Job ID = 5720864 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,927,548 reads read : 40,927,548 reads written : 40,927,548 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: 00:13:03 40927548 reads; of these: 40927548 (100.00%) were unpaired; of these: 1739000 (4.25%) aligned 0 times 27013351 (66.00%) aligned exactly 1 time 12175197 (29.75%) aligned >1 times 95.75% overall alignment rate Time searching: 00:13:03 Overall time: 00:13:03 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] 7124303 / 39188548 = 0.1818 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 03:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.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 03:02:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:02:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:02:31: 1000000 INFO @ Thu, 16 Apr 2020 03:02:37: 2000000 INFO @ Thu, 16 Apr 2020 03:02:42: 3000000 INFO @ Thu, 16 Apr 2020 03:02:47: 4000000 INFO @ Thu, 16 Apr 2020 03:02:52: 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 03:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.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 03:02:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:02:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:02:57: 6000000 INFO @ Thu, 16 Apr 2020 03:03:02: 1000000 INFO @ Thu, 16 Apr 2020 03:03:03: 7000000 INFO @ Thu, 16 Apr 2020 03:03:08: 2000000 INFO @ Thu, 16 Apr 2020 03:03:09: 8000000 INFO @ Thu, 16 Apr 2020 03:03:14: 3000000 INFO @ Thu, 16 Apr 2020 03:03:15: 9000000 INFO @ Thu, 16 Apr 2020 03:03:19: 4000000 INFO @ Thu, 16 Apr 2020 03:03:21: 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 @ Thu, 16 Apr 2020 03:03:25: 5000000 INFO @ Thu, 16 Apr 2020 03:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.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 03:03:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:03:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:03:27: 11000000 INFO @ Thu, 16 Apr 2020 03:03:32: 6000000 INFO @ Thu, 16 Apr 2020 03:03:33: 12000000 INFO @ Thu, 16 Apr 2020 03:03:34: 1000000 INFO @ Thu, 16 Apr 2020 03:03:38: 7000000 INFO @ Thu, 16 Apr 2020 03:03:39: 13000000 INFO @ Thu, 16 Apr 2020 03:03:41: 2000000 INFO @ Thu, 16 Apr 2020 03:03:44: 8000000 INFO @ Thu, 16 Apr 2020 03:03:46: 14000000 INFO @ Thu, 16 Apr 2020 03:03:48: 3000000 INFO @ Thu, 16 Apr 2020 03:03:51: 9000000 INFO @ Thu, 16 Apr 2020 03:03:52: 15000000 INFO @ Thu, 16 Apr 2020 03:03:55: 4000000 INFO @ Thu, 16 Apr 2020 03:03:57: 10000000 INFO @ Thu, 16 Apr 2020 03:03:58: 16000000 INFO @ Thu, 16 Apr 2020 03:04:02: 5000000 INFO @ Thu, 16 Apr 2020 03:04:03: 11000000 INFO @ Thu, 16 Apr 2020 03:04:05: 17000000 INFO @ Thu, 16 Apr 2020 03:04:09: 6000000 INFO @ Thu, 16 Apr 2020 03:04:10: 12000000 INFO @ Thu, 16 Apr 2020 03:04:11: 18000000 INFO @ Thu, 16 Apr 2020 03:04:16: 13000000 INFO @ Thu, 16 Apr 2020 03:04:17: 7000000 INFO @ Thu, 16 Apr 2020 03:04:17: 19000000 INFO @ Thu, 16 Apr 2020 03:04:22: 14000000 INFO @ Thu, 16 Apr 2020 03:04:24: 20000000 INFO @ Thu, 16 Apr 2020 03:04:24: 8000000 INFO @ Thu, 16 Apr 2020 03:04:29: 15000000 INFO @ Thu, 16 Apr 2020 03:04:30: 21000000 INFO @ Thu, 16 Apr 2020 03:04:31: 9000000 INFO @ Thu, 16 Apr 2020 03:04:35: 16000000 INFO @ Thu, 16 Apr 2020 03:04:36: 22000000 INFO @ Thu, 16 Apr 2020 03:04:39: 10000000 INFO @ Thu, 16 Apr 2020 03:04:41: 17000000 INFO @ Thu, 16 Apr 2020 03:04:43: 23000000 INFO @ Thu, 16 Apr 2020 03:04:46: 11000000 INFO @ Thu, 16 Apr 2020 03:04:47: 18000000 INFO @ Thu, 16 Apr 2020 03:04:49: 24000000 INFO @ Thu, 16 Apr 2020 03:04:53: 12000000 INFO @ Thu, 16 Apr 2020 03:04:54: 19000000 INFO @ Thu, 16 Apr 2020 03:04:55: 25000000 INFO @ Thu, 16 Apr 2020 03:05:00: 13000000 INFO @ Thu, 16 Apr 2020 03:05:00: 20000000 INFO @ Thu, 16 Apr 2020 03:05:02: 26000000 INFO @ Thu, 16 Apr 2020 03:05:06: 21000000 INFO @ Thu, 16 Apr 2020 03:05:07: 14000000 INFO @ Thu, 16 Apr 2020 03:05:08: 27000000 INFO @ Thu, 16 Apr 2020 03:05:13: 22000000 INFO @ Thu, 16 Apr 2020 03:05:14: 28000000 INFO @ Thu, 16 Apr 2020 03:05:15: 15000000 INFO @ Thu, 16 Apr 2020 03:05:19: 23000000 INFO @ Thu, 16 Apr 2020 03:05:21: 29000000 INFO @ Thu, 16 Apr 2020 03:05:22: 16000000 INFO @ Thu, 16 Apr 2020 03:05:25: 24000000 INFO @ Thu, 16 Apr 2020 03:05:27: 30000000 INFO @ Thu, 16 Apr 2020 03:05:29: 17000000 INFO @ Thu, 16 Apr 2020 03:05:32: 25000000 INFO @ Thu, 16 Apr 2020 03:05:33: 31000000 INFO @ Thu, 16 Apr 2020 03:05:36: 18000000 INFO @ Thu, 16 Apr 2020 03:05:38: 26000000 INFO @ Thu, 16 Apr 2020 03:05:40: 32000000 INFO @ Thu, 16 Apr 2020 03:05:40: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:05:40: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:05:40: #1 total tags in treatment: 32064245 INFO @ Thu, 16 Apr 2020 03:05:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:05:40: #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 03:05:41: #1 tags after filtering in treatment: 32064245 INFO @ Thu, 16 Apr 2020 03:05:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:05:41: #1 finished! INFO @ Thu, 16 Apr 2020 03:05:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:05:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:05:43: #2 number of paired peaks: 287 WARNING @ Thu, 16 Apr 2020 03:05:43: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Thu, 16 Apr 2020 03:05:43: start model_add_line... INFO @ Thu, 16 Apr 2020 03:05:43: start X-correlation... INFO @ Thu, 16 Apr 2020 03:05:43: end of X-cor INFO @ Thu, 16 Apr 2020 03:05:43: #2 finished! INFO @ Thu, 16 Apr 2020 03:05:43: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:05:43: #2 alternative fragment length(s) may be 1,597 bps INFO @ Thu, 16 Apr 2020 03:05:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.05_model.r WARNING @ Thu, 16 Apr 2020 03:05:43: #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 03:05:43: #2 You may need to consider one of the other alternative d(s): 1,597 WARNING @ Thu, 16 Apr 2020 03:05:43: #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 03:05:43: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:05:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:05:44: 19000000 INFO @ Thu, 16 Apr 2020 03:05:45: 27000000 INFO @ Thu, 16 Apr 2020 03:05:51: 20000000 INFO @ Thu, 16 Apr 2020 03:05:51: 28000000 INFO @ Thu, 16 Apr 2020 03:05:57: 29000000 INFO @ Thu, 16 Apr 2020 03:05:58: 21000000 INFO @ Thu, 16 Apr 2020 03:06:04: 30000000 INFO @ Thu, 16 Apr 2020 03:06:05: 22000000 INFO @ Thu, 16 Apr 2020 03:06:10: 31000000 INFO @ Thu, 16 Apr 2020 03:06:13: 23000000 INFO @ Thu, 16 Apr 2020 03:06:17: 32000000 INFO @ Thu, 16 Apr 2020 03:06:17: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:06:17: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:06:17: #1 total tags in treatment: 32064245 INFO @ Thu, 16 Apr 2020 03:06:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:06:17: #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 03:06:18: #1 tags after filtering in treatment: 32064245 INFO @ Thu, 16 Apr 2020 03:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:06:18: #1 finished! INFO @ Thu, 16 Apr 2020 03:06:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:06:20: #2 number of paired peaks: 287 WARNING @ Thu, 16 Apr 2020 03:06:20: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Thu, 16 Apr 2020 03:06:20: start model_add_line... INFO @ Thu, 16 Apr 2020 03:06:20: start X-correlation... INFO @ Thu, 16 Apr 2020 03:06:20: end of X-cor INFO @ Thu, 16 Apr 2020 03:06:20: #2 finished! INFO @ Thu, 16 Apr 2020 03:06:20: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:06:20: #2 alternative fragment length(s) may be 1,597 bps INFO @ Thu, 16 Apr 2020 03:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.10_model.r WARNING @ Thu, 16 Apr 2020 03:06:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:06:20: #2 You may need to consider one of the other alternative d(s): 1,597 WARNING @ Thu, 16 Apr 2020 03:06:20: #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 03:06:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:06:20: 24000000 INFO @ Thu, 16 Apr 2020 03:06:27: 25000000 INFO @ Thu, 16 Apr 2020 03:06:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:06:34: 26000000 INFO @ Thu, 16 Apr 2020 03:06:40: 27000000 INFO @ Thu, 16 Apr 2020 03:06:46: 28000000 INFO @ Thu, 16 Apr 2020 03:06:53: 29000000 INFO @ Thu, 16 Apr 2020 03:06:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:06:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:06:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.05_summits.bed INFO @ Thu, 16 Apr 2020 03:06:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:07:00: 30000000 INFO @ Thu, 16 Apr 2020 03:07:06: 31000000 INFO @ Thu, 16 Apr 2020 03:07:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:07:13: 32000000 INFO @ Thu, 16 Apr 2020 03:07:13: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:07:13: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:07:13: #1 total tags in treatment: 32064245 INFO @ Thu, 16 Apr 2020 03:07:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:07:13: #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 03:07:14: #1 tags after filtering in treatment: 32064245 INFO @ Thu, 16 Apr 2020 03:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:07:14: #1 finished! INFO @ Thu, 16 Apr 2020 03:07:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:07:16: #2 number of paired peaks: 287 WARNING @ Thu, 16 Apr 2020 03:07:16: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Thu, 16 Apr 2020 03:07:16: start model_add_line... INFO @ Thu, 16 Apr 2020 03:07:16: start X-correlation... INFO @ Thu, 16 Apr 2020 03:07:16: end of X-cor INFO @ Thu, 16 Apr 2020 03:07:16: #2 finished! INFO @ Thu, 16 Apr 2020 03:07:16: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:07:16: #2 alternative fragment length(s) may be 1,597 bps INFO @ Thu, 16 Apr 2020 03:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.20_model.r WARNING @ Thu, 16 Apr 2020 03:07:16: #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 03:07:16: #2 You may need to consider one of the other alternative d(s): 1,597 WARNING @ Thu, 16 Apr 2020 03:07:16: #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 03:07:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:07:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:07:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:07:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.10_summits.bed INFO @ Thu, 16 Apr 2020 03:07:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:08:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:08:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:08:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:08:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436053/SRX5436053.20_summits.bed INFO @ Thu, 16 Apr 2020 03:08:27: 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。