 2020 19:29:37: Done! pass1 - making usageList (760 chroms): 2 millis pass2 - checking and writing primary data (2323 records, 4 fields): 22 millis CompletedMACS2peakCalling