Job ID = 6455260 SRX = SRX287601 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:54:10 prefetch.2.10.7: 1) Downloading 'SRR869744'... 2020-06-21T09:54:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:56:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:56:43 prefetch.2.10.7: 1) 'SRR869744' was downloaded successfully Read 18421694 spots for SRR869744/SRR869744.sra Written 18421694 spots for SRR869744/SRR869744.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: 00:04:31 18421694 reads; of these: 18421694 (100.00%) were unpaired; of these: 1153160 (6.26%) aligned 0 times 15250928 (82.79%) aligned exactly 1 time 2017606 (10.95%) aligned >1 times 93.74% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 2471981 / 17268534 = 0.1431 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 19:07:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.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 19:07:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:16: 1000000 INFO @ Sun, 21 Jun 2020 19:07:22: 2000000 INFO @ Sun, 21 Jun 2020 19:07:27: 3000000 INFO @ Sun, 21 Jun 2020 19:07:33: 4000000 INFO @ Sun, 21 Jun 2020 19:07:39: 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 19:07:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.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 19:07:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:45: 6000000 INFO @ Sun, 21 Jun 2020 19:07:47: 1000000 INFO @ Sun, 21 Jun 2020 19:07:51: 7000000 INFO @ Sun, 21 Jun 2020 19:07:53: 2000000 INFO @ Sun, 21 Jun 2020 19:07:57: 8000000 INFO @ Sun, 21 Jun 2020 19:07:59: 3000000 INFO @ Sun, 21 Jun 2020 19:08:03: 9000000 INFO @ Sun, 21 Jun 2020 19:08:05: 4000000 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 19:08:09: 10000000 INFO @ Sun, 21 Jun 2020 19:08:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.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 19:08:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:11: 5000000 INFO @ Sun, 21 Jun 2020 19:08:16: 11000000 INFO @ Sun, 21 Jun 2020 19:08:17: 1000000 INFO @ Sun, 21 Jun 2020 19:08:18: 6000000 INFO @ Sun, 21 Jun 2020 19:08:22: 12000000 INFO @ Sun, 21 Jun 2020 19:08:24: 2000000 INFO @ Sun, 21 Jun 2020 19:08:25: 7000000 INFO @ Sun, 21 Jun 2020 19:08:29: 13000000 INFO @ Sun, 21 Jun 2020 19:08:31: 3000000 INFO @ Sun, 21 Jun 2020 19:08:31: 8000000 INFO @ Sun, 21 Jun 2020 19:08:36: 14000000 INFO @ Sun, 21 Jun 2020 19:08:38: 4000000 INFO @ Sun, 21 Jun 2020 19:08:38: 9000000 INFO @ Sun, 21 Jun 2020 19:08:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:08:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:08:41: #1 total tags in treatment: 14796553 INFO @ Sun, 21 Jun 2020 19:08:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:41: #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 19:08:42: #1 tags after filtering in treatment: 14796544 INFO @ Sun, 21 Jun 2020 19:08:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:43: #2 number of paired peaks: 1251 INFO @ Sun, 21 Jun 2020 19:08:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:43: #2 predicted fragment length is 282 bps INFO @ Sun, 21 Jun 2020 19:08:43: #2 alternative fragment length(s) may be 4,282 bps INFO @ Sun, 21 Jun 2020 19:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.05_model.r INFO @ Sun, 21 Jun 2020 19:08:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:45: 5000000 INFO @ Sun, 21 Jun 2020 19:08:45: 10000000 INFO @ Sun, 21 Jun 2020 19:08:51: 6000000 INFO @ Sun, 21 Jun 2020 19:08:51: 11000000 INFO @ Sun, 21 Jun 2020 19:08:58: 7000000 INFO @ Sun, 21 Jun 2020 19:08:58: 12000000 INFO @ Sun, 21 Jun 2020 19:09:05: 8000000 INFO @ Sun, 21 Jun 2020 19:09:05: 13000000 INFO @ Sun, 21 Jun 2020 19:09:12: 14000000 INFO @ Sun, 21 Jun 2020 19:09:12: 9000000 INFO @ Sun, 21 Jun 2020 19:09:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:18: #1 total tags in treatment: 14796553 INFO @ Sun, 21 Jun 2020 19:09:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:18: #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 19:09:18: #1 tags after filtering in treatment: 14796544 INFO @ Sun, 21 Jun 2020 19:09:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:19: 10000000 INFO @ Sun, 21 Jun 2020 19:09:20: #2 number of paired peaks: 1251 INFO @ Sun, 21 Jun 2020 19:09:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:20: #2 predicted fragment length is 282 bps INFO @ Sun, 21 Jun 2020 19:09:20: #2 alternative fragment length(s) may be 4,282 bps INFO @ Sun, 21 Jun 2020 19:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.10_model.r INFO @ Sun, 21 Jun 2020 19:09:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:09:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:25: 11000000 INFO @ Sun, 21 Jun 2020 19:09:32: 12000000 INFO @ Sun, 21 Jun 2020 19:09:39: 13000000 INFO @ Sun, 21 Jun 2020 19:09:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.05_summits.bed INFO @ Sun, 21 Jun 2020 19:09:43: Done! pass1 - making usageList (184 chroms): 2 millis pass2 - checking and writing primary data (6003 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:45: 14000000 INFO @ Sun, 21 Jun 2020 19:09:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:51: #1 total tags in treatment: 14796553 INFO @ Sun, 21 Jun 2020 19:09:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:51: #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 19:09:51: #1 tags after filtering in treatment: 14796544 INFO @ Sun, 21 Jun 2020 19:09:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:52: #2 number of paired peaks: 1251 INFO @ Sun, 21 Jun 2020 19:09:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:52: #2 predicted fragment length is 282 bps INFO @ Sun, 21 Jun 2020 19:09:52: #2 alternative fragment length(s) may be 4,282 bps INFO @ Sun, 21 Jun 2020 19:09:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.20_model.r INFO @ Sun, 21 Jun 2020 19:09:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.10_summits.bed INFO @ Sun, 21 Jun 2020 19:10:19: Done! pass1 - making usageList (123 chroms): 2 millis pass2 - checking and writing primary data (3289 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:10:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287601/SRX287601.20_summits.bed INFO @ Sun, 21 Jun 2020 19:10:51: Done! pass1 - making usageList (76 chroms): 2 millis pass2 - checking and writing primary data (1325 records, 4 fields): 5 millis CompletedMACS2peakCalling