Job ID = 6453072 SRX = SRX1032390 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:13:03 prefetch.2.10.7: 1) Downloading 'SRR2031895'... 2020-06-21T08:13:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:16:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:16:14 prefetch.2.10.7: 1) 'SRR2031895' was downloaded successfully Read 19412495 spots for SRR2031895/SRR2031895.sra Written 19412495 spots for SRR2031895/SRR2031895.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: 00:05:44 19412495 reads; of these: 19412495 (100.00%) were unpaired; of these: 863829 (4.45%) aligned 0 times 14085464 (72.56%) aligned exactly 1 time 4463202 (22.99%) aligned >1 times 95.55% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 6654856 / 18548666 = 0.3588 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 17:27:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.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 17:27:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:29: 1000000 INFO @ Sun, 21 Jun 2020 17:27:34: 2000000 INFO @ Sun, 21 Jun 2020 17:27:40: 3000000 INFO @ Sun, 21 Jun 2020 17:27:46: 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 17:27:52: 5000000 INFO @ Sun, 21 Jun 2020 17:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.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 17:27:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:58: 6000000 INFO @ Sun, 21 Jun 2020 17:28:00: 1000000 INFO @ Sun, 21 Jun 2020 17:28:05: 7000000 INFO @ Sun, 21 Jun 2020 17:28:06: 2000000 INFO @ Sun, 21 Jun 2020 17:28:11: 8000000 INFO @ Sun, 21 Jun 2020 17:28:13: 3000000 INFO @ Sun, 21 Jun 2020 17:28:18: 9000000 INFO @ Sun, 21 Jun 2020 17:28:19: 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 17:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.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 17:28:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:25: 10000000 INFO @ Sun, 21 Jun 2020 17:28:26: 5000000 INFO @ Sun, 21 Jun 2020 17:28:30: 1000000 INFO @ Sun, 21 Jun 2020 17:28:31: 11000000 INFO @ Sun, 21 Jun 2020 17:28:32: 6000000 INFO @ Sun, 21 Jun 2020 17:28:37: 2000000 INFO @ Sun, 21 Jun 2020 17:28:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:28:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:28:38: #1 total tags in treatment: 11893810 INFO @ Sun, 21 Jun 2020 17:28:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:38: #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 17:28:38: #1 tags after filtering in treatment: 11893809 INFO @ Sun, 21 Jun 2020 17:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:38: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:39: #2 number of paired peaks: 1467 INFO @ Sun, 21 Jun 2020 17:28:39: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:39: 7000000 INFO @ Sun, 21 Jun 2020 17:28:39: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:39: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:39: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:39: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 17:28:39: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 17:28:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.05_model.r INFO @ Sun, 21 Jun 2020 17:28:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:43: 3000000 INFO @ Sun, 21 Jun 2020 17:28:46: 8000000 INFO @ Sun, 21 Jun 2020 17:28:50: 4000000 INFO @ Sun, 21 Jun 2020 17:28:53: 9000000 INFO @ Sun, 21 Jun 2020 17:28:56: 5000000 INFO @ Sun, 21 Jun 2020 17:29:00: 10000000 INFO @ Sun, 21 Jun 2020 17:29:03: 6000000 INFO @ Sun, 21 Jun 2020 17:29:06: 11000000 INFO @ Sun, 21 Jun 2020 17:29:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:09: 7000000 INFO @ Sun, 21 Jun 2020 17:29:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:29:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:29:13: #1 total tags in treatment: 11893810 INFO @ Sun, 21 Jun 2020 17:29:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:13: #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 17:29:13: #1 tags after filtering in treatment: 11893809 INFO @ Sun, 21 Jun 2020 17:29:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:14: #2 number of paired peaks: 1467 INFO @ Sun, 21 Jun 2020 17:29:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:14: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 17:29:14: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 17:29:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.10_model.r INFO @ Sun, 21 Jun 2020 17:29:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:16: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:29:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.05_summits.bed INFO @ Sun, 21 Jun 2020 17:29:22: Done! INFO @ Sun, 21 Jun 2020 17:29:22: 9000000 pass1 - making usageList (605 chroms): 2 millis pass2 - checking and writing primary data (7587 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:29:28: 10000000 INFO @ Sun, 21 Jun 2020 17:29:34: 11000000 INFO @ Sun, 21 Jun 2020 17:29:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:29:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:29:39: #1 total tags in treatment: 11893810 INFO @ Sun, 21 Jun 2020 17:29:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:39: #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 17:29:40: #1 tags after filtering in treatment: 11893809 INFO @ Sun, 21 Jun 2020 17:29:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:40: #2 number of paired peaks: 1467 INFO @ Sun, 21 Jun 2020 17:29:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:41: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 17:29:41: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 17:29:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.20_model.r INFO @ Sun, 21 Jun 2020 17:29:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:29:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.10_summits.bed INFO @ Sun, 21 Jun 2020 17:29:54: Done! pass1 - making usageList (517 chroms): 2 millis pass2 - checking and writing primary data (4568 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:30:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032390/SRX1032390.20_summits.bed INFO @ Sun, 21 Jun 2020 17:30:22: Done! pass1 - making usageList (432 chroms): 1 millis pass2 - checking and writing primary data (2347 records, 4 fields): 14 millis CompletedMACS2peakCalling