Job ID = 6528156 SRX = SRX4923177 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:42:43 prefetch.2.10.7: 1) Downloading 'SRR8096327'... 2020-06-29T14:42:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:46:14 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:46:14 prefetch.2.10.7: 1) 'SRR8096327' was downloaded successfully 2020-06-29T14:46:14 prefetch.2.10.7: 'SRR8096327' has 0 unresolved dependencies Read 72748646 spots for SRR8096327/SRR8096327.sra Written 72748646 spots for SRR8096327/SRR8096327.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: 00:33:23 72748646 reads; of these: 72748646 (100.00%) were unpaired; of these: 1001280 (1.38%) aligned 0 times 21167794 (29.10%) aligned exactly 1 time 50579572 (69.53%) aligned >1 times 98.62% overall alignment rate Time searching: 00:33:23 Overall time: 00:33:23 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 32 files... [bam_rmdupse_core] 32033434 / 71747366 = 0.4465 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 @ Tue, 30 Jun 2020 00:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.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 @ Tue, 30 Jun 2020 00:49:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:49:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:49:56: 1000000 INFO @ Tue, 30 Jun 2020 00:50:03: 2000000 INFO @ Tue, 30 Jun 2020 00:50:09: 3000000 INFO @ Tue, 30 Jun 2020 00:50:14: 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 @ Tue, 30 Jun 2020 00:50:20: 5000000 INFO @ Tue, 30 Jun 2020 00:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.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 @ Tue, 30 Jun 2020 00:50:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:50:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:50:25: 6000000 INFO @ Tue, 30 Jun 2020 00:50:26: 1000000 INFO @ Tue, 30 Jun 2020 00:50:31: 7000000 INFO @ Tue, 30 Jun 2020 00:50:32: 2000000 INFO @ Tue, 30 Jun 2020 00:50:36: 8000000 INFO @ Tue, 30 Jun 2020 00:50:37: 3000000 INFO @ Tue, 30 Jun 2020 00:50:42: 9000000 INFO @ Tue, 30 Jun 2020 00:50:42: 4000000 INFO @ Tue, 30 Jun 2020 00:50:47: 10000000 INFO @ Tue, 30 Jun 2020 00:50:48: 5000000 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 @ Tue, 30 Jun 2020 00:50:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.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 @ Tue, 30 Jun 2020 00:50:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:50:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:50:52: 11000000 INFO @ Tue, 30 Jun 2020 00:50:54: 6000000 INFO @ Tue, 30 Jun 2020 00:50:56: 1000000 INFO @ Tue, 30 Jun 2020 00:50:58: 12000000 INFO @ Tue, 30 Jun 2020 00:50:59: 7000000 INFO @ Tue, 30 Jun 2020 00:51:02: 2000000 INFO @ Tue, 30 Jun 2020 00:51:03: 13000000 INFO @ Tue, 30 Jun 2020 00:51:05: 8000000 INFO @ Tue, 30 Jun 2020 00:51:08: 3000000 INFO @ Tue, 30 Jun 2020 00:51:09: 14000000 INFO @ Tue, 30 Jun 2020 00:51:10: 9000000 INFO @ Tue, 30 Jun 2020 00:51:13: 4000000 INFO @ Tue, 30 Jun 2020 00:51:15: 15000000 INFO @ Tue, 30 Jun 2020 00:51:16: 10000000 INFO @ Tue, 30 Jun 2020 00:51:19: 5000000 INFO @ Tue, 30 Jun 2020 00:51:20: 16000000 INFO @ Tue, 30 Jun 2020 00:51:22: 11000000 INFO @ Tue, 30 Jun 2020 00:51:25: 6000000 INFO @ Tue, 30 Jun 2020 00:51:26: 17000000 INFO @ Tue, 30 Jun 2020 00:51:27: 12000000 INFO @ Tue, 30 Jun 2020 00:51:31: 7000000 INFO @ Tue, 30 Jun 2020 00:51:32: 18000000 INFO @ Tue, 30 Jun 2020 00:51:33: 13000000 INFO @ Tue, 30 Jun 2020 00:51:36: 8000000 INFO @ Tue, 30 Jun 2020 00:51:37: 19000000 INFO @ Tue, 30 Jun 2020 00:51:38: 14000000 INFO @ Tue, 30 Jun 2020 00:51:42: 9000000 INFO @ Tue, 30 Jun 2020 00:51:43: 20000000 INFO @ Tue, 30 Jun 2020 00:51:44: 15000000 INFO @ Tue, 30 Jun 2020 00:51:47: 10000000 INFO @ Tue, 30 Jun 2020 00:51:49: 21000000 INFO @ Tue, 30 Jun 2020 00:51:49: 16000000 INFO @ Tue, 30 Jun 2020 00:51:53: 11000000 INFO @ Tue, 30 Jun 2020 00:51:54: 22000000 INFO @ Tue, 30 Jun 2020 00:51:55: 17000000 INFO @ Tue, 30 Jun 2020 00:51:58: 12000000 INFO @ Tue, 30 Jun 2020 00:52:00: 23000000 INFO @ Tue, 30 Jun 2020 00:52:00: 18000000 INFO @ Tue, 30 Jun 2020 00:52:04: 13000000 INFO @ Tue, 30 Jun 2020 00:52:06: 24000000 INFO @ Tue, 30 Jun 2020 00:52:06: 19000000 INFO @ Tue, 30 Jun 2020 00:52:10: 14000000 INFO @ Tue, 30 Jun 2020 00:52:11: 25000000 INFO @ Tue, 30 Jun 2020 00:52:11: 20000000 INFO @ Tue, 30 Jun 2020 00:52:15: 15000000 INFO @ Tue, 30 Jun 2020 00:52:17: 26000000 INFO @ Tue, 30 Jun 2020 00:52:17: 21000000 INFO @ Tue, 30 Jun 2020 00:52:21: 16000000 INFO @ Tue, 30 Jun 2020 00:52:22: 27000000 INFO @ Tue, 30 Jun 2020 00:52:22: 22000000 INFO @ Tue, 30 Jun 2020 00:52:26: 17000000 INFO @ Tue, 30 Jun 2020 00:52:28: 28000000 INFO @ Tue, 30 Jun 2020 00:52:28: 23000000 INFO @ Tue, 30 Jun 2020 00:52:32: 18000000 INFO @ Tue, 30 Jun 2020 00:52:33: 24000000 INFO @ Tue, 30 Jun 2020 00:52:33: 29000000 INFO @ Tue, 30 Jun 2020 00:52:37: 19000000 INFO @ Tue, 30 Jun 2020 00:52:38: 25000000 INFO @ Tue, 30 Jun 2020 00:52:39: 30000000 INFO @ Tue, 30 Jun 2020 00:52:43: 20000000 INFO @ Tue, 30 Jun 2020 00:52:44: 26000000 INFO @ Tue, 30 Jun 2020 00:52:44: 31000000 INFO @ Tue, 30 Jun 2020 00:52:48: 21000000 INFO @ Tue, 30 Jun 2020 00:52:49: 27000000 INFO @ Tue, 30 Jun 2020 00:52:50: 32000000 INFO @ Tue, 30 Jun 2020 00:52:54: 22000000 INFO @ Tue, 30 Jun 2020 00:52:54: 28000000 INFO @ Tue, 30 Jun 2020 00:52:55: 33000000 INFO @ Tue, 30 Jun 2020 00:52:59: 23000000 INFO @ Tue, 30 Jun 2020 00:53:00: 29000000 INFO @ Tue, 30 Jun 2020 00:53:00: 34000000 INFO @ Tue, 30 Jun 2020 00:53:05: 24000000 INFO @ Tue, 30 Jun 2020 00:53:05: 30000000 INFO @ Tue, 30 Jun 2020 00:53:06: 35000000 INFO @ Tue, 30 Jun 2020 00:53:10: 31000000 INFO @ Tue, 30 Jun 2020 00:53:10: 25000000 INFO @ Tue, 30 Jun 2020 00:53:11: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:53:16: 32000000 INFO @ Tue, 30 Jun 2020 00:53:16: 26000000 INFO @ Tue, 30 Jun 2020 00:53:17: 37000000 INFO @ Tue, 30 Jun 2020 00:53:21: 33000000 INFO @ Tue, 30 Jun 2020 00:53:21: 27000000 INFO @ Tue, 30 Jun 2020 00:53:23: 38000000 INFO @ Tue, 30 Jun 2020 00:53:26: 34000000 INFO @ Tue, 30 Jun 2020 00:53:27: 28000000 INFO @ Tue, 30 Jun 2020 00:53:28: 39000000 INFO @ Tue, 30 Jun 2020 00:53:32: 35000000 INFO @ Tue, 30 Jun 2020 00:53:32: 29000000 INFO @ Tue, 30 Jun 2020 00:53:33: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:53:33: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:53:33: #1 total tags in treatment: 39713932 INFO @ Tue, 30 Jun 2020 00:53:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:53:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:53:33: #1 tags after filtering in treatment: 39713932 INFO @ Tue, 30 Jun 2020 00:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:53:33: #1 finished! INFO @ Tue, 30 Jun 2020 00:53:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:53:36: #2 number of paired peaks: 1481 INFO @ Tue, 30 Jun 2020 00:53:36: start model_add_line... INFO @ Tue, 30 Jun 2020 00:53:36: start X-correlation... INFO @ Tue, 30 Jun 2020 00:53:36: end of X-cor INFO @ Tue, 30 Jun 2020 00:53:36: #2 finished! INFO @ Tue, 30 Jun 2020 00:53:36: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:53:36: #2 alternative fragment length(s) may be 1,53,69,72,89 bps INFO @ Tue, 30 Jun 2020 00:53:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.05_model.r WARNING @ Tue, 30 Jun 2020 00:53:36: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:53:36: #2 You may need to consider one of the other alternative d(s): 1,53,69,72,89 WARNING @ Tue, 30 Jun 2020 00:53:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:53:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:53:37: 36000000 INFO @ Tue, 30 Jun 2020 00:53:38: 30000000 INFO @ Tue, 30 Jun 2020 00:53:43: 37000000 INFO @ Tue, 30 Jun 2020 00:53:43: 31000000 INFO @ Tue, 30 Jun 2020 00:53:48: 38000000 INFO @ Tue, 30 Jun 2020 00:53:48: 32000000 INFO @ Tue, 30 Jun 2020 00:53:54: 39000000 INFO @ Tue, 30 Jun 2020 00:53:54: 33000000 INFO @ Tue, 30 Jun 2020 00:53:58: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:53:58: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:53:58: #1 total tags in treatment: 39713932 INFO @ Tue, 30 Jun 2020 00:53:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:53:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:53:59: #1 tags after filtering in treatment: 39713932 INFO @ Tue, 30 Jun 2020 00:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:53:59: #1 finished! INFO @ Tue, 30 Jun 2020 00:53:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:53:59: 34000000 INFO @ Tue, 30 Jun 2020 00:54:02: #2 number of paired peaks: 1481 INFO @ Tue, 30 Jun 2020 00:54:02: start model_add_line... INFO @ Tue, 30 Jun 2020 00:54:02: start X-correlation... INFO @ Tue, 30 Jun 2020 00:54:02: end of X-cor INFO @ Tue, 30 Jun 2020 00:54:02: #2 finished! INFO @ Tue, 30 Jun 2020 00:54:02: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:54:02: #2 alternative fragment length(s) may be 1,53,69,72,89 bps INFO @ Tue, 30 Jun 2020 00:54:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.10_model.r WARNING @ Tue, 30 Jun 2020 00:54:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:54:02: #2 You may need to consider one of the other alternative d(s): 1,53,69,72,89 WARNING @ Tue, 30 Jun 2020 00:54:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:54:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:54:05: 35000000 INFO @ Tue, 30 Jun 2020 00:54:10: 36000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:54:15: 37000000 INFO @ Tue, 30 Jun 2020 00:54:21: 38000000 INFO @ Tue, 30 Jun 2020 00:54:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:54:27: 39000000 INFO @ Tue, 30 Jun 2020 00:54:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:54:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:54:31: #1 total tags in treatment: 39713932 INFO @ Tue, 30 Jun 2020 00:54:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:54:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:54:32: #1 tags after filtering in treatment: 39713932 INFO @ Tue, 30 Jun 2020 00:54:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:54:32: #1 finished! INFO @ Tue, 30 Jun 2020 00:54:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:54:34: #2 number of paired peaks: 1481 INFO @ Tue, 30 Jun 2020 00:54:34: start model_add_line... INFO @ Tue, 30 Jun 2020 00:54:35: start X-correlation... INFO @ Tue, 30 Jun 2020 00:54:35: end of X-cor INFO @ Tue, 30 Jun 2020 00:54:35: #2 finished! INFO @ Tue, 30 Jun 2020 00:54:35: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:54:35: #2 alternative fragment length(s) may be 1,53,69,72,89 bps INFO @ Tue, 30 Jun 2020 00:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.20_model.r WARNING @ Tue, 30 Jun 2020 00:54:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:54:35: #2 You may need to consider one of the other alternative d(s): 1,53,69,72,89 WARNING @ Tue, 30 Jun 2020 00:54:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:54:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.05_summits.bed INFO @ Tue, 30 Jun 2020 00:54:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:54:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:55:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:55:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:55:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.10_summits.bed INFO @ Tue, 30 Jun 2020 00:55:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:55:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:55:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:55:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:55:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923177/SRX4923177.20_summits.bed INFO @ Tue, 30 Jun 2020 00:55:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling