Job ID = 6453404 SRX = SRX113332 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:23:17 prefetch.2.10.7: 1) Downloading 'SRR392953'... 2020-06-21T08:23:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:28:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:28:29 prefetch.2.10.7: 1) 'SRR392953' was downloaded successfully Read 22984833 spots for SRR392953/SRR392953.sra Written 22984833 spots for SRR392953/SRR392953.sra 2020-06-21T08:29:49 prefetch.2.10.7: 1) Downloading 'SRR392954'... 2020-06-21T08:29:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:46 prefetch.2.10.7: 1) 'SRR392954' was downloaded successfully Read 22005854 spots for SRR392954/SRR392954.sra Written 22005854 spots for SRR392954/SRR392954.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: 00:07:53 44990687 reads; of these: 44990687 (100.00%) were unpaired; of these: 3974503 (8.83%) aligned 0 times 37955989 (84.36%) aligned exactly 1 time 3060195 (6.80%) aligned >1 times 91.17% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 20825503 / 41016184 = 0.5077 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 17:50:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.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 17:50:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:50: 1000000 INFO @ Sun, 21 Jun 2020 17:50:55: 2000000 INFO @ Sun, 21 Jun 2020 17:51:00: 3000000 INFO @ Sun, 21 Jun 2020 17:51:06: 4000000 INFO @ Sun, 21 Jun 2020 17:51:11: 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 @ Sun, 21 Jun 2020 17:51:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.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 17:51:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:17: 6000000 INFO @ Sun, 21 Jun 2020 17:51:20: 1000000 INFO @ Sun, 21 Jun 2020 17:51:23: 7000000 INFO @ Sun, 21 Jun 2020 17:51:26: 2000000 INFO @ Sun, 21 Jun 2020 17:51:29: 8000000 INFO @ Sun, 21 Jun 2020 17:51:33: 3000000 INFO @ Sun, 21 Jun 2020 17:51:35: 9000000 INFO @ Sun, 21 Jun 2020 17:51:39: 4000000 INFO @ Sun, 21 Jun 2020 17:51:41: 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 @ Sun, 21 Jun 2020 17:51:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.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 17:51:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:45: 5000000 INFO @ Sun, 21 Jun 2020 17:51:47: 11000000 INFO @ Sun, 21 Jun 2020 17:51:50: 1000000 INFO @ Sun, 21 Jun 2020 17:51:51: 6000000 INFO @ Sun, 21 Jun 2020 17:51:53: 12000000 INFO @ Sun, 21 Jun 2020 17:51:56: 2000000 INFO @ Sun, 21 Jun 2020 17:51:57: 7000000 INFO @ Sun, 21 Jun 2020 17:51:59: 13000000 INFO @ Sun, 21 Jun 2020 17:52:02: 3000000 INFO @ Sun, 21 Jun 2020 17:52:03: 8000000 INFO @ Sun, 21 Jun 2020 17:52:05: 14000000 INFO @ Sun, 21 Jun 2020 17:52:09: 4000000 INFO @ Sun, 21 Jun 2020 17:52:09: 9000000 INFO @ Sun, 21 Jun 2020 17:52:11: 15000000 INFO @ Sun, 21 Jun 2020 17:52:15: 5000000 INFO @ Sun, 21 Jun 2020 17:52:15: 10000000 INFO @ Sun, 21 Jun 2020 17:52:17: 16000000 INFO @ Sun, 21 Jun 2020 17:52:21: 6000000 INFO @ Sun, 21 Jun 2020 17:52:21: 11000000 INFO @ Sun, 21 Jun 2020 17:52:23: 17000000 INFO @ Sun, 21 Jun 2020 17:52:27: 7000000 INFO @ Sun, 21 Jun 2020 17:52:27: 12000000 INFO @ Sun, 21 Jun 2020 17:52:30: 18000000 INFO @ Sun, 21 Jun 2020 17:52:33: 8000000 INFO @ Sun, 21 Jun 2020 17:52:34: 13000000 INFO @ Sun, 21 Jun 2020 17:52:36: 19000000 INFO @ Sun, 21 Jun 2020 17:52:39: 9000000 INFO @ Sun, 21 Jun 2020 17:52:40: 14000000 INFO @ Sun, 21 Jun 2020 17:52:42: 20000000 INFO @ Sun, 21 Jun 2020 17:52:44: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:52:44: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:52:44: #1 total tags in treatment: 20190681 INFO @ Sun, 21 Jun 2020 17:52:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:44: #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 17:52:44: #1 tags after filtering in treatment: 20190654 INFO @ Sun, 21 Jun 2020 17:52:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:45: 10000000 INFO @ Sun, 21 Jun 2020 17:52:46: 15000000 INFO @ Sun, 21 Jun 2020 17:52:46: #2 number of paired peaks: 2332 INFO @ Sun, 21 Jun 2020 17:52:46: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:46: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:46: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:46: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:46: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:52:46: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 17:52:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.05_model.r WARNING @ Sun, 21 Jun 2020 17:52:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:46: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 17:52:46: #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 17:52:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:51: 11000000 INFO @ Sun, 21 Jun 2020 17:52:52: 16000000 INFO @ Sun, 21 Jun 2020 17:52:57: 12000000 INFO @ Sun, 21 Jun 2020 17:52:58: 17000000 INFO @ Sun, 21 Jun 2020 17:53:03: 13000000 INFO @ Sun, 21 Jun 2020 17:53:04: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:53:09: 14000000 INFO @ Sun, 21 Jun 2020 17:53:10: 19000000 INFO @ Sun, 21 Jun 2020 17:53:15: 15000000 INFO @ Sun, 21 Jun 2020 17:53:16: 20000000 INFO @ Sun, 21 Jun 2020 17:53:17: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:53:17: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:53:17: #1 total tags in treatment: 20190681 INFO @ Sun, 21 Jun 2020 17:53:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:17: #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 17:53:18: #1 tags after filtering in treatment: 20190654 INFO @ Sun, 21 Jun 2020 17:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:19: #2 number of paired peaks: 2332 INFO @ Sun, 21 Jun 2020 17:53:19: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:20: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:53:20: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 17:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.10_model.r WARNING @ Sun, 21 Jun 2020 17:53:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:20: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 17:53:20: #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 17:53:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:21: 16000000 INFO @ Sun, 21 Jun 2020 17:53:27: 17000000 INFO @ Sun, 21 Jun 2020 17:53:32: 18000000 INFO @ Sun, 21 Jun 2020 17:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.05_summits.bed INFO @ Sun, 21 Jun 2020 17:53:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:53:38: 19000000 INFO @ Sun, 21 Jun 2020 17:53:43: 20000000 INFO @ Sun, 21 Jun 2020 17:53:44: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:53:44: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:53:44: #1 total tags in treatment: 20190681 INFO @ Sun, 21 Jun 2020 17:53:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:44: #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 17:53:45: #1 tags after filtering in treatment: 20190654 INFO @ Sun, 21 Jun 2020 17:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:47: #2 number of paired peaks: 2332 INFO @ Sun, 21 Jun 2020 17:53:47: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:47: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:47: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:47: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:47: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:53:47: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 17:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.20_model.r WARNING @ Sun, 21 Jun 2020 17:53:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:47: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 17:53:47: #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 17:53:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:53:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.10_summits.bed INFO @ Sun, 21 Jun 2020 17:54:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:54:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113332/SRX113332.20_summits.bed INFO @ Sun, 21 Jun 2020 17:54:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling