Job ID = 6453617 SRX = SRX1299940 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:24:17 prefetch.2.10.7: 1) Downloading 'SRR2546859'... 2020-06-21T08:24:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:55 prefetch.2.10.7: 'SRR2546859' is valid 2020-06-21T08:27:55 prefetch.2.10.7: 1) 'SRR2546859' was downloaded successfully Read 9520218 spots for SRR2546859/SRR2546859.sra Written 9520218 spots for SRR2546859/SRR2546859.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: 00:02:29 9520218 reads; of these: 9520218 (100.00%) were unpaired; of these: 1284509 (13.49%) aligned 0 times 5768172 (60.59%) aligned exactly 1 time 2467537 (25.92%) aligned >1 times 86.51% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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_rmdupse_core] 3841311 / 8235709 = 0.4664 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 17:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.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 17:33:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:33:15: 1000000 INFO @ Sun, 21 Jun 2020 17:33:21: 2000000 INFO @ Sun, 21 Jun 2020 17:33:26: 3000000 INFO @ Sun, 21 Jun 2020 17:33:31: 4000000 INFO @ Sun, 21 Jun 2020 17:33:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:33:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:33:33: #1 total tags in treatment: 4394398 INFO @ Sun, 21 Jun 2020 17:33:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:33:33: #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 17:33:34: #1 tags after filtering in treatment: 4394261 INFO @ Sun, 21 Jun 2020 17:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:33:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:33:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:33:34: #2 number of paired peaks: 3319 INFO @ Sun, 21 Jun 2020 17:33:34: start model_add_line... INFO @ Sun, 21 Jun 2020 17:33:34: start X-correlation... INFO @ Sun, 21 Jun 2020 17:33:34: end of X-cor INFO @ Sun, 21 Jun 2020 17:33:34: #2 finished! INFO @ Sun, 21 Jun 2020 17:33:34: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:33:34: #2 alternative fragment length(s) may be 4,126 bps INFO @ Sun, 21 Jun 2020 17:33:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.05_model.r INFO @ Sun, 21 Jun 2020 17:33:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:33:34: #3 Pre-compute pvalue-qvalue table... 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 17:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.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 17:33:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:33:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:33:45: 1000000 INFO @ Sun, 21 Jun 2020 17:33:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:33:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:33:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.05_summits.bed INFO @ Sun, 21 Jun 2020 17:33:50: Done! pass1 - making usageList (706 chroms): 1 millis pass2 - checking and writing primary data (2344 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:33:50: 2000000 INFO @ Sun, 21 Jun 2020 17:33:55: 3000000 INFO @ Sun, 21 Jun 2020 17:34:01: 4000000 INFO @ Sun, 21 Jun 2020 17:34:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:34:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:34:03: #1 total tags in treatment: 4394398 INFO @ Sun, 21 Jun 2020 17:34:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:03: #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 17:34:03: #1 tags after filtering in treatment: 4394261 INFO @ Sun, 21 Jun 2020 17:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:04: #2 number of paired peaks: 3319 INFO @ Sun, 21 Jun 2020 17:34:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:04: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:34:04: #2 alternative fragment length(s) may be 4,126 bps INFO @ Sun, 21 Jun 2020 17:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.10_model.r INFO @ Sun, 21 Jun 2020 17:34:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:04: #3 Pre-compute pvalue-qvalue table... 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 17:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.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 17:34:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:15: 1000000 INFO @ Sun, 21 Jun 2020 17:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.10_summits.bed INFO @ Sun, 21 Jun 2020 17:34:19: Done! pass1 - making usageList (576 chroms): 1 millis pass2 - checking and writing primary data (1348 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:34:20: 2000000 INFO @ Sun, 21 Jun 2020 17:34:25: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:34:30: 4000000 INFO @ Sun, 21 Jun 2020 17:34:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:34:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:34:32: #1 total tags in treatment: 4394398 INFO @ Sun, 21 Jun 2020 17:34:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:32: #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 17:34:33: #1 tags after filtering in treatment: 4394261 INFO @ Sun, 21 Jun 2020 17:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:33: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:33: #2 number of paired peaks: 3319 INFO @ Sun, 21 Jun 2020 17:34:33: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:33: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:33: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:33: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:33: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:34:33: #2 alternative fragment length(s) may be 4,126 bps INFO @ Sun, 21 Jun 2020 17:34:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.20_model.r INFO @ Sun, 21 Jun 2020 17:34:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:34:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299940/SRX1299940.20_summits.bed INFO @ Sun, 21 Jun 2020 17:34:48: Done! pass1 - making usageList (377 chroms): 1 millis pass2 - checking and writing primary data (652 records, 4 fields): 13 millis CompletedMACS2peakCalling