Job ID = 5720853 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,097,513 reads read : 34,097,513 reads written : 34,097,513 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:10:49 34097513 reads; of these: 34097513 (100.00%) were unpaired; of these: 1151853 (3.38%) aligned 0 times 22704987 (66.59%) aligned exactly 1 time 10240673 (30.03%) aligned >1 times 96.62% overall alignment rate Time searching: 00:10:49 Overall time: 00:10:49 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] 4820930 / 32945660 = 0.1463 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 @ Thu, 16 Apr 2020 02:41:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.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 @ Thu, 16 Apr 2020 02:41:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:41:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:42:02: 1000000 INFO @ Thu, 16 Apr 2020 02:42:07: 2000000 INFO @ Thu, 16 Apr 2020 02:42:11: 3000000 INFO @ Thu, 16 Apr 2020 02:42:16: 4000000 INFO @ Thu, 16 Apr 2020 02:42:21: 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 @ Thu, 16 Apr 2020 02:42:26: 6000000 INFO @ Thu, 16 Apr 2020 02:42:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.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 @ Thu, 16 Apr 2020 02:42:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:42:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:42:31: 7000000 INFO @ Thu, 16 Apr 2020 02:42:33: 1000000 INFO @ Thu, 16 Apr 2020 02:42:36: 8000000 INFO @ Thu, 16 Apr 2020 02:42:39: 2000000 INFO @ Thu, 16 Apr 2020 02:42:41: 9000000 INFO @ Thu, 16 Apr 2020 02:42:44: 3000000 INFO @ Thu, 16 Apr 2020 02:42:46: 10000000 INFO @ Thu, 16 Apr 2020 02:42:49: 4000000 INFO @ Thu, 16 Apr 2020 02:42:51: 11000000 INFO @ Thu, 16 Apr 2020 02:42:54: 5000000 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 @ Thu, 16 Apr 2020 02:42:57: 12000000 INFO @ Thu, 16 Apr 2020 02:42:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.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 @ Thu, 16 Apr 2020 02:42:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:42:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:42:59: 6000000 INFO @ Thu, 16 Apr 2020 02:43:02: 13000000 INFO @ Thu, 16 Apr 2020 02:43:02: 1000000 INFO @ Thu, 16 Apr 2020 02:43:05: 7000000 INFO @ Thu, 16 Apr 2020 02:43:07: 14000000 INFO @ Thu, 16 Apr 2020 02:43:08: 2000000 INFO @ Thu, 16 Apr 2020 02:43:10: 8000000 INFO @ Thu, 16 Apr 2020 02:43:12: 15000000 INFO @ Thu, 16 Apr 2020 02:43:13: 3000000 INFO @ Thu, 16 Apr 2020 02:43:15: 9000000 INFO @ Thu, 16 Apr 2020 02:43:17: 16000000 INFO @ Thu, 16 Apr 2020 02:43:18: 4000000 INFO @ Thu, 16 Apr 2020 02:43:20: 10000000 INFO @ Thu, 16 Apr 2020 02:43:22: 17000000 INFO @ Thu, 16 Apr 2020 02:43:23: 5000000 INFO @ Thu, 16 Apr 2020 02:43:25: 11000000 INFO @ Thu, 16 Apr 2020 02:43:27: 18000000 INFO @ Thu, 16 Apr 2020 02:43:29: 6000000 INFO @ Thu, 16 Apr 2020 02:43:31: 12000000 INFO @ Thu, 16 Apr 2020 02:43:32: 19000000 INFO @ Thu, 16 Apr 2020 02:43:34: 7000000 INFO @ Thu, 16 Apr 2020 02:43:36: 13000000 INFO @ Thu, 16 Apr 2020 02:43:38: 20000000 INFO @ Thu, 16 Apr 2020 02:43:39: 8000000 INFO @ Thu, 16 Apr 2020 02:43:41: 14000000 INFO @ Thu, 16 Apr 2020 02:43:43: 21000000 INFO @ Thu, 16 Apr 2020 02:43:44: 9000000 INFO @ Thu, 16 Apr 2020 02:43:46: 15000000 INFO @ Thu, 16 Apr 2020 02:43:48: 22000000 INFO @ Thu, 16 Apr 2020 02:43:49: 10000000 INFO @ Thu, 16 Apr 2020 02:43:51: 16000000 INFO @ Thu, 16 Apr 2020 02:43:53: 23000000 INFO @ Thu, 16 Apr 2020 02:43:55: 11000000 INFO @ Thu, 16 Apr 2020 02:43:56: 17000000 INFO @ Thu, 16 Apr 2020 02:43:58: 24000000 INFO @ Thu, 16 Apr 2020 02:44:00: 12000000 INFO @ Thu, 16 Apr 2020 02:44:01: 18000000 INFO @ Thu, 16 Apr 2020 02:44:03: 25000000 INFO @ Thu, 16 Apr 2020 02:44:05: 13000000 INFO @ Thu, 16 Apr 2020 02:44:06: 19000000 INFO @ Thu, 16 Apr 2020 02:44:09: 26000000 INFO @ Thu, 16 Apr 2020 02:44:10: 14000000 INFO @ Thu, 16 Apr 2020 02:44:11: 20000000 INFO @ Thu, 16 Apr 2020 02:44:14: 27000000 INFO @ Thu, 16 Apr 2020 02:44:15: 15000000 INFO @ Thu, 16 Apr 2020 02:44:17: 21000000 INFO @ Thu, 16 Apr 2020 02:44:19: 28000000 INFO @ Thu, 16 Apr 2020 02:44:20: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:44:20: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:44:20: #1 total tags in treatment: 28124730 INFO @ Thu, 16 Apr 2020 02:44:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:44:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 02:44:20: 16000000 INFO @ Thu, 16 Apr 2020 02:44:20: #1 tags after filtering in treatment: 28124730 INFO @ Thu, 16 Apr 2020 02:44:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:44:20: #1 finished! INFO @ Thu, 16 Apr 2020 02:44:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:44:22: 22000000 INFO @ Thu, 16 Apr 2020 02:44:22: #2 number of paired peaks: 369 WARNING @ Thu, 16 Apr 2020 02:44:22: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Thu, 16 Apr 2020 02:44:22: start model_add_line... INFO @ Thu, 16 Apr 2020 02:44:22: start X-correlation... INFO @ Thu, 16 Apr 2020 02:44:22: end of X-cor INFO @ Thu, 16 Apr 2020 02:44:22: #2 finished! INFO @ Thu, 16 Apr 2020 02:44:22: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:44:22: #2 alternative fragment length(s) may be 1,30 bps INFO @ Thu, 16 Apr 2020 02:44:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.05_model.r WARNING @ Thu, 16 Apr 2020 02:44:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:44:22: #2 You may need to consider one of the other alternative d(s): 1,30 WARNING @ Thu, 16 Apr 2020 02:44:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 02:44:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:44:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:44:25: 17000000 INFO @ Thu, 16 Apr 2020 02:44:27: 23000000 INFO @ Thu, 16 Apr 2020 02:44:31: 18000000 INFO @ Thu, 16 Apr 2020 02:44:32: 24000000 INFO @ Thu, 16 Apr 2020 02:44:36: 19000000 INFO @ Thu, 16 Apr 2020 02:44:37: 25000000 INFO @ Thu, 16 Apr 2020 02:44:41: 20000000 INFO @ Thu, 16 Apr 2020 02:44:42: 26000000 INFO @ Thu, 16 Apr 2020 02:44:46: 21000000 INFO @ Thu, 16 Apr 2020 02:44:48: 27000000 INFO @ Thu, 16 Apr 2020 02:44:51: 22000000 INFO @ Thu, 16 Apr 2020 02:44:53: 28000000 INFO @ Thu, 16 Apr 2020 02:44:54: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:44:54: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:44:54: #1 total tags in treatment: 28124730 INFO @ Thu, 16 Apr 2020 02:44:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:44:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 02:44:54: #1 tags after filtering in treatment: 28124730 INFO @ Thu, 16 Apr 2020 02:44:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:44:54: #1 finished! INFO @ Thu, 16 Apr 2020 02:44:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:44:56: #2 number of paired peaks: 369 WARNING @ Thu, 16 Apr 2020 02:44:56: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Thu, 16 Apr 2020 02:44:56: start model_add_line... INFO @ Thu, 16 Apr 2020 02:44:56: 23000000 INFO @ Thu, 16 Apr 2020 02:44:56: start X-correlation... INFO @ Thu, 16 Apr 2020 02:44:56: end of X-cor INFO @ Thu, 16 Apr 2020 02:44:56: #2 finished! INFO @ Thu, 16 Apr 2020 02:44:56: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:44:56: #2 alternative fragment length(s) may be 1,30 bps INFO @ Thu, 16 Apr 2020 02:44:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.10_model.r WARNING @ Thu, 16 Apr 2020 02:44:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:44:56: #2 You may need to consider one of the other alternative d(s): 1,30 WARNING @ Thu, 16 Apr 2020 02:44:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 02:44:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:44:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:45:01: 24000000 INFO @ Thu, 16 Apr 2020 02:45:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:45:06: 25000000 INFO @ Thu, 16 Apr 2020 02:45:11: 26000000 INFO @ Thu, 16 Apr 2020 02:45:16: 27000000 INFO @ Thu, 16 Apr 2020 02:45:21: 28000000 INFO @ Thu, 16 Apr 2020 02:45:22: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:45:22: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:45:22: #1 total tags in treatment: 28124730 INFO @ Thu, 16 Apr 2020 02:45:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:45:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 02:45:22: #1 tags after filtering in treatment: 28124730 INFO @ Thu, 16 Apr 2020 02:45:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:45:22: #1 finished! INFO @ Thu, 16 Apr 2020 02:45:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:45:24: #2 number of paired peaks: 369 WARNING @ Thu, 16 Apr 2020 02:45:24: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Thu, 16 Apr 2020 02:45:24: start model_add_line... INFO @ Thu, 16 Apr 2020 02:45:24: start X-correlation... INFO @ Thu, 16 Apr 2020 02:45:24: end of X-cor INFO @ Thu, 16 Apr 2020 02:45:24: #2 finished! INFO @ Thu, 16 Apr 2020 02:45:24: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:45:24: #2 alternative fragment length(s) may be 1,30 bps INFO @ Thu, 16 Apr 2020 02:45:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.20_model.r WARNING @ Thu, 16 Apr 2020 02:45:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:45:24: #2 You may need to consider one of the other alternative d(s): 1,30 WARNING @ Thu, 16 Apr 2020 02:45:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 02:45:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.05_summits.bed INFO @ Thu, 16 Apr 2020 02:45:26: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:45:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.10_summits.bed INFO @ Thu, 16 Apr 2020 02:45:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:46:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:46:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:46:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:46:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436046/SRX5436046.20_summits.bed INFO @ Thu, 16 Apr 2020 02:46:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。