Job ID = 5720854 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,425,834 reads read : 33,425,834 reads written : 33,425,834 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: 00:10:35 33425834 reads; of these: 33425834 (100.00%) were unpaired; of these: 1126411 (3.37%) aligned 0 times 22098483 (66.11%) aligned exactly 1 time 10200940 (30.52%) aligned >1 times 96.63% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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] 4711472 / 32299423 = 0.1459 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 02:43:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.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 02:43:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:43:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:43:05: 1000000 INFO @ Thu, 16 Apr 2020 02:43:10: 2000000 INFO @ Thu, 16 Apr 2020 02:43:15: 3000000 INFO @ Thu, 16 Apr 2020 02:43:20: 4000000 INFO @ Thu, 16 Apr 2020 02:43:25: 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 02:43:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.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 02:43:29: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:43:29: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:43:30: 6000000 INFO @ Thu, 16 Apr 2020 02:43:35: 7000000 INFO @ Thu, 16 Apr 2020 02:43:36: 1000000 INFO @ Thu, 16 Apr 2020 02:43:41: 8000000 INFO @ Thu, 16 Apr 2020 02:43:42: 2000000 INFO @ Thu, 16 Apr 2020 02:43:47: 9000000 INFO @ Thu, 16 Apr 2020 02:43:49: 3000000 INFO @ Thu, 16 Apr 2020 02:43:52: 10000000 INFO @ Thu, 16 Apr 2020 02:43:56: 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 @ Thu, 16 Apr 2020 02:43:58: 11000000 INFO @ Thu, 16 Apr 2020 02:43:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.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 02:43:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:43:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:44:02: 5000000 INFO @ Thu, 16 Apr 2020 02:44:04: 12000000 INFO @ Thu, 16 Apr 2020 02:44:05: 1000000 INFO @ Thu, 16 Apr 2020 02:44:09: 6000000 INFO @ Thu, 16 Apr 2020 02:44:09: 13000000 INFO @ Thu, 16 Apr 2020 02:44:11: 2000000 INFO @ Thu, 16 Apr 2020 02:44:15: 14000000 INFO @ Thu, 16 Apr 2020 02:44:16: 7000000 INFO @ Thu, 16 Apr 2020 02:44:17: 3000000 INFO @ Thu, 16 Apr 2020 02:44:20: 15000000 INFO @ Thu, 16 Apr 2020 02:44:22: 8000000 INFO @ Thu, 16 Apr 2020 02:44:23: 4000000 INFO @ Thu, 16 Apr 2020 02:44:26: 16000000 INFO @ Thu, 16 Apr 2020 02:44:29: 9000000 INFO @ Thu, 16 Apr 2020 02:44:30: 5000000 INFO @ Thu, 16 Apr 2020 02:44:32: 17000000 INFO @ Thu, 16 Apr 2020 02:44:35: 6000000 INFO @ Thu, 16 Apr 2020 02:44:35: 10000000 INFO @ Thu, 16 Apr 2020 02:44:37: 18000000 INFO @ Thu, 16 Apr 2020 02:44:42: 7000000 INFO @ Thu, 16 Apr 2020 02:44:42: 11000000 INFO @ Thu, 16 Apr 2020 02:44:43: 19000000 INFO @ Thu, 16 Apr 2020 02:44:48: 8000000 INFO @ Thu, 16 Apr 2020 02:44:48: 12000000 INFO @ Thu, 16 Apr 2020 02:44:49: 20000000 INFO @ Thu, 16 Apr 2020 02:44:54: 21000000 INFO @ Thu, 16 Apr 2020 02:44:54: 9000000 INFO @ Thu, 16 Apr 2020 02:44:55: 13000000 INFO @ Thu, 16 Apr 2020 02:45:00: 22000000 INFO @ Thu, 16 Apr 2020 02:45:00: 10000000 INFO @ Thu, 16 Apr 2020 02:45:01: 14000000 INFO @ Thu, 16 Apr 2020 02:45:06: 23000000 INFO @ Thu, 16 Apr 2020 02:45:06: 11000000 INFO @ Thu, 16 Apr 2020 02:45:08: 15000000 INFO @ Thu, 16 Apr 2020 02:45:11: 24000000 INFO @ Thu, 16 Apr 2020 02:45:13: 12000000 INFO @ Thu, 16 Apr 2020 02:45:14: 16000000 INFO @ Thu, 16 Apr 2020 02:45:17: 25000000 INFO @ Thu, 16 Apr 2020 02:45:19: 13000000 INFO @ Thu, 16 Apr 2020 02:45:21: 17000000 INFO @ Thu, 16 Apr 2020 02:45:23: 26000000 INFO @ Thu, 16 Apr 2020 02:45:25: 14000000 INFO @ Thu, 16 Apr 2020 02:45:27: 18000000 INFO @ Thu, 16 Apr 2020 02:45:29: 27000000 INFO @ Thu, 16 Apr 2020 02:45:32: 15000000 INFO @ Thu, 16 Apr 2020 02:45:32: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:45:32: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:45:32: #1 total tags in treatment: 27587951 INFO @ Thu, 16 Apr 2020 02:45:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:45:32: #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 02:45:33: #1 tags after filtering in treatment: 27587951 INFO @ Thu, 16 Apr 2020 02:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:45:33: #1 finished! INFO @ Thu, 16 Apr 2020 02:45:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:45:34: 19000000 INFO @ Thu, 16 Apr 2020 02:45:34: #2 number of paired peaks: 383 WARNING @ Thu, 16 Apr 2020 02:45:34: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 16 Apr 2020 02:45:34: start model_add_line... INFO @ Thu, 16 Apr 2020 02:45:35: start X-correlation... INFO @ Thu, 16 Apr 2020 02:45:35: end of X-cor INFO @ Thu, 16 Apr 2020 02:45:35: #2 finished! INFO @ Thu, 16 Apr 2020 02:45:35: #2 predicted fragment length is 2 bps INFO @ Thu, 16 Apr 2020 02:45:35: #2 alternative fragment length(s) may be 2,32 bps INFO @ Thu, 16 Apr 2020 02:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.05_model.r WARNING @ Thu, 16 Apr 2020 02:45:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:45:35: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Thu, 16 Apr 2020 02:45:35: #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 02:45:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:45:38: 16000000 INFO @ Thu, 16 Apr 2020 02:45:40: 20000000 INFO @ Thu, 16 Apr 2020 02:45:44: 17000000 INFO @ Thu, 16 Apr 2020 02:45:47: 21000000 INFO @ Thu, 16 Apr 2020 02:45:50: 18000000 INFO @ Thu, 16 Apr 2020 02:45:53: 22000000 INFO @ Thu, 16 Apr 2020 02:45:57: 19000000 INFO @ Thu, 16 Apr 2020 02:46:00: 23000000 INFO @ Thu, 16 Apr 2020 02:46:03: 20000000 INFO @ Thu, 16 Apr 2020 02:46:06: 24000000 INFO @ Thu, 16 Apr 2020 02:46:09: 21000000 INFO @ Thu, 16 Apr 2020 02:46:13: 25000000 INFO @ Thu, 16 Apr 2020 02:46:16: 22000000 INFO @ Thu, 16 Apr 2020 02:46:19: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:46:19: 26000000 INFO @ Thu, 16 Apr 2020 02:46:22: 23000000 INFO @ Thu, 16 Apr 2020 02:46:26: 27000000 INFO @ Thu, 16 Apr 2020 02:46:28: 24000000 INFO @ Thu, 16 Apr 2020 02:46:30: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:46:30: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:46:30: #1 total tags in treatment: 27587951 INFO @ Thu, 16 Apr 2020 02:46:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:46:30: #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 02:46:30: #1 tags after filtering in treatment: 27587951 INFO @ Thu, 16 Apr 2020 02:46:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:46:30: #1 finished! INFO @ Thu, 16 Apr 2020 02:46:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:46:32: #2 number of paired peaks: 383 WARNING @ Thu, 16 Apr 2020 02:46:32: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 16 Apr 2020 02:46:32: start model_add_line... INFO @ Thu, 16 Apr 2020 02:46:32: start X-correlation... INFO @ Thu, 16 Apr 2020 02:46:32: end of X-cor INFO @ Thu, 16 Apr 2020 02:46:32: #2 finished! INFO @ Thu, 16 Apr 2020 02:46:32: #2 predicted fragment length is 2 bps INFO @ Thu, 16 Apr 2020 02:46:32: #2 alternative fragment length(s) may be 2,32 bps INFO @ Thu, 16 Apr 2020 02:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.10_model.r WARNING @ Thu, 16 Apr 2020 02:46:32: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:46:32: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Thu, 16 Apr 2020 02:46:32: #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 02:46:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:46:34: 25000000 INFO @ Thu, 16 Apr 2020 02:46:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:46:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:46:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.05_summits.bed INFO @ Thu, 16 Apr 2020 02:46:39: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:46:40: 26000000 INFO @ Thu, 16 Apr 2020 02:46:47: 27000000 INFO @ Thu, 16 Apr 2020 02:46:50: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:46:50: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:46:50: #1 total tags in treatment: 27587951 INFO @ Thu, 16 Apr 2020 02:46:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:46:50: #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 02:46:51: #1 tags after filtering in treatment: 27587951 INFO @ Thu, 16 Apr 2020 02:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:46:51: #1 finished! INFO @ Thu, 16 Apr 2020 02:46:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:46:53: #2 number of paired peaks: 383 WARNING @ Thu, 16 Apr 2020 02:46:53: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 16 Apr 2020 02:46:53: start model_add_line... INFO @ Thu, 16 Apr 2020 02:46:53: start X-correlation... INFO @ Thu, 16 Apr 2020 02:46:53: end of X-cor INFO @ Thu, 16 Apr 2020 02:46:53: #2 finished! INFO @ Thu, 16 Apr 2020 02:46:53: #2 predicted fragment length is 2 bps INFO @ Thu, 16 Apr 2020 02:46:53: #2 alternative fragment length(s) may be 2,32 bps INFO @ Thu, 16 Apr 2020 02:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.20_model.r WARNING @ Thu, 16 Apr 2020 02:46:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:46:53: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Thu, 16 Apr 2020 02:46:53: #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 02:46:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:47:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:47:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:47:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:47:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:47:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.10_summits.bed INFO @ Thu, 16 Apr 2020 02:47:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436047/SRX5436047.20_summits.bed INFO @ Thu, 16 Apr 2020 02:47:57: Done! pass1 - making usageList (0 chroms): 0 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。