Job ID = 6457643 SRX = SRX467051 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:08:22 prefetch.2.10.7: 1) Downloading 'SRR1164475'... 2020-06-21T12:08:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:12:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:12:23 prefetch.2.10.7: 1) 'SRR1164475' was downloaded successfully Read 34009141 spots for SRR1164475/SRR1164475.sra Written 34009141 spots for SRR1164475/SRR1164475.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: 00:08:22 34009141 reads; of these: 34009141 (100.00%) were unpaired; of these: 1611011 (4.74%) aligned 0 times 25913161 (76.19%) aligned exactly 1 time 6484969 (19.07%) aligned >1 times 95.26% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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 16 files... [bam_rmdupse_core] 11044343 / 32398130 = 0.3409 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 21:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.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 21:31:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:20: 1000000 INFO @ Sun, 21 Jun 2020 21:31:26: 2000000 INFO @ Sun, 21 Jun 2020 21:31:32: 3000000 INFO @ Sun, 21 Jun 2020 21:31:37: 4000000 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 21:31:43: 5000000 INFO @ Sun, 21 Jun 2020 21:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.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 21:31:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:48: 6000000 INFO @ Sun, 21 Jun 2020 21:31:50: 1000000 INFO @ Sun, 21 Jun 2020 21:31:54: 7000000 INFO @ Sun, 21 Jun 2020 21:31:56: 2000000 INFO @ Sun, 21 Jun 2020 21:32:00: 8000000 INFO @ Sun, 21 Jun 2020 21:32:02: 3000000 INFO @ Sun, 21 Jun 2020 21:32:05: 9000000 INFO @ Sun, 21 Jun 2020 21:32:07: 4000000 INFO @ Sun, 21 Jun 2020 21:32:11: 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 21:32:13: 5000000 INFO @ Sun, 21 Jun 2020 21:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.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 21:32:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:16: 11000000 INFO @ Sun, 21 Jun 2020 21:32:19: 6000000 INFO @ Sun, 21 Jun 2020 21:32:21: 1000000 INFO @ Sun, 21 Jun 2020 21:32:22: 12000000 INFO @ Sun, 21 Jun 2020 21:32:25: 7000000 INFO @ Sun, 21 Jun 2020 21:32:27: 13000000 INFO @ Sun, 21 Jun 2020 21:32:28: 2000000 INFO @ Sun, 21 Jun 2020 21:32:31: 8000000 INFO @ Sun, 21 Jun 2020 21:32:32: 14000000 INFO @ Sun, 21 Jun 2020 21:32:34: 3000000 INFO @ Sun, 21 Jun 2020 21:32:37: 9000000 INFO @ Sun, 21 Jun 2020 21:32:38: 15000000 INFO @ Sun, 21 Jun 2020 21:32:41: 4000000 INFO @ Sun, 21 Jun 2020 21:32:43: 10000000 INFO @ Sun, 21 Jun 2020 21:32:43: 16000000 INFO @ Sun, 21 Jun 2020 21:32:47: 5000000 INFO @ Sun, 21 Jun 2020 21:32:49: 11000000 INFO @ Sun, 21 Jun 2020 21:32:49: 17000000 INFO @ Sun, 21 Jun 2020 21:32:53: 6000000 INFO @ Sun, 21 Jun 2020 21:32:54: 12000000 INFO @ Sun, 21 Jun 2020 21:32:55: 18000000 INFO @ Sun, 21 Jun 2020 21:32:59: 7000000 INFO @ Sun, 21 Jun 2020 21:33:00: 13000000 INFO @ Sun, 21 Jun 2020 21:33:01: 19000000 INFO @ Sun, 21 Jun 2020 21:33:05: 8000000 INFO @ Sun, 21 Jun 2020 21:33:06: 14000000 INFO @ Sun, 21 Jun 2020 21:33:06: 20000000 INFO @ Sun, 21 Jun 2020 21:33:11: 9000000 INFO @ Sun, 21 Jun 2020 21:33:12: 21000000 INFO @ Sun, 21 Jun 2020 21:33:12: 15000000 INFO @ Sun, 21 Jun 2020 21:33:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:14: #1 total tags in treatment: 21353787 INFO @ Sun, 21 Jun 2020 21:33:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:14: #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 21:33:15: #1 tags after filtering in treatment: 21353786 INFO @ Sun, 21 Jun 2020 21:33:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:15: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:16: #2 number of paired peaks: 140 WARNING @ Sun, 21 Jun 2020 21:33:16: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 21 Jun 2020 21:33:16: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:17: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:33:17: #2 alternative fragment length(s) may be 2,46,71,110,126,188,234,342,359,423,476,497,515,552,589 bps INFO @ Sun, 21 Jun 2020 21:33:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.05_model.r WARNING @ Sun, 21 Jun 2020 21:33:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:17: #2 You may need to consider one of the other alternative d(s): 2,46,71,110,126,188,234,342,359,423,476,497,515,552,589 WARNING @ Sun, 21 Jun 2020 21:33:17: #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 21:33:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:17: 10000000 INFO @ Sun, 21 Jun 2020 21:33:18: 16000000 INFO @ Sun, 21 Jun 2020 21:33:23: 11000000 INFO @ Sun, 21 Jun 2020 21:33:24: 17000000 INFO @ Sun, 21 Jun 2020 21:33:29: 12000000 INFO @ Sun, 21 Jun 2020 21:33:31: 18000000 INFO @ Sun, 21 Jun 2020 21:33:35: 13000000 INFO @ Sun, 21 Jun 2020 21:33:37: 19000000 INFO @ Sun, 21 Jun 2020 21:33:41: 14000000 INFO @ Sun, 21 Jun 2020 21:33:42: 20000000 INFO @ Sun, 21 Jun 2020 21:33:46: 15000000 INFO @ Sun, 21 Jun 2020 21:33:48: 21000000 INFO @ Sun, 21 Jun 2020 21:33:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:51: #1 total tags in treatment: 21353787 INFO @ Sun, 21 Jun 2020 21:33:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:51: #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 21:33:52: #1 tags after filtering in treatment: 21353786 INFO @ Sun, 21 Jun 2020 21:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:52: 16000000 INFO @ Sun, 21 Jun 2020 21:33:53: #2 number of paired peaks: 140 WARNING @ Sun, 21 Jun 2020 21:33:53: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 21 Jun 2020 21:33:53: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:53: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:53: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:53: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:53: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:33:53: #2 alternative fragment length(s) may be 2,46,71,110,126,188,234,342,359,423,476,497,515,552,589 bps INFO @ Sun, 21 Jun 2020 21:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.10_model.r WARNING @ Sun, 21 Jun 2020 21:33:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:53: #2 You may need to consider one of the other alternative d(s): 2,46,71,110,126,188,234,342,359,423,476,497,515,552,589 WARNING @ Sun, 21 Jun 2020 21:33:53: #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 21:33:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:57: 17000000 INFO @ Sun, 21 Jun 2020 21:34:04: 18000000 INFO @ Sun, 21 Jun 2020 21:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.05_summits.bed INFO @ Sun, 21 Jun 2020 21:34:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:34:09: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:34:14: 20000000 INFO @ Sun, 21 Jun 2020 21:34:20: 21000000 INFO @ Sun, 21 Jun 2020 21:34:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:34:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:34:22: #1 total tags in treatment: 21353787 INFO @ Sun, 21 Jun 2020 21:34:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:22: #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 21:34:23: #1 tags after filtering in treatment: 21353786 INFO @ Sun, 21 Jun 2020 21:34:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:23: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:34:24: #2 number of paired peaks: 140 WARNING @ Sun, 21 Jun 2020 21:34:24: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 21 Jun 2020 21:34:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:34:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:34:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:34:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:34:24: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:34:24: #2 alternative fragment length(s) may be 2,46,71,110,126,188,234,342,359,423,476,497,515,552,589 bps INFO @ Sun, 21 Jun 2020 21:34:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.20_model.r WARNING @ Sun, 21 Jun 2020 21:34:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:34:24: #2 You may need to consider one of the other alternative d(s): 2,46,71,110,126,188,234,342,359,423,476,497,515,552,589 WARNING @ Sun, 21 Jun 2020 21:34:24: #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 21:34:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:34:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.10_summits.bed INFO @ Sun, 21 Jun 2020 21:34:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:34:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467051/SRX467051.20_summits.bed INFO @ Sun, 21 Jun 2020 21:35:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。