Job ID = 6456446 SRX = SRX3404043 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:52:16 prefetch.2.10.7: 1) Downloading 'SRR6303520'... 2020-06-21T10:52:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:54:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:54:59 prefetch.2.10.7: 'SRR6303520' is valid 2020-06-21T10:54:59 prefetch.2.10.7: 1) 'SRR6303520' was downloaded successfully 2020-06-21T10:54:59 prefetch.2.10.7: 'SRR6303520' has 0 unresolved dependencies Read 18987942 spots for SRR6303520/SRR6303520.sra Written 18987942 spots for SRR6303520/SRR6303520.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: 00:05:09 18987942 reads; of these: 18987942 (100.00%) were unpaired; of these: 529016 (2.79%) aligned 0 times 13434357 (70.75%) aligned exactly 1 time 5024569 (26.46%) aligned >1 times 97.21% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 4039881 / 18458926 = 0.2189 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 20:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.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 20:05:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:18: 1000000 INFO @ Sun, 21 Jun 2020 20:05:25: 2000000 INFO @ Sun, 21 Jun 2020 20:05:32: 3000000 INFO @ Sun, 21 Jun 2020 20:05:39: 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 @ Sun, 21 Jun 2020 20:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.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 20:05:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:46: 5000000 INFO @ Sun, 21 Jun 2020 20:05:49: 1000000 INFO @ Sun, 21 Jun 2020 20:05:54: 6000000 INFO @ Sun, 21 Jun 2020 20:05:57: 2000000 INFO @ Sun, 21 Jun 2020 20:06:01: 7000000 INFO @ Sun, 21 Jun 2020 20:06:05: 3000000 INFO @ Sun, 21 Jun 2020 20:06:09: 8000000 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 20:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.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 20:06:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:12: 4000000 INFO @ Sun, 21 Jun 2020 20:06:17: 9000000 INFO @ Sun, 21 Jun 2020 20:06:19: 1000000 INFO @ Sun, 21 Jun 2020 20:06:20: 5000000 INFO @ Sun, 21 Jun 2020 20:06:24: 10000000 INFO @ Sun, 21 Jun 2020 20:06:27: 2000000 INFO @ Sun, 21 Jun 2020 20:06:29: 6000000 INFO @ Sun, 21 Jun 2020 20:06:32: 11000000 INFO @ Sun, 21 Jun 2020 20:06:35: 3000000 INFO @ Sun, 21 Jun 2020 20:06:37: 7000000 INFO @ Sun, 21 Jun 2020 20:06:40: 12000000 INFO @ Sun, 21 Jun 2020 20:06:43: 4000000 INFO @ Sun, 21 Jun 2020 20:06:45: 8000000 INFO @ Sun, 21 Jun 2020 20:06:48: 13000000 INFO @ Sun, 21 Jun 2020 20:06:51: 5000000 INFO @ Sun, 21 Jun 2020 20:06:52: 9000000 INFO @ Sun, 21 Jun 2020 20:06:56: 14000000 INFO @ Sun, 21 Jun 2020 20:06:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:06:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:06:59: #1 total tags in treatment: 14419045 INFO @ Sun, 21 Jun 2020 20:06:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:59: #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 20:06:59: 6000000 INFO @ Sun, 21 Jun 2020 20:07:00: 10000000 INFO @ Sun, 21 Jun 2020 20:07:00: #1 tags after filtering in treatment: 14418950 INFO @ Sun, 21 Jun 2020 20:07:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:00: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:01: #2 number of paired peaks: 2433 INFO @ Sun, 21 Jun 2020 20:07:01: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:01: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:01: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:01: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 20:07:01: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 20:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.05_model.r INFO @ Sun, 21 Jun 2020 20:07:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:07: 11000000 INFO @ Sun, 21 Jun 2020 20:07:08: 7000000 INFO @ Sun, 21 Jun 2020 20:07:15: 12000000 INFO @ Sun, 21 Jun 2020 20:07:16: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:07:23: 9000000 INFO @ Sun, 21 Jun 2020 20:07:23: 13000000 INFO @ Sun, 21 Jun 2020 20:07:31: 10000000 INFO @ Sun, 21 Jun 2020 20:07:31: 14000000 INFO @ Sun, 21 Jun 2020 20:07:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:07:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:07:35: #1 total tags in treatment: 14419045 INFO @ Sun, 21 Jun 2020 20:07:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:35: #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 20:07:35: #1 tags after filtering in treatment: 14418950 INFO @ Sun, 21 Jun 2020 20:07:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:37: #2 number of paired peaks: 2433 INFO @ Sun, 21 Jun 2020 20:07:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:37: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 20:07:37: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 20:07:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.10_model.r INFO @ Sun, 21 Jun 2020 20:07:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:38: 11000000 INFO @ Sun, 21 Jun 2020 20:07:45: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.05_summits.bed INFO @ Sun, 21 Jun 2020 20:07:53: Done! pass1 - making usageList (635 chroms): 2 millis pass2 - checking and writing primary data (5706 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:07:53: 13000000 INFO @ Sun, 21 Jun 2020 20:08:00: 14000000 INFO @ Sun, 21 Jun 2020 20:08:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:08:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:08:04: #1 total tags in treatment: 14419045 INFO @ Sun, 21 Jun 2020 20:08:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:04: #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 20:08:04: #1 tags after filtering in treatment: 14418950 INFO @ Sun, 21 Jun 2020 20:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:05: #2 number of paired peaks: 2433 INFO @ Sun, 21 Jun 2020 20:08:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:05: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 20:08:05: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 20:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.20_model.r INFO @ Sun, 21 Jun 2020 20:08:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.10_summits.bed INFO @ Sun, 21 Jun 2020 20:08:28: Done! pass1 - making usageList (459 chroms): 2 millis pass2 - checking and writing primary data (4358 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:08:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404043/SRX3404043.20_summits.bed INFO @ Sun, 21 Jun 2020 20:08:56: Done! pass1 - making usageList (247 chroms): 1 millis pass2 - checking and writing primary data (3274 records, 4 fields): 10 millis CompletedMACS2peakCalling