Job ID = 6456033 SRX = SRX3159489 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:25:06 prefetch.2.10.7: 1) Downloading 'SRR6004219'... 2020-06-21T10:25:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:55 prefetch.2.10.7: 'SRR6004219' is valid 2020-06-21T10:26:55 prefetch.2.10.7: 1) 'SRR6004219' was downloaded successfully 2020-06-21T10:26:55 prefetch.2.10.7: 'SRR6004219' has 0 unresolved dependencies Read 20270512 spots for SRR6004219/SRR6004219.sra Written 20270512 spots for SRR6004219/SRR6004219.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: 00:04:56 20270512 reads; of these: 20270512 (100.00%) were unpaired; of these: 1342912 (6.62%) aligned 0 times 16074554 (79.30%) aligned exactly 1 time 2853046 (14.07%) aligned >1 times 93.38% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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 8 files... [bam_rmdupse_core] 5873353 / 18927600 = 0.3103 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 19:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.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 19:36:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:35: 1000000 INFO @ Sun, 21 Jun 2020 19:36:40: 2000000 INFO @ Sun, 21 Jun 2020 19:36:45: 3000000 INFO @ Sun, 21 Jun 2020 19:36:49: 4000000 INFO @ Sun, 21 Jun 2020 19:36:54: 5000000 INFO @ Sun, 21 Jun 2020 19:36:59: 6000000 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 19:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.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 19:37:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:03: 7000000 INFO @ Sun, 21 Jun 2020 19:37:05: 1000000 INFO @ Sun, 21 Jun 2020 19:37:08: 8000000 INFO @ Sun, 21 Jun 2020 19:37:10: 2000000 INFO @ Sun, 21 Jun 2020 19:37:13: 9000000 INFO @ Sun, 21 Jun 2020 19:37:15: 3000000 INFO @ Sun, 21 Jun 2020 19:37:18: 10000000 INFO @ Sun, 21 Jun 2020 19:37:19: 4000000 INFO @ Sun, 21 Jun 2020 19:37:23: 11000000 INFO @ Sun, 21 Jun 2020 19:37:24: 5000000 INFO @ Sun, 21 Jun 2020 19:37:28: 12000000 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 19:37:29: 6000000 INFO @ Sun, 21 Jun 2020 19:37:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.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 19:37:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:33: 13000000 INFO @ Sun, 21 Jun 2020 19:37:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:37:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:37:33: #1 total tags in treatment: 13054247 INFO @ Sun, 21 Jun 2020 19:37:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:33: #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 19:37:34: 7000000 INFO @ Sun, 21 Jun 2020 19:37:34: #1 tags after filtering in treatment: 13054244 INFO @ Sun, 21 Jun 2020 19:37:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:35: #2 number of paired peaks: 4199 INFO @ Sun, 21 Jun 2020 19:37:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:35: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 19:37:35: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 19:37:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.05_model.r INFO @ Sun, 21 Jun 2020 19:37:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:36: 1000000 INFO @ Sun, 21 Jun 2020 19:37:39: 8000000 INFO @ Sun, 21 Jun 2020 19:37:41: 2000000 INFO @ Sun, 21 Jun 2020 19:37:43: 9000000 INFO @ Sun, 21 Jun 2020 19:37:47: 3000000 INFO @ Sun, 21 Jun 2020 19:37:48: 10000000 INFO @ Sun, 21 Jun 2020 19:37:52: 4000000 INFO @ Sun, 21 Jun 2020 19:37:53: 11000000 INFO @ Sun, 21 Jun 2020 19:37:57: 5000000 INFO @ Sun, 21 Jun 2020 19:37:58: 12000000 INFO @ Sun, 21 Jun 2020 19:38:03: 6000000 INFO @ Sun, 21 Jun 2020 19:38:03: 13000000 INFO @ Sun, 21 Jun 2020 19:38:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:38:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:38:04: #1 total tags in treatment: 13054247 INFO @ Sun, 21 Jun 2020 19:38:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:04: #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 19:38:04: #1 tags after filtering in treatment: 13054244 INFO @ Sun, 21 Jun 2020 19:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:05: #2 number of paired peaks: 4199 INFO @ Sun, 21 Jun 2020 19:38:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:05: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 19:38:05: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 19:38:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.10_model.r INFO @ Sun, 21 Jun 2020 19:38:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:08: 7000000 INFO @ Sun, 21 Jun 2020 19:38:13: 8000000 INFO @ Sun, 21 Jun 2020 19:38:18: 9000000 INFO @ Sun, 21 Jun 2020 19:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:20: Done! pass1 - making usageList (424 chroms): 2 millis pass2 - checking and writing primary data (8263 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:24: 10000000 INFO @ Sun, 21 Jun 2020 19:38:29: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:38:35: 12000000 INFO @ Sun, 21 Jun 2020 19:38:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:40: 13000000 INFO @ Sun, 21 Jun 2020 19:38:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:38:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:38:40: #1 total tags in treatment: 13054247 INFO @ Sun, 21 Jun 2020 19:38:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:40: #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 19:38:41: #1 tags after filtering in treatment: 13054244 INFO @ Sun, 21 Jun 2020 19:38:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:42: #2 number of paired peaks: 4199 INFO @ Sun, 21 Jun 2020 19:38:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:42: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 19:38:42: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 19:38:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.20_model.r INFO @ Sun, 21 Jun 2020 19:38:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.10_summits.bed INFO @ Sun, 21 Jun 2020 19:38:50: Done! pass1 - making usageList (290 chroms): 1 millis pass2 - checking and writing primary data (6690 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:39:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159489/SRX3159489.20_summits.bed INFO @ Sun, 21 Jun 2020 19:39:29: Done! pass1 - making usageList (132 chroms): 1 millis pass2 - checking and writing primary data (5008 records, 4 fields): 10 millis CompletedMACS2peakCalling