Job ID = 14519071 SRX = ERX2745123 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 88450733 spots for ERR2731898/ERR2731898.sra Written 88450733 spots for ERR2731898/ERR2731898.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: 00:00:01 Multiseed full-index search: 00:40:33 88450733 reads; of these: 88450733 (100.00%) were unpaired; of these: 3391127 (3.83%) aligned 0 times 71529139 (80.87%) aligned exactly 1 time 13530467 (15.30%) aligned >1 times 96.17% overall alignment rate Time searching: 00:40:37 Overall time: 00:40:37 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 36 files... [bam_rmdupse_core] 39362923 / 85059606 = 0.4628 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 15:27:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.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 @ Sat, 15 Jan 2022 15:27:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 15:27:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 15:27:09: 1000000 INFO @ Sat, 15 Jan 2022 15:27:16: 2000000 INFO @ Sat, 15 Jan 2022 15:27:23: 3000000 INFO @ Sat, 15 Jan 2022 15:27:30: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 15:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.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 @ Sat, 15 Jan 2022 15:27:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 15:27:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 15:27:37: 5000000 INFO @ Sat, 15 Jan 2022 15:27:40: 1000000 INFO @ Sat, 15 Jan 2022 15:27:44: 6000000 INFO @ Sat, 15 Jan 2022 15:27:46: 2000000 INFO @ Sat, 15 Jan 2022 15:27:52: 7000000 INFO @ Sat, 15 Jan 2022 15:27:53: 3000000 INFO @ Sat, 15 Jan 2022 15:27:59: 8000000 INFO @ Sat, 15 Jan 2022 15:28:00: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 15:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.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 @ Sat, 15 Jan 2022 15:28:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 15:28:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 15:28:07: 9000000 INFO @ Sat, 15 Jan 2022 15:28:07: 5000000 INFO @ Sat, 15 Jan 2022 15:28:10: 1000000 INFO @ Sat, 15 Jan 2022 15:28:14: 10000000 INFO @ Sat, 15 Jan 2022 15:28:14: 6000000 INFO @ Sat, 15 Jan 2022 15:28:17: 2000000 INFO @ Sat, 15 Jan 2022 15:28:22: 7000000 INFO @ Sat, 15 Jan 2022 15:28:22: 11000000 INFO @ Sat, 15 Jan 2022 15:28:24: 3000000 INFO @ Sat, 15 Jan 2022 15:28:29: 8000000 INFO @ Sat, 15 Jan 2022 15:28:30: 12000000 INFO @ Sat, 15 Jan 2022 15:28:31: 4000000 INFO @ Sat, 15 Jan 2022 15:28:36: 9000000 INFO @ Sat, 15 Jan 2022 15:28:37: 13000000 INFO @ Sat, 15 Jan 2022 15:28:38: 5000000 INFO @ Sat, 15 Jan 2022 15:28:43: 10000000 INFO @ Sat, 15 Jan 2022 15:28:45: 14000000 INFO @ Sat, 15 Jan 2022 15:28:46: 6000000 INFO @ Sat, 15 Jan 2022 15:28:50: 11000000 INFO @ Sat, 15 Jan 2022 15:28:53: 15000000 INFO @ Sat, 15 Jan 2022 15:28:53: 7000000 INFO @ Sat, 15 Jan 2022 15:28:57: 12000000 INFO @ Sat, 15 Jan 2022 15:29:00: 8000000 INFO @ Sat, 15 Jan 2022 15:29:00: 16000000 INFO @ Sat, 15 Jan 2022 15:29:04: 13000000 INFO @ Sat, 15 Jan 2022 15:29:07: 9000000 INFO @ Sat, 15 Jan 2022 15:29:08: 17000000 INFO @ Sat, 15 Jan 2022 15:29:12: 14000000 INFO @ Sat, 15 Jan 2022 15:29:14: 10000000 INFO @ Sat, 15 Jan 2022 15:29:15: 18000000 INFO @ Sat, 15 Jan 2022 15:29:19: 15000000 INFO @ Sat, 15 Jan 2022 15:29:21: 11000000 INFO @ Sat, 15 Jan 2022 15:29:23: 19000000 INFO @ Sat, 15 Jan 2022 15:29:26: 16000000 INFO @ Sat, 15 Jan 2022 15:29:28: 12000000 INFO @ Sat, 15 Jan 2022 15:29:30: 20000000 INFO @ Sat, 15 Jan 2022 15:29:33: 17000000 INFO @ Sat, 15 Jan 2022 15:29:36: 13000000 INFO @ Sat, 15 Jan 2022 15:29:38: 21000000 INFO @ Sat, 15 Jan 2022 15:29:40: 18000000 INFO @ Sat, 15 Jan 2022 15:29:43: 14000000 INFO @ Sat, 15 Jan 2022 15:29:45: 22000000 INFO @ Sat, 15 Jan 2022 15:29:47: 19000000 INFO @ Sat, 15 Jan 2022 15:29:50: 15000000 INFO @ Sat, 15 Jan 2022 15:29:53: 23000000 INFO @ Sat, 15 Jan 2022 15:29:55: 20000000 INFO @ Sat, 15 Jan 2022 15:29:57: 16000000 INFO @ Sat, 15 Jan 2022 15:30:00: 24000000 INFO @ Sat, 15 Jan 2022 15:30:02: 21000000 INFO @ Sat, 15 Jan 2022 15:30:04: 17000000 INFO @ Sat, 15 Jan 2022 15:30:08: 25000000 INFO @ Sat, 15 Jan 2022 15:30:09: 22000000 INFO @ Sat, 15 Jan 2022 15:30:11: 18000000 INFO @ Sat, 15 Jan 2022 15:30:15: 26000000 INFO @ Sat, 15 Jan 2022 15:30:16: 23000000 INFO @ Sat, 15 Jan 2022 15:30:19: 19000000 INFO @ Sat, 15 Jan 2022 15:30:23: 27000000 INFO @ Sat, 15 Jan 2022 15:30:23: 24000000 INFO @ Sat, 15 Jan 2022 15:30:26: 20000000 INFO @ Sat, 15 Jan 2022 15:30:30: 28000000 INFO @ Sat, 15 Jan 2022 15:30:30: 25000000 INFO @ Sat, 15 Jan 2022 15:30:33: 21000000 INFO @ Sat, 15 Jan 2022 15:30:37: 26000000 INFO @ Sat, 15 Jan 2022 15:30:38: 29000000 INFO @ Sat, 15 Jan 2022 15:30:40: 22000000 INFO @ Sat, 15 Jan 2022 15:30:45: 27000000 INFO @ Sat, 15 Jan 2022 15:30:45: 30000000 INFO @ Sat, 15 Jan 2022 15:30:47: 23000000 INFO @ Sat, 15 Jan 2022 15:30:52: 28000000 INFO @ Sat, 15 Jan 2022 15:30:53: 31000000 INFO @ Sat, 15 Jan 2022 15:30:54: 24000000 INFO @ Sat, 15 Jan 2022 15:30:59: 29000000 INFO @ Sat, 15 Jan 2022 15:31:00: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 15:31:02: 25000000 INFO @ Sat, 15 Jan 2022 15:31:06: 30000000 INFO @ Sat, 15 Jan 2022 15:31:08: 33000000 INFO @ Sat, 15 Jan 2022 15:31:09: 26000000 INFO @ Sat, 15 Jan 2022 15:31:13: 31000000 INFO @ Sat, 15 Jan 2022 15:31:15: 34000000 INFO @ Sat, 15 Jan 2022 15:31:16: 27000000 INFO @ Sat, 15 Jan 2022 15:31:20: 32000000 INFO @ Sat, 15 Jan 2022 15:31:23: 35000000 INFO @ Sat, 15 Jan 2022 15:31:23: 28000000 INFO @ Sat, 15 Jan 2022 15:31:28: 33000000 INFO @ Sat, 15 Jan 2022 15:31:30: 29000000 INFO @ Sat, 15 Jan 2022 15:31:30: 36000000 INFO @ Sat, 15 Jan 2022 15:31:35: 34000000 INFO @ Sat, 15 Jan 2022 15:31:37: 30000000 INFO @ Sat, 15 Jan 2022 15:31:38: 37000000 INFO @ Sat, 15 Jan 2022 15:31:42: 35000000 INFO @ Sat, 15 Jan 2022 15:31:45: 31000000 INFO @ Sat, 15 Jan 2022 15:31:45: 38000000 INFO @ Sat, 15 Jan 2022 15:31:49: 36000000 INFO @ Sat, 15 Jan 2022 15:31:52: 32000000 INFO @ Sat, 15 Jan 2022 15:31:53: 39000000 INFO @ Sat, 15 Jan 2022 15:31:56: 37000000 INFO @ Sat, 15 Jan 2022 15:31:59: 33000000 INFO @ Sat, 15 Jan 2022 15:32:01: 40000000 INFO @ Sat, 15 Jan 2022 15:32:03: 38000000 INFO @ Sat, 15 Jan 2022 15:32:06: 34000000 INFO @ Sat, 15 Jan 2022 15:32:08: 41000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 15:32:11: 39000000 INFO @ Sat, 15 Jan 2022 15:32:13: 35000000 INFO @ Sat, 15 Jan 2022 15:32:16: 42000000 INFO @ Sat, 15 Jan 2022 15:32:18: 40000000 INFO @ Sat, 15 Jan 2022 15:32:20: 36000000 INFO @ Sat, 15 Jan 2022 15:32:23: 43000000 INFO @ Sat, 15 Jan 2022 15:32:25: 41000000 INFO @ Sat, 15 Jan 2022 15:32:28: 37000000 INFO @ Sat, 15 Jan 2022 15:32:31: 44000000 INFO @ Sat, 15 Jan 2022 15:32:32: 42000000 INFO @ Sat, 15 Jan 2022 15:32:35: 38000000 INFO @ Sat, 15 Jan 2022 15:32:38: 45000000 INFO @ Sat, 15 Jan 2022 15:32:39: 43000000 INFO @ Sat, 15 Jan 2022 15:32:42: 39000000 INFO @ Sat, 15 Jan 2022 15:32:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 15:32:44: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 15:32:44: #1 total tags in treatment: 45696683 INFO @ Sat, 15 Jan 2022 15:32:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 15:32:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 15:32:45: #1 tags after filtering in treatment: 45696517 INFO @ Sat, 15 Jan 2022 15:32:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 15:32:45: #1 finished! INFO @ Sat, 15 Jan 2022 15:32:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 15:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 15:32:46: 44000000 INFO @ Sat, 15 Jan 2022 15:32:49: 40000000 INFO @ Sat, 15 Jan 2022 15:32:52: #2 number of paired peaks: 102812 INFO @ Sat, 15 Jan 2022 15:32:52: start model_add_line... INFO @ Sat, 15 Jan 2022 15:32:53: 45000000 INFO @ Sat, 15 Jan 2022 15:32:53: start X-correlation... INFO @ Sat, 15 Jan 2022 15:32:53: end of X-cor INFO @ Sat, 15 Jan 2022 15:32:53: #2 finished! INFO @ Sat, 15 Jan 2022 15:32:53: #2 predicted fragment length is 208 bps INFO @ Sat, 15 Jan 2022 15:32:53: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 15 Jan 2022 15:32:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05_model.r INFO @ Sat, 15 Jan 2022 15:32:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 15:32:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 15:32:55: 41000000 INFO @ Sat, 15 Jan 2022 15:32:58: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 15:32:58: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 15:32:58: #1 total tags in treatment: 45696683 INFO @ Sat, 15 Jan 2022 15:32:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 15:32:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 15:32:59: #1 tags after filtering in treatment: 45696517 INFO @ Sat, 15 Jan 2022 15:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 15:32:59: #1 finished! INFO @ Sat, 15 Jan 2022 15:32:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 15:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 15:33:02: 42000000 INFO @ Sat, 15 Jan 2022 15:33:07: #2 number of paired peaks: 102812 INFO @ Sat, 15 Jan 2022 15:33:07: start model_add_line... INFO @ Sat, 15 Jan 2022 15:33:07: start X-correlation... INFO @ Sat, 15 Jan 2022 15:33:07: end of X-cor INFO @ Sat, 15 Jan 2022 15:33:07: #2 finished! INFO @ Sat, 15 Jan 2022 15:33:07: #2 predicted fragment length is 208 bps INFO @ Sat, 15 Jan 2022 15:33:07: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 15 Jan 2022 15:33:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10_model.r INFO @ Sat, 15 Jan 2022 15:33:07: #3 Call peaks... INFO @ Sat, 15 Jan 2022 15:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 15:33:07: 43000000 INFO @ Sat, 15 Jan 2022 15:33:13: 44000000 INFO @ Sat, 15 Jan 2022 15:33:19: 45000000 INFO @ Sat, 15 Jan 2022 15:33:23: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 15:33:23: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 15:33:23: #1 total tags in treatment: 45696683 INFO @ Sat, 15 Jan 2022 15:33:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 15:33:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 15:33:24: #1 tags after filtering in treatment: 45696517 INFO @ Sat, 15 Jan 2022 15:33:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 15:33:24: #1 finished! INFO @ Sat, 15 Jan 2022 15:33:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 15:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 15:33:31: #2 number of paired peaks: 102812 INFO @ Sat, 15 Jan 2022 15:33:31: start model_add_line... INFO @ Sat, 15 Jan 2022 15:33:32: start X-correlation... INFO @ Sat, 15 Jan 2022 15:33:32: end of X-cor INFO @ Sat, 15 Jan 2022 15:33:32: #2 finished! INFO @ Sat, 15 Jan 2022 15:33:32: #2 predicted fragment length is 208 bps INFO @ Sat, 15 Jan 2022 15:33:32: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 15 Jan 2022 15:33:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20_model.r INFO @ Sat, 15 Jan 2022 15:33:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 15:33:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 15:34:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 15:34:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 15:35:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 15:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05_peaks.xls INFO @ Sat, 15 Jan 2022 15:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 15:35:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.05_summits.bed INFO @ Sat, 15 Jan 2022 15:35:34: Done! pass1 - making usageList (228 chroms): 8 millis pass2 - checking and writing primary data (58458 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 15:35:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10_peaks.xls INFO @ Sat, 15 Jan 2022 15:35:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 15:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.10_summits.bed INFO @ Sat, 15 Jan 2022 15:35:45: Done! pass1 - making usageList (196 chroms): 7 millis pass2 - checking and writing primary data (45790 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 15:36:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20_peaks.xls INFO @ Sat, 15 Jan 2022 15:36:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 15:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745123/ERX2745123.20_summits.bed INFO @ Sat, 15 Jan 2022 15:36:20: Done! pass1 - making usageList (163 chroms): 5 millis pass2 - checking and writing primary data (32548 records, 4 fields): 34 millis CompletedMACS2peakCalling