Job ID = 6458774 SRX = SRX5436047 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:37:29 prefetch.2.10.7: 1) Downloading 'SRR8637379'... 2020-06-21T12:37:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:44:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:44:54 prefetch.2.10.7: 1) 'SRR8637379' was downloaded successfully Read 33425834 spots for SRR8637379/SRR8637379.sra Written 33425834 spots for SRR8637379/SRR8637379.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: 00:09:21 33425834 reads; of these: 33425834 (100.00%) were unpaired; of these: 1392295 (4.17%) aligned 0 times 22121109 (66.18%) aligned exactly 1 time 9912430 (29.65%) aligned >1 times 95.83% overall alignment rate Time searching: 00:09:21 Overall time: 00:09:21 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] 5323823 / 32033539 = 0.1662 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 22:02:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/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 @ Sun, 21 Jun 2020 22:02:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:04: 1000000 INFO @ Sun, 21 Jun 2020 22:03:12: 2000000 INFO @ Sun, 21 Jun 2020 22:03:19: 3000000 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 22:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/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 @ Sun, 21 Jun 2020 22:03:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:27: 4000000 INFO @ Sun, 21 Jun 2020 22:03:35: 1000000 INFO @ Sun, 21 Jun 2020 22:03:35: 5000000 INFO @ Sun, 21 Jun 2020 22:03:44: 2000000 INFO @ Sun, 21 Jun 2020 22:03:44: 6000000 INFO @ Sun, 21 Jun 2020 22:03:52: 3000000 INFO @ Sun, 21 Jun 2020 22:03:52: 7000000 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 22:03:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/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 @ Sun, 21 Jun 2020 22:03:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:01: 4000000 INFO @ Sun, 21 Jun 2020 22:04:01: 8000000 INFO @ Sun, 21 Jun 2020 22:04:06: 1000000 INFO @ Sun, 21 Jun 2020 22:04:10: 9000000 INFO @ Sun, 21 Jun 2020 22:04:10: 5000000 INFO @ Sun, 21 Jun 2020 22:04:15: 2000000 INFO @ Sun, 21 Jun 2020 22:04:19: 10000000 INFO @ Sun, 21 Jun 2020 22:04:20: 6000000 INFO @ Sun, 21 Jun 2020 22:04:23: 3000000 INFO @ Sun, 21 Jun 2020 22:04:28: 11000000 INFO @ Sun, 21 Jun 2020 22:04:29: 7000000 INFO @ Sun, 21 Jun 2020 22:04:32: 4000000 INFO @ Sun, 21 Jun 2020 22:04:37: 12000000 INFO @ Sun, 21 Jun 2020 22:04:38: 8000000 INFO @ Sun, 21 Jun 2020 22:04:41: 5000000 INFO @ Sun, 21 Jun 2020 22:04:46: 13000000 INFO @ Sun, 21 Jun 2020 22:04:47: 9000000 INFO @ Sun, 21 Jun 2020 22:04:50: 6000000 INFO @ Sun, 21 Jun 2020 22:04:55: 14000000 INFO @ Sun, 21 Jun 2020 22:04:56: 10000000 INFO @ Sun, 21 Jun 2020 22:04:59: 7000000 INFO @ Sun, 21 Jun 2020 22:05:05: 15000000 INFO @ Sun, 21 Jun 2020 22:05:05: 11000000 INFO @ Sun, 21 Jun 2020 22:05:08: 8000000 INFO @ Sun, 21 Jun 2020 22:05:14: 16000000 INFO @ Sun, 21 Jun 2020 22:05:14: 12000000 INFO @ Sun, 21 Jun 2020 22:05:17: 9000000 INFO @ Sun, 21 Jun 2020 22:05:22: 17000000 INFO @ Sun, 21 Jun 2020 22:05:23: 13000000 INFO @ Sun, 21 Jun 2020 22:05:26: 10000000 INFO @ Sun, 21 Jun 2020 22:05:31: 18000000 INFO @ Sun, 21 Jun 2020 22:05:32: 14000000 INFO @ Sun, 21 Jun 2020 22:05:35: 11000000 INFO @ Sun, 21 Jun 2020 22:05:40: 19000000 INFO @ Sun, 21 Jun 2020 22:05:42: 15000000 INFO @ Sun, 21 Jun 2020 22:05:44: 12000000 INFO @ Sun, 21 Jun 2020 22:05:49: 20000000 INFO @ Sun, 21 Jun 2020 22:05:51: 16000000 INFO @ Sun, 21 Jun 2020 22:05:53: 13000000 INFO @ Sun, 21 Jun 2020 22:05:58: 21000000 INFO @ Sun, 21 Jun 2020 22:06:00: 17000000 INFO @ Sun, 21 Jun 2020 22:06:02: 14000000 INFO @ Sun, 21 Jun 2020 22:06:07: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:06:09: 18000000 INFO @ Sun, 21 Jun 2020 22:06:12: 15000000 INFO @ Sun, 21 Jun 2020 22:06:16: 23000000 INFO @ Sun, 21 Jun 2020 22:06:19: 19000000 INFO @ Sun, 21 Jun 2020 22:06:21: 16000000 INFO @ Sun, 21 Jun 2020 22:06:25: 24000000 INFO @ Sun, 21 Jun 2020 22:06:28: 20000000 INFO @ Sun, 21 Jun 2020 22:06:30: 17000000 INFO @ Sun, 21 Jun 2020 22:06:34: 25000000 INFO @ Sun, 21 Jun 2020 22:06:37: 21000000 INFO @ Sun, 21 Jun 2020 22:06:39: 18000000 INFO @ Sun, 21 Jun 2020 22:06:43: 26000000 INFO @ Sun, 21 Jun 2020 22:06:46: 22000000 INFO @ Sun, 21 Jun 2020 22:06:48: 19000000 INFO @ Sun, 21 Jun 2020 22:06:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:06:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:06:50: #1 total tags in treatment: 26709716 INFO @ Sun, 21 Jun 2020 22:06:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:50: #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 22:06:50: #1 tags after filtering in treatment: 26709659 INFO @ Sun, 21 Jun 2020 22:06:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:50: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:52: #2 number of paired peaks: 935 WARNING @ Sun, 21 Jun 2020 22:06:52: Fewer paired peaks (935) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 935 pairs to build model! INFO @ Sun, 21 Jun 2020 22:06:52: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:53: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:53: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:53: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:53: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:06:53: #2 alternative fragment length(s) may be 1,36 bps INFO @ Sun, 21 Jun 2020 22:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.05_model.r WARNING @ Sun, 21 Jun 2020 22:06:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:53: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Sun, 21 Jun 2020 22:06:53: #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 22:06:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:56: 23000000 INFO @ Sun, 21 Jun 2020 22:06:57: 20000000 INFO @ Sun, 21 Jun 2020 22:07:05: 24000000 INFO @ Sun, 21 Jun 2020 22:07:06: 21000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:07:14: 25000000 INFO @ Sun, 21 Jun 2020 22:07:15: 22000000 INFO @ Sun, 21 Jun 2020 22:07:22: 26000000 INFO @ Sun, 21 Jun 2020 22:07:24: 23000000 INFO @ Sun, 21 Jun 2020 22:07:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:07:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:07:29: #1 total tags in treatment: 26709716 INFO @ Sun, 21 Jun 2020 22:07:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:29: #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 22:07:29: #1 tags after filtering in treatment: 26709659 INFO @ Sun, 21 Jun 2020 22:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:29: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:31: #2 number of paired peaks: 935 WARNING @ Sun, 21 Jun 2020 22:07:31: Fewer paired peaks (935) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 935 pairs to build model! INFO @ Sun, 21 Jun 2020 22:07:31: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:31: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:31: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:31: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:31: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:07:31: #2 alternative fragment length(s) may be 1,36 bps INFO @ Sun, 21 Jun 2020 22:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.10_model.r WARNING @ Sun, 21 Jun 2020 22:07:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:07:31: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Sun, 21 Jun 2020 22:07:31: #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 22:07:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:07:33: 24000000 INFO @ Sun, 21 Jun 2020 22:07:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:41: 25000000 INFO @ Sun, 21 Jun 2020 22:07:48: 26000000 INFO @ Sun, 21 Jun 2020 22:07:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:07:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:07:54: #1 total tags in treatment: 26709716 INFO @ Sun, 21 Jun 2020 22:07:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:54: #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 22:07:55: #1 tags after filtering in treatment: 26709659 INFO @ Sun, 21 Jun 2020 22:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:55: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:57: #2 number of paired peaks: 935 WARNING @ Sun, 21 Jun 2020 22:07:57: Fewer paired peaks (935) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 935 pairs to build model! INFO @ Sun, 21 Jun 2020 22:07:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:57: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:07:57: #2 alternative fragment length(s) may be 1,36 bps INFO @ Sun, 21 Jun 2020 22:07:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.20_model.r WARNING @ Sun, 21 Jun 2020 22:07:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:07:57: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Sun, 21 Jun 2020 22:07:57: #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 22:07:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.05_summits.bed INFO @ Sun, 21 Jun 2020 22:08:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:08:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.10_summits.bed INFO @ Sun, 21 Jun 2020 22:08:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:08:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:09:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436047/SRX5436047.20_summits.bed INFO @ Sun, 21 Jun 2020 22:09:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling