Job ID = 6528062 SRX = SRX3981697 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:23:06 prefetch.2.10.7: 1) Downloading 'SRR7050483'... 2020-06-29T14:23:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:23:44 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:23:44 prefetch.2.10.7: 'SRR7050483' is valid 2020-06-29T14:23:44 prefetch.2.10.7: 1) 'SRR7050483' was downloaded successfully 2020-06-29T14:23:44 prefetch.2.10.7: 'SRR7050483' has 0 unresolved dependencies Read 8186490 spots for SRR7050483/SRR7050483.sra Written 8186490 spots for SRR7050483/SRR7050483.sra 2020-06-29T14:24:24 prefetch.2.10.7: 1) Downloading 'SRR7050484'... 2020-06-29T14:24:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:25:11 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:25:12 prefetch.2.10.7: 'SRR7050484' is valid 2020-06-29T14:25:12 prefetch.2.10.7: 1) 'SRR7050484' was downloaded successfully 2020-06-29T14:25:12 prefetch.2.10.7: 'SRR7050484' has 0 unresolved dependencies Read 8180234 spots for SRR7050484/SRR7050484.sra Written 8180234 spots for SRR7050484/SRR7050484.sra 2020-06-29T14:25:50 prefetch.2.10.7: 1) Downloading 'SRR7050485'... 2020-06-29T14:25:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:27:00 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:27:01 prefetch.2.10.7: 'SRR7050485' is valid 2020-06-29T14:27:01 prefetch.2.10.7: 1) 'SRR7050485' was downloaded successfully 2020-06-29T14:27:01 prefetch.2.10.7: 'SRR7050485' has 0 unresolved dependencies Read 8209203 spots for SRR7050485/SRR7050485.sra Written 8209203 spots for SRR7050485/SRR7050485.sra 2020-06-29T14:27:39 prefetch.2.10.7: 1) Downloading 'SRR7050486'... 2020-06-29T14:27:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:28:46 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:28:46 prefetch.2.10.7: 'SRR7050486' is valid 2020-06-29T14:28:46 prefetch.2.10.7: 1) 'SRR7050486' was downloaded successfully 2020-06-29T14:28:46 prefetch.2.10.7: 'SRR7050486' has 0 unresolved dependencies Read 8254049 spots for SRR7050486/SRR7050486.sra Written 8254049 spots for SRR7050486/SRR7050486.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: 00:09:05 32829976 reads; of these: 32829976 (100.00%) were unpaired; of these: 896138 (2.73%) aligned 0 times 24728053 (75.32%) aligned exactly 1 time 7205785 (21.95%) aligned >1 times 97.27% overall alignment rate Time searching: 00:09:05 Overall time: 00:09:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 3839997 / 31933838 = 0.1202 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 @ Mon, 29 Jun 2020 23:51:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.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 @ Mon, 29 Jun 2020 23:51:27: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:51:27: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:51:32: 1000000 INFO @ Mon, 29 Jun 2020 23:51:37: 2000000 INFO @ Mon, 29 Jun 2020 23:51:42: 3000000 INFO @ Mon, 29 Jun 2020 23:51:46: 4000000 INFO @ Mon, 29 Jun 2020 23:51:51: 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 @ Mon, 29 Jun 2020 23:51:56: 6000000 INFO @ Mon, 29 Jun 2020 23:51:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.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 @ Mon, 29 Jun 2020 23:51:57: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:51:57: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:52:00: 7000000 INFO @ Mon, 29 Jun 2020 23:52:03: 1000000 INFO @ Mon, 29 Jun 2020 23:52:05: 8000000 INFO @ Mon, 29 Jun 2020 23:52:08: 2000000 INFO @ Mon, 29 Jun 2020 23:52:10: 9000000 INFO @ Mon, 29 Jun 2020 23:52:14: 3000000 INFO @ Mon, 29 Jun 2020 23:52:15: 10000000 INFO @ Mon, 29 Jun 2020 23:52:19: 4000000 INFO @ Mon, 29 Jun 2020 23:52:20: 11000000 INFO @ Mon, 29 Jun 2020 23:52:25: 5000000 INFO @ Mon, 29 Jun 2020 23:52:25: 12000000 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 @ Mon, 29 Jun 2020 23:52:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.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 @ Mon, 29 Jun 2020 23:52:27: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:52:27: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:52:30: 13000000 INFO @ Mon, 29 Jun 2020 23:52:30: 6000000 INFO @ Mon, 29 Jun 2020 23:52:33: 1000000 INFO @ Mon, 29 Jun 2020 23:52:35: 14000000 INFO @ Mon, 29 Jun 2020 23:52:36: 7000000 INFO @ Mon, 29 Jun 2020 23:52:39: 2000000 INFO @ Mon, 29 Jun 2020 23:52:40: 15000000 INFO @ Mon, 29 Jun 2020 23:52:41: 8000000 INFO @ Mon, 29 Jun 2020 23:52:44: 3000000 INFO @ Mon, 29 Jun 2020 23:52:45: 16000000 INFO @ Mon, 29 Jun 2020 23:52:47: 9000000 INFO @ Mon, 29 Jun 2020 23:52:49: 4000000 INFO @ Mon, 29 Jun 2020 23:52:50: 17000000 INFO @ Mon, 29 Jun 2020 23:52:52: 10000000 INFO @ Mon, 29 Jun 2020 23:52:54: 5000000 INFO @ Mon, 29 Jun 2020 23:52:54: 18000000 INFO @ Mon, 29 Jun 2020 23:52:58: 11000000 INFO @ Mon, 29 Jun 2020 23:52:59: 6000000 INFO @ Mon, 29 Jun 2020 23:52:59: 19000000 INFO @ Mon, 29 Jun 2020 23:53:04: 12000000 INFO @ Mon, 29 Jun 2020 23:53:04: 7000000 INFO @ Mon, 29 Jun 2020 23:53:04: 20000000 INFO @ Mon, 29 Jun 2020 23:53:09: 8000000 INFO @ Mon, 29 Jun 2020 23:53:09: 13000000 INFO @ Mon, 29 Jun 2020 23:53:09: 21000000 INFO @ Mon, 29 Jun 2020 23:53:14: 9000000 INFO @ Mon, 29 Jun 2020 23:53:14: 22000000 INFO @ Mon, 29 Jun 2020 23:53:15: 14000000 INFO @ Mon, 29 Jun 2020 23:53:19: 10000000 INFO @ Mon, 29 Jun 2020 23:53:19: 23000000 INFO @ Mon, 29 Jun 2020 23:53:21: 15000000 INFO @ Mon, 29 Jun 2020 23:53:24: 11000000 INFO @ Mon, 29 Jun 2020 23:53:25: 24000000 INFO @ Mon, 29 Jun 2020 23:53:26: 16000000 INFO @ Mon, 29 Jun 2020 23:53:29: 12000000 INFO @ Mon, 29 Jun 2020 23:53:30: 25000000 INFO @ Mon, 29 Jun 2020 23:53:32: 17000000 INFO @ Mon, 29 Jun 2020 23:53:34: 13000000 INFO @ Mon, 29 Jun 2020 23:53:34: 26000000 INFO @ Mon, 29 Jun 2020 23:53:37: 18000000 INFO @ Mon, 29 Jun 2020 23:53:39: 14000000 INFO @ Mon, 29 Jun 2020 23:53:39: 27000000 INFO @ Mon, 29 Jun 2020 23:53:43: 19000000 INFO @ Mon, 29 Jun 2020 23:53:44: 15000000 INFO @ Mon, 29 Jun 2020 23:53:44: 28000000 INFO @ Mon, 29 Jun 2020 23:53:45: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:53:45: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:53:45: #1 total tags in treatment: 28093841 INFO @ Mon, 29 Jun 2020 23:53:45: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:53:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:53:46: #1 tags after filtering in treatment: 28093841 INFO @ Mon, 29 Jun 2020 23:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:53:46: #1 finished! INFO @ Mon, 29 Jun 2020 23:53:46: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:53:47: #2 number of paired peaks: 123 WARNING @ Mon, 29 Jun 2020 23:53:47: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Mon, 29 Jun 2020 23:53:47: start model_add_line... INFO @ Mon, 29 Jun 2020 23:53:47: start X-correlation... INFO @ Mon, 29 Jun 2020 23:53:47: end of X-cor INFO @ Mon, 29 Jun 2020 23:53:47: #2 finished! INFO @ Mon, 29 Jun 2020 23:53:47: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:53:47: #2 alternative fragment length(s) may be 2,12,32,48 bps INFO @ Mon, 29 Jun 2020 23:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.05_model.r WARNING @ Mon, 29 Jun 2020 23:53:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:53:47: #2 You may need to consider one of the other alternative d(s): 2,12,32,48 WARNING @ Mon, 29 Jun 2020 23:53:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:53:47: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:53:49: 20000000 INFO @ Mon, 29 Jun 2020 23:53:49: 16000000 INFO @ Mon, 29 Jun 2020 23:53:54: 17000000 INFO @ Mon, 29 Jun 2020 23:53:54: 21000000 INFO @ Mon, 29 Jun 2020 23:53:59: 18000000 INFO @ Mon, 29 Jun 2020 23:54:00: 22000000 INFO @ Mon, 29 Jun 2020 23:54:04: 19000000 INFO @ Mon, 29 Jun 2020 23:54:06: 23000000 INFO @ Mon, 29 Jun 2020 23:54:09: 20000000 INFO @ Mon, 29 Jun 2020 23:54:11: 24000000 INFO @ Mon, 29 Jun 2020 23:54:14: 21000000 INFO @ Mon, 29 Jun 2020 23:54:17: 25000000 INFO @ Mon, 29 Jun 2020 23:54:19: 22000000 INFO @ Mon, 29 Jun 2020 23:54:23: 26000000 INFO @ Mon, 29 Jun 2020 23:54:24: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:54:29: 24000000 INFO @ Mon, 29 Jun 2020 23:54:29: 27000000 INFO @ Mon, 29 Jun 2020 23:54:29: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:54:34: 25000000 INFO @ Mon, 29 Jun 2020 23:54:35: 28000000 INFO @ Mon, 29 Jun 2020 23:54:35: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:54:35: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:54:35: #1 total tags in treatment: 28093841 INFO @ Mon, 29 Jun 2020 23:54:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:54:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:54:36: #1 tags after filtering in treatment: 28093841 INFO @ Mon, 29 Jun 2020 23:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:54:36: #1 finished! INFO @ Mon, 29 Jun 2020 23:54:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:54:38: #2 number of paired peaks: 123 WARNING @ Mon, 29 Jun 2020 23:54:38: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Mon, 29 Jun 2020 23:54:38: start model_add_line... INFO @ Mon, 29 Jun 2020 23:54:38: start X-correlation... INFO @ Mon, 29 Jun 2020 23:54:38: end of X-cor INFO @ Mon, 29 Jun 2020 23:54:38: #2 finished! INFO @ Mon, 29 Jun 2020 23:54:38: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:54:38: #2 alternative fragment length(s) may be 2,12,32,48 bps INFO @ Mon, 29 Jun 2020 23:54:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.10_model.r WARNING @ Mon, 29 Jun 2020 23:54:38: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:54:38: #2 You may need to consider one of the other alternative d(s): 2,12,32,48 WARNING @ Mon, 29 Jun 2020 23:54:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:54:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:54:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:54:39: 26000000 INFO @ Mon, 29 Jun 2020 23:54:43: 27000000 INFO @ Mon, 29 Jun 2020 23:54:48: 28000000 INFO @ Mon, 29 Jun 2020 23:54:49: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:54:49: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:54:49: #1 total tags in treatment: 28093841 INFO @ Mon, 29 Jun 2020 23:54:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:54:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.05_summits.bed INFO @ Mon, 29 Jun 2020 23:54:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:54:49: #1 tags after filtering in treatment: 28093841 INFO @ Mon, 29 Jun 2020 23:54:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:54:49: #1 finished! INFO @ Mon, 29 Jun 2020 23:54:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:54:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:54:51: #2 number of paired peaks: 123 WARNING @ Mon, 29 Jun 2020 23:54:51: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Mon, 29 Jun 2020 23:54:51: start model_add_line... INFO @ Mon, 29 Jun 2020 23:54:51: start X-correlation... INFO @ Mon, 29 Jun 2020 23:54:51: end of X-cor INFO @ Mon, 29 Jun 2020 23:54:51: #2 finished! INFO @ Mon, 29 Jun 2020 23:54:51: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:54:51: #2 alternative fragment length(s) may be 2,12,32,48 bps INFO @ Mon, 29 Jun 2020 23:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.20_model.r WARNING @ Mon, 29 Jun 2020 23:54:51: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:54:51: #2 You may need to consider one of the other alternative d(s): 2,12,32,48 WARNING @ Mon, 29 Jun 2020 23:54:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:54:51: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:55:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:55:33: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.10_summits.bed INFO @ Mon, 29 Jun 2020 23:55:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:55:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:55:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:55:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981697/SRX3981697.20_summits.bed INFO @ Mon, 29 Jun 2020 23:55:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling