Job ID = 14518187 SRX = SRX9430854 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5210987 spots for SRR12979033/SRR12979033.sra Written 5210987 spots for SRR12979033/SRR12979033.sra Read 6689462 spots for SRR12979034/SRR12979034.sra Written 6689462 spots for SRR12979034/SRR12979034.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: 00:00:00 Multiseed full-index search: 00:36:48 11900449 reads; of these: 11900449 (100.00%) were unpaired; of these: 1485335 (12.48%) aligned 0 times 6271606 (52.70%) aligned exactly 1 time 4143508 (34.82%) aligned >1 times 87.52% overall alignment rate Time searching: 00:36:50 Overall time: 00:36:50 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 8 files... [bam_rmdupse_core] 2238168 / 10415114 = 0.2149 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 11:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.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 11:30:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:30:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:31:00: 1000000 INFO @ Sat, 15 Jan 2022 11:31:07: 2000000 INFO @ Sat, 15 Jan 2022 11:31:13: 3000000 INFO @ Sat, 15 Jan 2022 11:31:20: 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 11:31:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.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 11:31:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:31:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:31:26: 5000000 INFO @ Sat, 15 Jan 2022 11:31:30: 1000000 INFO @ Sat, 15 Jan 2022 11:31:33: 6000000 INFO @ Sat, 15 Jan 2022 11:31:37: 2000000 INFO @ Sat, 15 Jan 2022 11:31:40: 7000000 INFO @ Sat, 15 Jan 2022 11:31:43: 3000000 INFO @ Sat, 15 Jan 2022 11:31:48: 8000000 INFO @ Sat, 15 Jan 2022 11:31:49: #1 tag size is determined as 57 bps INFO @ Sat, 15 Jan 2022 11:31:49: #1 tag size = 57 INFO @ Sat, 15 Jan 2022 11:31:49: #1 total tags in treatment: 8176946 INFO @ Sat, 15 Jan 2022 11:31:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:31:49: #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 11:31:49: #1 tags after filtering in treatment: 8176750 INFO @ Sat, 15 Jan 2022 11:31:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:31:49: #1 finished! INFO @ Sat, 15 Jan 2022 11:31:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:31:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:31:49: 4000000 INFO @ Sat, 15 Jan 2022 11:31:51: #2 number of paired peaks: 31935 INFO @ Sat, 15 Jan 2022 11:31:51: start model_add_line... INFO @ Sat, 15 Jan 2022 11:31:51: start X-correlation... INFO @ Sat, 15 Jan 2022 11:31:51: end of X-cor INFO @ Sat, 15 Jan 2022 11:31:51: #2 finished! INFO @ Sat, 15 Jan 2022 11:31:51: #2 predicted fragment length is 118 bps INFO @ Sat, 15 Jan 2022 11:31:51: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 15 Jan 2022 11:31:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.05_model.r INFO @ Sat, 15 Jan 2022 11:31:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:31:51: #3 Pre-compute pvalue-qvalue table... 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 11:31:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.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 11:31:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:31:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:31:55: 5000000 INFO @ Sat, 15 Jan 2022 11:32:00: 1000000 INFO @ Sat, 15 Jan 2022 11:32:02: 6000000 INFO @ Sat, 15 Jan 2022 11:32:07: 2000000 INFO @ Sat, 15 Jan 2022 11:32:08: 7000000 INFO @ Sat, 15 Jan 2022 11:32:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:32:14: 3000000 INFO @ Sat, 15 Jan 2022 11:32:14: 8000000 INFO @ Sat, 15 Jan 2022 11:32:16: #1 tag size is determined as 57 bps INFO @ Sat, 15 Jan 2022 11:32:16: #1 tag size = 57 INFO @ Sat, 15 Jan 2022 11:32:16: #1 total tags in treatment: 8176946 INFO @ Sat, 15 Jan 2022 11:32:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:32:16: #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 11:32:16: #1 tags after filtering in treatment: 8176750 INFO @ Sat, 15 Jan 2022 11:32:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:32:16: #1 finished! INFO @ Sat, 15 Jan 2022 11:32:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:32:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:32:18: #2 number of paired peaks: 31935 INFO @ Sat, 15 Jan 2022 11:32:18: start model_add_line... INFO @ Sat, 15 Jan 2022 11:32:18: start X-correlation... INFO @ Sat, 15 Jan 2022 11:32:18: end of X-cor INFO @ Sat, 15 Jan 2022 11:32:18: #2 finished! INFO @ Sat, 15 Jan 2022 11:32:18: #2 predicted fragment length is 118 bps INFO @ Sat, 15 Jan 2022 11:32:18: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 15 Jan 2022 11:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.10_model.r INFO @ Sat, 15 Jan 2022 11:32:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.05_peaks.xls INFO @ Sat, 15 Jan 2022 11:32:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.05_summits.bed INFO @ Sat, 15 Jan 2022 11:32:19: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (9315 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:32:21: 4000000 INFO @ Sat, 15 Jan 2022 11:32:27: 5000000 INFO @ Sat, 15 Jan 2022 11:32:34: 6000000 INFO @ Sat, 15 Jan 2022 11:32:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:32:41: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 11:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.10_peaks.xls INFO @ Sat, 15 Jan 2022 11:32:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.10_summits.bed INFO @ Sat, 15 Jan 2022 11:32:47: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (2293 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:32:47: 8000000 INFO @ Sat, 15 Jan 2022 11:32:48: #1 tag size is determined as 57 bps INFO @ Sat, 15 Jan 2022 11:32:48: #1 tag size = 57 INFO @ Sat, 15 Jan 2022 11:32:48: #1 total tags in treatment: 8176946 INFO @ Sat, 15 Jan 2022 11:32:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:32:48: #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 11:32:48: #1 tags after filtering in treatment: 8176750 INFO @ Sat, 15 Jan 2022 11:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:32:48: #1 finished! INFO @ Sat, 15 Jan 2022 11:32:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:32:50: #2 number of paired peaks: 31935 INFO @ Sat, 15 Jan 2022 11:32:50: start model_add_line... INFO @ Sat, 15 Jan 2022 11:32:50: start X-correlation... INFO @ Sat, 15 Jan 2022 11:32:50: end of X-cor INFO @ Sat, 15 Jan 2022 11:32:50: #2 finished! INFO @ Sat, 15 Jan 2022 11:32:50: #2 predicted fragment length is 118 bps INFO @ Sat, 15 Jan 2022 11:32:50: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 15 Jan 2022 11:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.20_model.r INFO @ Sat, 15 Jan 2022 11:32:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:32:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 11:33:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:33:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.20_peaks.xls INFO @ Sat, 15 Jan 2022 11:33:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:33:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430854/SRX9430854.20_summits.bed INFO @ Sat, 15 Jan 2022 11:33:18: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 3 millis CompletedMACS2peakCalling