Job ID = 10223653 SRX = ERX2745128 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T20:02:12 prefetch.2.10.7: 1) Downloading 'ERR2731903'... 2020-10-15T20:02:12 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T20:03:17 prefetch.2.10.7: HTTPS download succeed 2020-10-15T20:03:17 prefetch.2.10.7: 1) 'ERR2731903' was downloaded successfully Read 45015276 spots for ERR2731903/ERR2731903.sra Written 45015276 spots for ERR2731903/ERR2731903.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:43 45015276 reads; of these: 45015276 (100.00%) were unpaired; of these: 5612760 (12.47%) aligned 0 times 32843092 (72.96%) aligned exactly 1 time 6559424 (14.57%) aligned >1 times 87.53% overall alignment rate Time searching: 00:20:45 Overall time: 00:20:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 21946802 / 39402516 = 0.5570 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 @ Fri, 16 Oct 2020 05:31:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 16 Oct 2020 05:31:40: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:31:40: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:31:45: 1000000 INFO @ Fri, 16 Oct 2020 05:31:49: 2000000 INFO @ Fri, 16 Oct 2020 05:31:54: 3000000 INFO @ Fri, 16 Oct 2020 05:31:59: 4000000 INFO @ Fri, 16 Oct 2020 05:32:03: 5000000 INFO @ Fri, 16 Oct 2020 05:32:08: 6000000 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 @ Fri, 16 Oct 2020 05:32:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 16 Oct 2020 05:32:10: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:32:10: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:32:13: 7000000 INFO @ Fri, 16 Oct 2020 05:32:15: 1000000 INFO @ Fri, 16 Oct 2020 05:32:18: 8000000 INFO @ Fri, 16 Oct 2020 05:32:20: 2000000 INFO @ Fri, 16 Oct 2020 05:32:23: 9000000 INFO @ Fri, 16 Oct 2020 05:32:25: 3000000 INFO @ Fri, 16 Oct 2020 05:32:28: 10000000 INFO @ Fri, 16 Oct 2020 05:32:30: 4000000 INFO @ Fri, 16 Oct 2020 05:32:33: 11000000 INFO @ Fri, 16 Oct 2020 05:32:35: 5000000 INFO @ Fri, 16 Oct 2020 05:32:37: 12000000 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 @ Fri, 16 Oct 2020 05:32:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 16 Oct 2020 05:32:40: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:32:40: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:32:40: 6000000 INFO @ Fri, 16 Oct 2020 05:32:42: 13000000 INFO @ Fri, 16 Oct 2020 05:32:45: 7000000 INFO @ Fri, 16 Oct 2020 05:32:46: 1000000 INFO @ Fri, 16 Oct 2020 05:32:47: 14000000 INFO @ Fri, 16 Oct 2020 05:32:50: 8000000 INFO @ Fri, 16 Oct 2020 05:32:52: 2000000 INFO @ Fri, 16 Oct 2020 05:32:52: 15000000 INFO @ Fri, 16 Oct 2020 05:32:55: 9000000 INFO @ Fri, 16 Oct 2020 05:32:57: 16000000 INFO @ Fri, 16 Oct 2020 05:32:58: 3000000 INFO @ Fri, 16 Oct 2020 05:33:00: 10000000 INFO @ Fri, 16 Oct 2020 05:33:02: 17000000 INFO @ Fri, 16 Oct 2020 05:33:04: 4000000 INFO @ Fri, 16 Oct 2020 05:33:05: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:33:05: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:33:05: #1 total tags in treatment: 17455714 INFO @ Fri, 16 Oct 2020 05:33:05: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:33:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 05:33:05: #1 tags after filtering in treatment: 17455541 INFO @ Fri, 16 Oct 2020 05:33:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:33:05: #1 finished! INFO @ Fri, 16 Oct 2020 05:33:05: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:33:05: 11000000 INFO @ Fri, 16 Oct 2020 05:33:08: #2 number of paired peaks: 27606 INFO @ Fri, 16 Oct 2020 05:33:08: start model_add_line... INFO @ Fri, 16 Oct 2020 05:33:08: start X-correlation... INFO @ Fri, 16 Oct 2020 05:33:08: end of X-cor INFO @ Fri, 16 Oct 2020 05:33:08: #2 finished! INFO @ Fri, 16 Oct 2020 05:33:08: #2 predicted fragment length is 250 bps INFO @ Fri, 16 Oct 2020 05:33:08: #2 alternative fragment length(s) may be 250 bps INFO @ Fri, 16 Oct 2020 05:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.05_model.r INFO @ Fri, 16 Oct 2020 05:33:08: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:33:10: 5000000 INFO @ Fri, 16 Oct 2020 05:33:10: 12000000 INFO @ Fri, 16 Oct 2020 05:33:15: 13000000 INFO @ Fri, 16 Oct 2020 05:33:16: 6000000 INFO @ Fri, 16 Oct 2020 05:33:20: 14000000 INFO @ Fri, 16 Oct 2020 05:33:21: 7000000 INFO @ Fri, 16 Oct 2020 05:33:25: 15000000 INFO @ Fri, 16 Oct 2020 05:33:27: 8000000 INFO @ Fri, 16 Oct 2020 05:33:30: 16000000 INFO @ Fri, 16 Oct 2020 05:33:33: 9000000 INFO @ Fri, 16 Oct 2020 05:33:35: 17000000 INFO @ Fri, 16 Oct 2020 05:33:38: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:33:38: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:33:38: #1 total tags in treatment: 17455714 INFO @ Fri, 16 Oct 2020 05:33:38: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:33:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 05:33:38: #1 tags after filtering in treatment: 17455541 INFO @ Fri, 16 Oct 2020 05:33:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:33:38: #1 finished! INFO @ Fri, 16 Oct 2020 05:33:38: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:33:39: 10000000 INFO @ Fri, 16 Oct 2020 05:33:40: #2 number of paired peaks: 27606 INFO @ Fri, 16 Oct 2020 05:33:40: start model_add_line... INFO @ Fri, 16 Oct 2020 05:33:41: start X-correlation... INFO @ Fri, 16 Oct 2020 05:33:41: end of X-cor INFO @ Fri, 16 Oct 2020 05:33:41: #2 finished! INFO @ Fri, 16 Oct 2020 05:33:41: #2 predicted fragment length is 250 bps INFO @ Fri, 16 Oct 2020 05:33:41: #2 alternative fragment length(s) may be 250 bps INFO @ Fri, 16 Oct 2020 05:33:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.10_model.r INFO @ Fri, 16 Oct 2020 05:33:41: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:33:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:33:45: 11000000 INFO @ Fri, 16 Oct 2020 05:33:50: 12000000 INFO @ Fri, 16 Oct 2020 05:33:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:33:56: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 05:34:02: 14000000 INFO @ Fri, 16 Oct 2020 05:34:07: 15000000 INFO @ Fri, 16 Oct 2020 05:34:13: 16000000 INFO @ Fri, 16 Oct 2020 05:34:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.05_peaks.xls INFO @ Fri, 16 Oct 2020 05:34:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:34:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.05_summits.bed INFO @ Fri, 16 Oct 2020 05:34:14: Done! pass1 - making usageList (123 chroms): 3 millis pass2 - checking and writing primary data (18225 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:34:18: 17000000 INFO @ Fri, 16 Oct 2020 05:34:21: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:34:21: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:34:21: #1 total tags in treatment: 17455714 INFO @ Fri, 16 Oct 2020 05:34:21: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:34:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 05:34:21: #1 tags after filtering in treatment: 17455541 INFO @ Fri, 16 Oct 2020 05:34:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:34:21: #1 finished! INFO @ Fri, 16 Oct 2020 05:34:21: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:34:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:34:23: #2 number of paired peaks: 27606 INFO @ Fri, 16 Oct 2020 05:34:23: start model_add_line... INFO @ Fri, 16 Oct 2020 05:34:24: start X-correlation... INFO @ Fri, 16 Oct 2020 05:34:24: end of X-cor INFO @ Fri, 16 Oct 2020 05:34:24: #2 finished! INFO @ Fri, 16 Oct 2020 05:34:24: #2 predicted fragment length is 250 bps INFO @ Fri, 16 Oct 2020 05:34:24: #2 alternative fragment length(s) may be 250 bps INFO @ Fri, 16 Oct 2020 05:34:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.20_model.r INFO @ Fri, 16 Oct 2020 05:34:24: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:34:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:34:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 05:34:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.10_peaks.xls INFO @ Fri, 16 Oct 2020 05:34:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:34:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.10_summits.bed INFO @ Fri, 16 Oct 2020 05:34:47: Done! pass1 - making usageList (109 chroms): 2 millis pass2 - checking and writing primary data (16157 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:35:07: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:35:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.20_peaks.xls INFO @ Fri, 16 Oct 2020 05:35:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:35:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745128/ERX2745128.20_summits.bed INFO @ Fri, 16 Oct 2020 05:35:31: Done! pass1 - making usageList (91 chroms): 3 millis pass2 - checking and writing primary data (13731 records, 4 fields): 15 millis CompletedMACS2peakCalling