Job ID = 10223648 SRX = ERX2745124 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T19:51:59 prefetch.2.10.7: 1) Downloading 'ERR2731899'... 2020-10-15T19:51:59 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T19:53:27 prefetch.2.10.7: HTTPS download succeed 2020-10-15T19:53:27 prefetch.2.10.7: 1) 'ERR2731899' was downloaded successfully Read 65333517 spots for ERR2731899/ERR2731899.sra Written 65333517 spots for ERR2731899/ERR2731899.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:25:24 65333517 reads; of these: 65333517 (100.00%) were unpaired; of these: 3343168 (5.12%) aligned 0 times 55999869 (85.71%) aligned exactly 1 time 5990480 (9.17%) aligned >1 times 94.88% overall alignment rate Time searching: 00:25:30 Overall time: 00:25:30 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 28 files... [bam_rmdupse_core] 38909811 / 61990349 = 0.6277 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 05:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.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 05:30:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:30:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:30:26: 1000000 INFO @ Fri, 16 Oct 2020 05:30:33: 2000000 INFO @ Fri, 16 Oct 2020 05:30:40: 3000000 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 05:30:46: 4000000 INFO @ Fri, 16 Oct 2020 05:30:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.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 05:30:48: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:30:48: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:30:55: 1000000 INFO @ Fri, 16 Oct 2020 05:30:57: 5000000 INFO @ Fri, 16 Oct 2020 05:31:02: 2000000 INFO @ Fri, 16 Oct 2020 05:31:09: 3000000 INFO @ Fri, 16 Oct 2020 05:31:13: 6000000 INFO @ Fri, 16 Oct 2020 05:31:16: 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 @ Fri, 16 Oct 2020 05:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.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 05:31:18: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:31:18: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:31:23: 5000000 INFO @ Fri, 16 Oct 2020 05:31:26: 1000000 INFO @ Fri, 16 Oct 2020 05:31:28: 7000000 INFO @ Fri, 16 Oct 2020 05:31:30: 6000000 INFO @ Fri, 16 Oct 2020 05:31:34: 2000000 INFO @ Fri, 16 Oct 2020 05:31:37: 7000000 INFO @ Fri, 16 Oct 2020 05:31:42: 3000000 INFO @ Fri, 16 Oct 2020 05:31:42: 8000000 INFO @ Fri, 16 Oct 2020 05:31:44: 8000000 INFO @ Fri, 16 Oct 2020 05:31:50: 4000000 INFO @ Fri, 16 Oct 2020 05:31:52: 9000000 INFO @ Fri, 16 Oct 2020 05:31:56: 9000000 INFO @ Fri, 16 Oct 2020 05:31:58: 5000000 INFO @ Fri, 16 Oct 2020 05:31:59: 10000000 INFO @ Fri, 16 Oct 2020 05:32:06: 6000000 INFO @ Fri, 16 Oct 2020 05:32:06: 11000000 INFO @ Fri, 16 Oct 2020 05:32:10: 10000000 INFO @ Fri, 16 Oct 2020 05:32:13: 12000000 INFO @ Fri, 16 Oct 2020 05:32:13: 7000000 INFO @ Fri, 16 Oct 2020 05:32:20: 13000000 INFO @ Fri, 16 Oct 2020 05:32:21: 8000000 INFO @ Fri, 16 Oct 2020 05:32:23: 11000000 INFO @ Fri, 16 Oct 2020 05:32:27: 14000000 INFO @ Fri, 16 Oct 2020 05:32:29: 9000000 INFO @ Fri, 16 Oct 2020 05:32:35: 15000000 INFO @ Fri, 16 Oct 2020 05:32:36: 12000000 INFO @ Fri, 16 Oct 2020 05:32:36: 10000000 INFO @ Fri, 16 Oct 2020 05:32:42: 16000000 INFO @ Fri, 16 Oct 2020 05:32:44: 11000000 INFO @ Fri, 16 Oct 2020 05:32:49: 13000000 INFO @ Fri, 16 Oct 2020 05:32:49: 17000000 INFO @ Fri, 16 Oct 2020 05:32:52: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 05:32:56: 18000000 INFO @ Fri, 16 Oct 2020 05:32:59: 13000000 INFO @ Fri, 16 Oct 2020 05:33:02: 14000000 INFO @ Fri, 16 Oct 2020 05:33:03: 19000000 INFO @ Fri, 16 Oct 2020 05:33:07: 14000000 INFO @ Fri, 16 Oct 2020 05:33:10: 20000000 INFO @ Fri, 16 Oct 2020 05:33:15: 15000000 INFO @ Fri, 16 Oct 2020 05:33:15: 15000000 INFO @ Fri, 16 Oct 2020 05:33:17: 21000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 05:33:22: 16000000 INFO @ Fri, 16 Oct 2020 05:33:24: 22000000 INFO @ Fri, 16 Oct 2020 05:33:29: 16000000 INFO @ Fri, 16 Oct 2020 05:33:30: 17000000 INFO @ Fri, 16 Oct 2020 05:33:31: 23000000 INFO @ Fri, 16 Oct 2020 05:33:32: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:33:32: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:33:32: #1 total tags in treatment: 23080538 INFO @ Fri, 16 Oct 2020 05:33:32: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:33:32: #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 05:33:32: #1 tags after filtering in treatment: 23080265 INFO @ Fri, 16 Oct 2020 05:33:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:33:32: #1 finished! INFO @ Fri, 16 Oct 2020 05:33:32: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:33:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:33:35: #2 number of paired peaks: 26966 INFO @ Fri, 16 Oct 2020 05:33:35: start model_add_line... INFO @ Fri, 16 Oct 2020 05:33:35: start X-correlation... INFO @ Fri, 16 Oct 2020 05:33:35: end of X-cor INFO @ Fri, 16 Oct 2020 05:33:35: #2 finished! INFO @ Fri, 16 Oct 2020 05:33:35: #2 predicted fragment length is 214 bps INFO @ Fri, 16 Oct 2020 05:33:35: #2 alternative fragment length(s) may be 214 bps INFO @ Fri, 16 Oct 2020 05:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.10_model.r INFO @ Fri, 16 Oct 2020 05:33:35: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:33:38: 18000000 INFO @ Fri, 16 Oct 2020 05:33:43: 17000000 INFO @ Fri, 16 Oct 2020 05:33:45: 19000000 INFO @ Fri, 16 Oct 2020 05:33:52: 20000000 INFO @ Fri, 16 Oct 2020 05:33:56: 18000000 INFO @ Fri, 16 Oct 2020 05:33:59: 21000000 INFO @ Fri, 16 Oct 2020 05:34:06: 22000000 INFO @ Fri, 16 Oct 2020 05:34:10: 19000000 INFO @ Fri, 16 Oct 2020 05:34:13: 23000000 INFO @ Fri, 16 Oct 2020 05:34:14: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:34:14: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:34:14: #1 total tags in treatment: 23080538 INFO @ Fri, 16 Oct 2020 05:34:14: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:34:14: #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 05:34:14: #1 tags after filtering in treatment: 23080265 INFO @ Fri, 16 Oct 2020 05:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:34:14: #1 finished! INFO @ Fri, 16 Oct 2020 05:34:14: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:34:17: #2 number of paired peaks: 26966 INFO @ Fri, 16 Oct 2020 05:34:17: start model_add_line... INFO @ Fri, 16 Oct 2020 05:34:17: start X-correlation... INFO @ Fri, 16 Oct 2020 05:34:17: end of X-cor INFO @ Fri, 16 Oct 2020 05:34:17: #2 finished! INFO @ Fri, 16 Oct 2020 05:34:17: #2 predicted fragment length is 214 bps INFO @ Fri, 16 Oct 2020 05:34:17: #2 alternative fragment length(s) may be 214 bps INFO @ Fri, 16 Oct 2020 05:34:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.20_model.r INFO @ Fri, 16 Oct 2020 05:34:17: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:34:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:34:22: 20000000 INFO @ Fri, 16 Oct 2020 05:34:30: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:34:32: 21000000 INFO @ Fri, 16 Oct 2020 05:34:43: 22000000 INFO @ Fri, 16 Oct 2020 05:34:54: 23000000 INFO @ Fri, 16 Oct 2020 05:34:55: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:34:55: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:34:55: #1 total tags in treatment: 23080538 INFO @ Fri, 16 Oct 2020 05:34:55: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:34:55: #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 05:34:55: #1 tags after filtering in treatment: 23080265 INFO @ Fri, 16 Oct 2020 05:34:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:34:55: #1 finished! INFO @ Fri, 16 Oct 2020 05:34:55: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:34:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:34:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.10_peaks.xls INFO @ Fri, 16 Oct 2020 05:34:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.10_summits.bed INFO @ Fri, 16 Oct 2020 05:34:57: Done! INFO @ Fri, 16 Oct 2020 05:34:58: #2 number of paired peaks: 26966 INFO @ Fri, 16 Oct 2020 05:34:58: start model_add_line... INFO @ Fri, 16 Oct 2020 05:34:58: start X-correlation... INFO @ Fri, 16 Oct 2020 05:34:58: end of X-cor INFO @ Fri, 16 Oct 2020 05:34:58: #2 finished! INFO @ Fri, 16 Oct 2020 05:34:58: #2 predicted fragment length is 214 bps INFO @ Fri, 16 Oct 2020 05:34:58: #2 alternative fragment length(s) may be 214 bps INFO @ Fri, 16 Oct 2020 05:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.05_model.r INFO @ Fri, 16 Oct 2020 05:34:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:34:58: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (122 chroms): 4 millis pass2 - checking and writing primary data (21394 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:35:14: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:35:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.20_peaks.xls INFO @ Fri, 16 Oct 2020 05:35:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:35:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.20_summits.bed INFO @ Fri, 16 Oct 2020 05:35:42: Done! pass1 - making usageList (114 chroms): 4 millis pass2 - checking and writing primary data (19089 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:35:54: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.05_peaks.xls INFO @ Fri, 16 Oct 2020 05:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745124/ERX2745124.05_summits.bed INFO @ Fri, 16 Oct 2020 05:36:23: Done! pass1 - making usageList (137 chroms): 4 millis pass2 - checking and writing primary data (23712 records, 4 fields): 25 millis CompletedMACS2peakCalling