Job ID = 6456415 SRX = SRX3404011 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:55:01 prefetch.2.10.7: 1) Downloading 'SRR6303488'... 2020-06-21T10:55:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:57:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:57:06 prefetch.2.10.7: 'SRR6303488' is valid 2020-06-21T10:57:06 prefetch.2.10.7: 1) 'SRR6303488' was downloaded successfully 2020-06-21T10:57:06 prefetch.2.10.7: 'SRR6303488' has 0 unresolved dependencies Read 19411300 spots for SRR6303488/SRR6303488.sra Written 19411300 spots for SRR6303488/SRR6303488.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: 00:05:05 19411300 reads; of these: 19411300 (100.00%) were unpaired; of these: 523139 (2.70%) aligned 0 times 14437388 (74.38%) aligned exactly 1 time 4450773 (22.93%) aligned >1 times 97.30% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 3373485 / 18888161 = 0.1786 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 20:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.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 20:07:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:04: 1000000 INFO @ Sun, 21 Jun 2020 20:08:09: 2000000 INFO @ Sun, 21 Jun 2020 20:08:14: 3000000 INFO @ Sun, 21 Jun 2020 20:08:19: 4000000 INFO @ Sun, 21 Jun 2020 20:08:24: 5000000 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 20:08:29: 6000000 INFO @ Sun, 21 Jun 2020 20:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.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 20:08:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:34: 7000000 INFO @ Sun, 21 Jun 2020 20:08:35: 1000000 INFO @ Sun, 21 Jun 2020 20:08:39: 8000000 INFO @ Sun, 21 Jun 2020 20:08:40: 2000000 INFO @ Sun, 21 Jun 2020 20:08:43: 9000000 INFO @ Sun, 21 Jun 2020 20:08:45: 3000000 INFO @ Sun, 21 Jun 2020 20:08:48: 10000000 INFO @ Sun, 21 Jun 2020 20:08:50: 4000000 INFO @ Sun, 21 Jun 2020 20:08:53: 11000000 INFO @ Sun, 21 Jun 2020 20:08:55: 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 @ Sun, 21 Jun 2020 20:08:58: 12000000 INFO @ Sun, 21 Jun 2020 20:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.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 20:09:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:00: 6000000 INFO @ Sun, 21 Jun 2020 20:09:03: 13000000 INFO @ Sun, 21 Jun 2020 20:09:05: 1000000 INFO @ Sun, 21 Jun 2020 20:09:05: 7000000 INFO @ Sun, 21 Jun 2020 20:09:09: 14000000 INFO @ Sun, 21 Jun 2020 20:09:10: 8000000 INFO @ Sun, 21 Jun 2020 20:09:10: 2000000 INFO @ Sun, 21 Jun 2020 20:09:14: 15000000 INFO @ Sun, 21 Jun 2020 20:09:15: 9000000 INFO @ Sun, 21 Jun 2020 20:09:15: 3000000 INFO @ Sun, 21 Jun 2020 20:09:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:09:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:09:17: #1 total tags in treatment: 15514676 INFO @ Sun, 21 Jun 2020 20:09:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:17: #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 20:09:17: #1 tags after filtering in treatment: 15514568 INFO @ Sun, 21 Jun 2020 20:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:19: #2 number of paired peaks: 1564 INFO @ Sun, 21 Jun 2020 20:09:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:19: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 20:09:19: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 20:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.05_model.r INFO @ Sun, 21 Jun 2020 20:09:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:20: 10000000 INFO @ Sun, 21 Jun 2020 20:09:20: 4000000 INFO @ Sun, 21 Jun 2020 20:09:25: 11000000 INFO @ Sun, 21 Jun 2020 20:09:25: 5000000 INFO @ Sun, 21 Jun 2020 20:09:29: 12000000 INFO @ Sun, 21 Jun 2020 20:09:30: 6000000 INFO @ Sun, 21 Jun 2020 20:09:35: 13000000 INFO @ Sun, 21 Jun 2020 20:09:36: 7000000 INFO @ Sun, 21 Jun 2020 20:09:40: 14000000 INFO @ Sun, 21 Jun 2020 20:09:41: 8000000 INFO @ Sun, 21 Jun 2020 20:09:45: 15000000 INFO @ Sun, 21 Jun 2020 20:09:46: 9000000 INFO @ Sun, 21 Jun 2020 20:09:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:09:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:09:48: #1 total tags in treatment: 15514676 INFO @ Sun, 21 Jun 2020 20:09:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:48: #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 20:09:48: #1 tags after filtering in treatment: 15514568 INFO @ Sun, 21 Jun 2020 20:09:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:50: #2 number of paired peaks: 1564 INFO @ Sun, 21 Jun 2020 20:09:50: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:50: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:50: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:50: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:50: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 20:09:50: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 20:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.10_model.r INFO @ Sun, 21 Jun 2020 20:09:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:51: 10000000 INFO @ Sun, 21 Jun 2020 20:09:55: 11000000 INFO @ Sun, 21 Jun 2020 20:09:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:00: 12000000 INFO @ Sun, 21 Jun 2020 20:10:05: 13000000 INFO @ Sun, 21 Jun 2020 20:10:11: 14000000 INFO @ Sun, 21 Jun 2020 20:10:16: 15000000 INFO @ Sun, 21 Jun 2020 20:10:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:10:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:10:19: #1 total tags in treatment: 15514676 INFO @ Sun, 21 Jun 2020 20:10:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:19: #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 20:10:19: #1 tags after filtering in treatment: 15514568 INFO @ Sun, 21 Jun 2020 20:10:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:19: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.05_summits.bed INFO @ Sun, 21 Jun 2020 20:10:20: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (480 chroms): 2 millis pass2 - checking and writing primary data (5820 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:10:20: #2 number of paired peaks: 1564 INFO @ Sun, 21 Jun 2020 20:10:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:21: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 20:10:21: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 20:10:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.20_model.r INFO @ Sun, 21 Jun 2020 20:10:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.10_summits.bed INFO @ Sun, 21 Jun 2020 20:10:49: Done! pass1 - making usageList (339 chroms): 1 millis pass2 - checking and writing primary data (3726 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:11:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404011/SRX3404011.20_summits.bed INFO @ Sun, 21 Jun 2020 20:11:20: Done! pass1 - making usageList (209 chroms): 2 millis pass2 - checking and writing primary data (2589 records, 4 fields): 9 millis CompletedMACS2peakCalling