Job ID = 6527423 SRX = ERX102366 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:36:52 prefetch.2.10.7: 1) Downloading 'ERR126230'... 2020-06-29T12:36:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:44:31 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:44:31 prefetch.2.10.7: 1) 'ERR126230' was downloaded successfully Read 39663849 spots for ERR126230/ERR126230.sra Written 39663849 spots for ERR126230/ERR126230.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: 00:20:20 39663849 reads; of these: 39663849 (100.00%) were unpaired; of these: 584773 (1.47%) aligned 0 times 27512924 (69.37%) aligned exactly 1 time 11566152 (29.16%) aligned >1 times 98.53% overall alignment rate Time searching: 00:20:20 Overall time: 00:20:20 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] 6226268 / 39079076 = 0.1593 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 22:37:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.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 22:37:07: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:37:07: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:37:14: 1000000 INFO @ Mon, 29 Jun 2020 22:37:21: 2000000 INFO @ Mon, 29 Jun 2020 22:37:28: 3000000 INFO @ Mon, 29 Jun 2020 22:37:34: 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 22:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.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 22:37:37: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:37:37: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:37:42: 5000000 INFO @ Mon, 29 Jun 2020 22:37:46: 1000000 INFO @ Mon, 29 Jun 2020 22:37:50: 6000000 INFO @ Mon, 29 Jun 2020 22:37:54: 2000000 INFO @ Mon, 29 Jun 2020 22:37:57: 7000000 INFO @ Mon, 29 Jun 2020 22:38:03: 3000000 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 22:38:05: 8000000 INFO @ Mon, 29 Jun 2020 22:38:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.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 22:38:07: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:38:07: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:38:11: 4000000 INFO @ Mon, 29 Jun 2020 22:38:13: 9000000 INFO @ Mon, 29 Jun 2020 22:38:15: 1000000 INFO @ Mon, 29 Jun 2020 22:38:20: 5000000 INFO @ Mon, 29 Jun 2020 22:38:21: 10000000 INFO @ Mon, 29 Jun 2020 22:38:24: 2000000 INFO @ Mon, 29 Jun 2020 22:38:29: 6000000 INFO @ Mon, 29 Jun 2020 22:38:29: 11000000 INFO @ Mon, 29 Jun 2020 22:38:32: 3000000 INFO @ Mon, 29 Jun 2020 22:38:37: 12000000 INFO @ Mon, 29 Jun 2020 22:38:38: 7000000 INFO @ Mon, 29 Jun 2020 22:38:40: 4000000 INFO @ Mon, 29 Jun 2020 22:38:45: 13000000 INFO @ Mon, 29 Jun 2020 22:38:46: 8000000 INFO @ Mon, 29 Jun 2020 22:38:48: 5000000 INFO @ Mon, 29 Jun 2020 22:38:54: 14000000 INFO @ Mon, 29 Jun 2020 22:38:55: 9000000 INFO @ Mon, 29 Jun 2020 22:38:56: 6000000 INFO @ Mon, 29 Jun 2020 22:39:02: 15000000 INFO @ Mon, 29 Jun 2020 22:39:04: 10000000 INFO @ Mon, 29 Jun 2020 22:39:04: 7000000 INFO @ Mon, 29 Jun 2020 22:39:10: 16000000 INFO @ Mon, 29 Jun 2020 22:39:12: 8000000 INFO @ Mon, 29 Jun 2020 22:39:12: 11000000 INFO @ Mon, 29 Jun 2020 22:39:18: 17000000 INFO @ Mon, 29 Jun 2020 22:39:19: 9000000 INFO @ Mon, 29 Jun 2020 22:39:21: 12000000 INFO @ Mon, 29 Jun 2020 22:39:25: 18000000 INFO @ Mon, 29 Jun 2020 22:39:27: 10000000 INFO @ Mon, 29 Jun 2020 22:39:30: 13000000 INFO @ Mon, 29 Jun 2020 22:39:33: 19000000 INFO @ Mon, 29 Jun 2020 22:39:35: 11000000 INFO @ Mon, 29 Jun 2020 22:39:39: 14000000 INFO @ Mon, 29 Jun 2020 22:39:41: 20000000 INFO @ Mon, 29 Jun 2020 22:39:43: 12000000 INFO @ Mon, 29 Jun 2020 22:39:47: 15000000 INFO @ Mon, 29 Jun 2020 22:39:49: 21000000 INFO @ Mon, 29 Jun 2020 22:39:51: 13000000 INFO @ Mon, 29 Jun 2020 22:39:56: 16000000 INFO @ Mon, 29 Jun 2020 22:39:56: 22000000 INFO @ Mon, 29 Jun 2020 22:39:59: 14000000 INFO @ Mon, 29 Jun 2020 22:40:04: 23000000 INFO @ Mon, 29 Jun 2020 22:40:04: 17000000 INFO @ Mon, 29 Jun 2020 22:40:06: 15000000 INFO @ Mon, 29 Jun 2020 22:40:11: 24000000 INFO @ Mon, 29 Jun 2020 22:40:12: 18000000 INFO @ Mon, 29 Jun 2020 22:40:14: 16000000 INFO @ Mon, 29 Jun 2020 22:40:19: 25000000 INFO @ Mon, 29 Jun 2020 22:40:21: 19000000 INFO @ Mon, 29 Jun 2020 22:40:22: 17000000 INFO @ Mon, 29 Jun 2020 22:40:27: 26000000 INFO @ Mon, 29 Jun 2020 22:40:29: 20000000 INFO @ Mon, 29 Jun 2020 22:40:29: 18000000 INFO @ Mon, 29 Jun 2020 22:40:35: 27000000 INFO @ Mon, 29 Jun 2020 22:40:37: 19000000 INFO @ Mon, 29 Jun 2020 22:40:37: 21000000 INFO @ Mon, 29 Jun 2020 22:40:42: 28000000 INFO @ Mon, 29 Jun 2020 22:40:44: 20000000 INFO @ Mon, 29 Jun 2020 22:40:45: 22000000 INFO @ Mon, 29 Jun 2020 22:40:50: 29000000 INFO @ Mon, 29 Jun 2020 22:40:52: 21000000 INFO @ Mon, 29 Jun 2020 22:40:53: 23000000 INFO @ Mon, 29 Jun 2020 22:40:58: 30000000 INFO @ Mon, 29 Jun 2020 22:41:00: 22000000 INFO @ Mon, 29 Jun 2020 22:41:01: 24000000 INFO @ Mon, 29 Jun 2020 22:41:05: 31000000 INFO @ Mon, 29 Jun 2020 22:41:07: 23000000 INFO @ Mon, 29 Jun 2020 22:41:09: 25000000 INFO @ Mon, 29 Jun 2020 22:41:13: 32000000 INFO @ Mon, 29 Jun 2020 22:41:15: 24000000 INFO @ Mon, 29 Jun 2020 22:41:17: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:41:20: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 22:41:20: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 22:41:20: #1 total tags in treatment: 32852808 INFO @ Mon, 29 Jun 2020 22:41:20: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:41:20: #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 22:41:20: #1 tags after filtering in treatment: 32852808 INFO @ Mon, 29 Jun 2020 22:41:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:41:20: #1 finished! INFO @ Mon, 29 Jun 2020 22:41:20: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:41:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:41:22: #2 number of paired peaks: 208 WARNING @ Mon, 29 Jun 2020 22:41:22: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 29 Jun 2020 22:41:22: start model_add_line... INFO @ Mon, 29 Jun 2020 22:41:23: 25000000 INFO @ Mon, 29 Jun 2020 22:41:23: start X-correlation... INFO @ Mon, 29 Jun 2020 22:41:23: end of X-cor INFO @ Mon, 29 Jun 2020 22:41:23: #2 finished! INFO @ Mon, 29 Jun 2020 22:41:23: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:41:23: #2 alternative fragment length(s) may be 2,39,48 bps INFO @ Mon, 29 Jun 2020 22:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.05_model.r WARNING @ Mon, 29 Jun 2020 22:41:23: #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 22:41:23: #2 You may need to consider one of the other alternative d(s): 2,39,48 WARNING @ Mon, 29 Jun 2020 22:41:23: #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 22:41:23: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:41:25: 27000000 INFO @ Mon, 29 Jun 2020 22:41:30: 26000000 INFO @ Mon, 29 Jun 2020 22:41:33: 28000000 INFO @ Mon, 29 Jun 2020 22:41:37: 27000000 INFO @ Mon, 29 Jun 2020 22:41:42: 29000000 INFO @ Mon, 29 Jun 2020 22:41:45: 28000000 INFO @ Mon, 29 Jun 2020 22:41:50: 30000000 INFO @ Mon, 29 Jun 2020 22:41:52: 29000000 INFO @ Mon, 29 Jun 2020 22:41:58: 31000000 INFO @ Mon, 29 Jun 2020 22:42:00: 30000000 INFO @ Mon, 29 Jun 2020 22:42:06: 32000000 INFO @ Mon, 29 Jun 2020 22:42:07: 31000000 INFO @ Mon, 29 Jun 2020 22:42:13: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 22:42:13: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 22:42:13: #1 total tags in treatment: 32852808 INFO @ Mon, 29 Jun 2020 22:42:13: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:42:13: #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 22:42:13: #1 tags after filtering in treatment: 32852808 INFO @ Mon, 29 Jun 2020 22:42:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:42:13: #1 finished! INFO @ Mon, 29 Jun 2020 22:42:13: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:42:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:42:14: 32000000 INFO @ Mon, 29 Jun 2020 22:42:15: #2 number of paired peaks: 208 WARNING @ Mon, 29 Jun 2020 22:42:15: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 29 Jun 2020 22:42:15: start model_add_line... INFO @ Mon, 29 Jun 2020 22:42:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:42:16: start X-correlation... INFO @ Mon, 29 Jun 2020 22:42:16: end of X-cor INFO @ Mon, 29 Jun 2020 22:42:16: #2 finished! INFO @ Mon, 29 Jun 2020 22:42:16: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:42:16: #2 alternative fragment length(s) may be 2,39,48 bps INFO @ Mon, 29 Jun 2020 22:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.10_model.r WARNING @ Mon, 29 Jun 2020 22:42:16: #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 22:42:16: #2 You may need to consider one of the other alternative d(s): 2,39,48 WARNING @ Mon, 29 Jun 2020 22:42:16: #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 22:42:16: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:42:20: #1 tag size is determined as 75 bps INFO @ Mon, 29 Jun 2020 22:42:20: #1 tag size = 75 INFO @ Mon, 29 Jun 2020 22:42:20: #1 total tags in treatment: 32852808 INFO @ Mon, 29 Jun 2020 22:42:20: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:42:20: #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 22:42:21: #1 tags after filtering in treatment: 32852808 INFO @ Mon, 29 Jun 2020 22:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:42:21: #1 finished! INFO @ Mon, 29 Jun 2020 22:42:21: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:42:23: #2 number of paired peaks: 208 WARNING @ Mon, 29 Jun 2020 22:42:23: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 29 Jun 2020 22:42:23: start model_add_line... INFO @ Mon, 29 Jun 2020 22:42:23: start X-correlation... INFO @ Mon, 29 Jun 2020 22:42:23: end of X-cor INFO @ Mon, 29 Jun 2020 22:42:23: #2 finished! INFO @ Mon, 29 Jun 2020 22:42:23: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:42:23: #2 alternative fragment length(s) may be 2,39,48 bps INFO @ Mon, 29 Jun 2020 22:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.20_model.r WARNING @ Mon, 29 Jun 2020 22:42:23: #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 22:42:23: #2 You may need to consider one of the other alternative d(s): 2,39,48 WARNING @ Mon, 29 Jun 2020 22:42:23: #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 22:42:23: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:42:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:42:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:42:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:42:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.05_summits.bed INFO @ Mon, 29 Jun 2020 22:42:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:43:08: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:43:16: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:43:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:43:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:43:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.10_summits.bed INFO @ Mon, 29 Jun 2020 22:43:32: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:43:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:43:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:43:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102366/ERX102366.20_summits.bed INFO @ Mon, 29 Jun 2020 22:43:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling