Job ID = 6527627 SRX = SRX159169 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:37:38 prefetch.2.10.7: 1) Downloading 'SRR520450'... 2020-06-29T12:37:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:43:52 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:43:52 prefetch.2.10.7: 1) 'SRR520450' was downloaded successfully Read 43707761 spots for SRR520450/SRR520450.sra Written 43707761 spots for SRR520450/SRR520450.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: 00:11:55 43707761 reads; of these: 43707761 (100.00%) were unpaired; of these: 10444404 (23.90%) aligned 0 times 23828022 (54.52%) aligned exactly 1 time 9435335 (21.59%) aligned >1 times 76.10% overall alignment rate Time searching: 00:11:55 Overall time: 00:11:55 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] 3808782 / 33263357 = 0.1145 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 @ Mon, 29 Jun 2020 22:15:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.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 @ Mon, 29 Jun 2020 22:15:16: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:15:16: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:15:22: 1000000 INFO @ Mon, 29 Jun 2020 22:15:29: 2000000 INFO @ Mon, 29 Jun 2020 22:15:35: 3000000 INFO @ Mon, 29 Jun 2020 22:15:42: 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 @ Mon, 29 Jun 2020 22:15:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.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 @ Mon, 29 Jun 2020 22:15:46: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:15:46: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:15:48: 5000000 INFO @ Mon, 29 Jun 2020 22:15:53: 1000000 INFO @ Mon, 29 Jun 2020 22:15:55: 6000000 INFO @ Mon, 29 Jun 2020 22:16:00: 2000000 INFO @ Mon, 29 Jun 2020 22:16:02: 7000000 INFO @ Mon, 29 Jun 2020 22:16:07: 3000000 INFO @ Mon, 29 Jun 2020 22:16:09: 8000000 INFO @ Mon, 29 Jun 2020 22:16:14: 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 @ Mon, 29 Jun 2020 22:16:16: 9000000 INFO @ Mon, 29 Jun 2020 22:16:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.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 @ Mon, 29 Jun 2020 22:16:16: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:16:16: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:16:21: 5000000 INFO @ Mon, 29 Jun 2020 22:16:23: 10000000 INFO @ Mon, 29 Jun 2020 22:16:23: 1000000 INFO @ Mon, 29 Jun 2020 22:16:28: 6000000 INFO @ Mon, 29 Jun 2020 22:16:30: 11000000 INFO @ Mon, 29 Jun 2020 22:16:30: 2000000 INFO @ Mon, 29 Jun 2020 22:16:35: 7000000 INFO @ Mon, 29 Jun 2020 22:16:37: 12000000 INFO @ Mon, 29 Jun 2020 22:16:37: 3000000 INFO @ Mon, 29 Jun 2020 22:16:42: 8000000 INFO @ Mon, 29 Jun 2020 22:16:44: 13000000 INFO @ Mon, 29 Jun 2020 22:16:44: 4000000 INFO @ Mon, 29 Jun 2020 22:16:49: 9000000 INFO @ Mon, 29 Jun 2020 22:16:50: 14000000 INFO @ Mon, 29 Jun 2020 22:16:51: 5000000 INFO @ Mon, 29 Jun 2020 22:16:56: 10000000 INFO @ Mon, 29 Jun 2020 22:16:57: 15000000 INFO @ Mon, 29 Jun 2020 22:16:58: 6000000 INFO @ Mon, 29 Jun 2020 22:17:03: 11000000 INFO @ Mon, 29 Jun 2020 22:17:04: 16000000 INFO @ Mon, 29 Jun 2020 22:17:05: 7000000 INFO @ Mon, 29 Jun 2020 22:17:10: 12000000 INFO @ Mon, 29 Jun 2020 22:17:11: 17000000 INFO @ Mon, 29 Jun 2020 22:17:12: 8000000 INFO @ Mon, 29 Jun 2020 22:17:17: 13000000 INFO @ Mon, 29 Jun 2020 22:17:18: 18000000 INFO @ Mon, 29 Jun 2020 22:17:19: 9000000 INFO @ Mon, 29 Jun 2020 22:17:24: 14000000 INFO @ Mon, 29 Jun 2020 22:17:25: 19000000 INFO @ Mon, 29 Jun 2020 22:17:26: 10000000 INFO @ Mon, 29 Jun 2020 22:17:31: 15000000 INFO @ Mon, 29 Jun 2020 22:17:31: 20000000 INFO @ Mon, 29 Jun 2020 22:17:33: 11000000 INFO @ Mon, 29 Jun 2020 22:17:38: 16000000 INFO @ Mon, 29 Jun 2020 22:17:38: 21000000 INFO @ Mon, 29 Jun 2020 22:17:40: 12000000 INFO @ Mon, 29 Jun 2020 22:17:44: 17000000 INFO @ Mon, 29 Jun 2020 22:17:45: 22000000 INFO @ Mon, 29 Jun 2020 22:17:47: 13000000 INFO @ Mon, 29 Jun 2020 22:17:51: 18000000 INFO @ Mon, 29 Jun 2020 22:17:51: 23000000 INFO @ Mon, 29 Jun 2020 22:17:54: 14000000 INFO @ Mon, 29 Jun 2020 22:17:58: 19000000 INFO @ Mon, 29 Jun 2020 22:17:58: 24000000 INFO @ Mon, 29 Jun 2020 22:18:00: 15000000 INFO @ Mon, 29 Jun 2020 22:18:04: 20000000 INFO @ Mon, 29 Jun 2020 22:18:04: 25000000 INFO @ Mon, 29 Jun 2020 22:18:07: 16000000 INFO @ Mon, 29 Jun 2020 22:18:11: 21000000 INFO @ Mon, 29 Jun 2020 22:18:11: 26000000 INFO @ Mon, 29 Jun 2020 22:18:14: 17000000 INFO @ Mon, 29 Jun 2020 22:18:17: 22000000 INFO @ Mon, 29 Jun 2020 22:18:18: 27000000 INFO @ Mon, 29 Jun 2020 22:18:20: 18000000 INFO @ Mon, 29 Jun 2020 22:18:24: 23000000 INFO @ Mon, 29 Jun 2020 22:18:24: 28000000 INFO @ Mon, 29 Jun 2020 22:18:27: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:18:31: 24000000 INFO @ Mon, 29 Jun 2020 22:18:31: 29000000 INFO @ Mon, 29 Jun 2020 22:18:33: 20000000 INFO @ Mon, 29 Jun 2020 22:18:34: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:18:34: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:18:34: #1 total tags in treatment: 29454575 INFO @ Mon, 29 Jun 2020 22:18:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:18:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:18:34: #1 tags after filtering in treatment: 29454575 INFO @ Mon, 29 Jun 2020 22:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:18:34: #1 finished! INFO @ Mon, 29 Jun 2020 22:18:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:18:36: #2 number of paired peaks: 256 WARNING @ Mon, 29 Jun 2020 22:18:36: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Mon, 29 Jun 2020 22:18:36: start model_add_line... INFO @ Mon, 29 Jun 2020 22:18:37: start X-correlation... INFO @ Mon, 29 Jun 2020 22:18:37: end of X-cor INFO @ Mon, 29 Jun 2020 22:18:37: #2 finished! INFO @ Mon, 29 Jun 2020 22:18:37: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:18:37: #2 alternative fragment length(s) may be 2,36 bps INFO @ Mon, 29 Jun 2020 22:18:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.05_model.r WARNING @ Mon, 29 Jun 2020 22:18:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:18:37: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Mon, 29 Jun 2020 22:18:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:18:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:18:37: 25000000 INFO @ Mon, 29 Jun 2020 22:18:40: 21000000 INFO @ Mon, 29 Jun 2020 22:18:44: 26000000 INFO @ Mon, 29 Jun 2020 22:18:47: 22000000 INFO @ Mon, 29 Jun 2020 22:18:51: 27000000 INFO @ Mon, 29 Jun 2020 22:18:53: 23000000 INFO @ Mon, 29 Jun 2020 22:18:57: 28000000 INFO @ Mon, 29 Jun 2020 22:19:00: 24000000 INFO @ Mon, 29 Jun 2020 22:19:04: 29000000 INFO @ Mon, 29 Jun 2020 22:19:06: 25000000 INFO @ Mon, 29 Jun 2020 22:19:07: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:19:07: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:19:07: #1 total tags in treatment: 29454575 INFO @ Mon, 29 Jun 2020 22:19:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:19:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:19:08: #1 tags after filtering in treatment: 29454575 INFO @ Mon, 29 Jun 2020 22:19:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:19:08: #1 finished! INFO @ Mon, 29 Jun 2020 22:19:08: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:19:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:19:10: #2 number of paired peaks: 256 WARNING @ Mon, 29 Jun 2020 22:19:10: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Mon, 29 Jun 2020 22:19:10: start model_add_line... INFO @ Mon, 29 Jun 2020 22:19:10: start X-correlation... INFO @ Mon, 29 Jun 2020 22:19:10: end of X-cor INFO @ Mon, 29 Jun 2020 22:19:10: #2 finished! INFO @ Mon, 29 Jun 2020 22:19:10: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:19:10: #2 alternative fragment length(s) may be 2,36 bps INFO @ Mon, 29 Jun 2020 22:19:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.10_model.r WARNING @ Mon, 29 Jun 2020 22:19:10: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:19:10: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Mon, 29 Jun 2020 22:19:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:19:10: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:19:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:19:12: 26000000 INFO @ Mon, 29 Jun 2020 22:19:18: 27000000 INFO @ Mon, 29 Jun 2020 22:19:24: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:19:24: 28000000 INFO @ Mon, 29 Jun 2020 22:19:31: 29000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:19:33: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:19:33: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:19:33: #1 total tags in treatment: 29454575 INFO @ Mon, 29 Jun 2020 22:19:33: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:19:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:19:34: #1 tags after filtering in treatment: 29454575 INFO @ Mon, 29 Jun 2020 22:19:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:19:34: #1 finished! INFO @ Mon, 29 Jun 2020 22:19:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:19:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:19:36: #2 number of paired peaks: 256 WARNING @ Mon, 29 Jun 2020 22:19:36: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Mon, 29 Jun 2020 22:19:36: start model_add_line... INFO @ Mon, 29 Jun 2020 22:19:36: start X-correlation... INFO @ Mon, 29 Jun 2020 22:19:36: end of X-cor INFO @ Mon, 29 Jun 2020 22:19:36: #2 finished! INFO @ Mon, 29 Jun 2020 22:19:36: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:19:36: #2 alternative fragment length(s) may be 2,36 bps INFO @ Mon, 29 Jun 2020 22:19:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.20_model.r WARNING @ Mon, 29 Jun 2020 22:19:36: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:19:36: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Mon, 29 Jun 2020 22:19:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:19:36: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:19:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.05_summits.bed INFO @ Mon, 29 Jun 2020 22:19:46: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:19:58: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.10_summits.bed INFO @ Mon, 29 Jun 2020 22:20:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:20:23: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159169/SRX159169.20_summits.bed INFO @ Mon, 29 Jun 2020 22:20:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling