Job ID = 14519553 SRX = SRX9963484 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32711722 spots for SRR13565200/SRR13565200.sra Written 32711722 spots for SRR13565200/SRR13565200.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: 00:30:52 32711722 reads; of these: 32711722 (100.00%) were unpaired; of these: 4020980 (12.29%) aligned 0 times 25482661 (77.90%) aligned exactly 1 time 3208081 (9.81%) aligned >1 times 87.71% overall alignment rate Time searching: 00:30:54 Overall time: 00:30:54 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 12 files... [bam_rmdupse_core] 8759763 / 28690742 = 0.3053 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 16:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.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 16:48:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:48:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:48:12: 1000000 INFO @ Sat, 15 Jan 2022 16:48:18: 2000000 INFO @ Sat, 15 Jan 2022 16:48:24: 3000000 INFO @ Sat, 15 Jan 2022 16:48:30: 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 16:48:35: 5000000 INFO @ Sat, 15 Jan 2022 16:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.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 16:48:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:48:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:48:42: 6000000 INFO @ Sat, 15 Jan 2022 16:48:43: 1000000 INFO @ Sat, 15 Jan 2022 16:48:48: 7000000 INFO @ Sat, 15 Jan 2022 16:48:49: 2000000 INFO @ Sat, 15 Jan 2022 16:48:55: 8000000 INFO @ Sat, 15 Jan 2022 16:48:56: 3000000 INFO @ Sat, 15 Jan 2022 16:49:01: 9000000 INFO @ Sat, 15 Jan 2022 16:49:02: 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 16:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.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 16:49:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:49:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:49:08: 10000000 INFO @ Sat, 15 Jan 2022 16:49:09: 5000000 INFO @ Sat, 15 Jan 2022 16:49:14: 1000000 INFO @ Sat, 15 Jan 2022 16:49:15: 11000000 INFO @ Sat, 15 Jan 2022 16:49:16: 6000000 INFO @ Sat, 15 Jan 2022 16:49:22: 2000000 INFO @ Sat, 15 Jan 2022 16:49:22: 12000000 INFO @ Sat, 15 Jan 2022 16:49:23: 7000000 INFO @ Sat, 15 Jan 2022 16:49:29: 13000000 INFO @ Sat, 15 Jan 2022 16:49:30: 3000000 INFO @ Sat, 15 Jan 2022 16:49:30: 8000000 INFO @ Sat, 15 Jan 2022 16:49:36: 14000000 INFO @ Sat, 15 Jan 2022 16:49:37: 9000000 INFO @ Sat, 15 Jan 2022 16:49:38: 4000000 INFO @ Sat, 15 Jan 2022 16:49:43: 15000000 INFO @ Sat, 15 Jan 2022 16:49:44: 10000000 INFO @ Sat, 15 Jan 2022 16:49:46: 5000000 INFO @ Sat, 15 Jan 2022 16:49:50: 16000000 INFO @ Sat, 15 Jan 2022 16:49:51: 11000000 INFO @ Sat, 15 Jan 2022 16:49:54: 6000000 INFO @ Sat, 15 Jan 2022 16:49:57: 17000000 INFO @ Sat, 15 Jan 2022 16:49:58: 12000000 INFO @ Sat, 15 Jan 2022 16:50:03: 7000000 INFO @ Sat, 15 Jan 2022 16:50:04: 18000000 INFO @ Sat, 15 Jan 2022 16:50:06: 13000000 INFO @ Sat, 15 Jan 2022 16:50:11: 8000000 INFO @ Sat, 15 Jan 2022 16:50:12: 19000000 INFO @ Sat, 15 Jan 2022 16:50:13: 14000000 INFO @ Sat, 15 Jan 2022 16:50:18: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 16:50:18: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 16:50:18: #1 total tags in treatment: 19930979 INFO @ Sat, 15 Jan 2022 16:50:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:50:18: #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 16:50:19: #1 tags after filtering in treatment: 19930720 INFO @ Sat, 15 Jan 2022 16:50:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:50:19: #1 finished! INFO @ Sat, 15 Jan 2022 16:50:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:50:19: 9000000 INFO @ Sat, 15 Jan 2022 16:50:20: 15000000 INFO @ Sat, 15 Jan 2022 16:50:21: #2 number of paired peaks: 37626 INFO @ Sat, 15 Jan 2022 16:50:21: start model_add_line... INFO @ Sat, 15 Jan 2022 16:50:22: start X-correlation... INFO @ Sat, 15 Jan 2022 16:50:22: end of X-cor INFO @ Sat, 15 Jan 2022 16:50:22: #2 finished! INFO @ Sat, 15 Jan 2022 16:50:22: #2 predicted fragment length is 211 bps INFO @ Sat, 15 Jan 2022 16:50:22: #2 alternative fragment length(s) may be 4,211 bps INFO @ Sat, 15 Jan 2022 16:50:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.05_model.r INFO @ Sat, 15 Jan 2022 16:50:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:50:27: 16000000 INFO @ Sat, 15 Jan 2022 16:50:27: 10000000 INFO @ Sat, 15 Jan 2022 16:50:34: 17000000 INFO @ Sat, 15 Jan 2022 16:50:35: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 16:50:41: 18000000 INFO @ Sat, 15 Jan 2022 16:50:43: 12000000 INFO @ Sat, 15 Jan 2022 16:50:48: 19000000 INFO @ Sat, 15 Jan 2022 16:50:51: 13000000 INFO @ Sat, 15 Jan 2022 16:50:55: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 16:50:55: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 16:50:55: #1 total tags in treatment: 19930979 INFO @ Sat, 15 Jan 2022 16:50:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:50:55: #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 16:50:55: #1 tags after filtering in treatment: 19930720 INFO @ Sat, 15 Jan 2022 16:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:50:55: #1 finished! INFO @ Sat, 15 Jan 2022 16:50:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:50:58: #2 number of paired peaks: 37626 INFO @ Sat, 15 Jan 2022 16:50:58: start model_add_line... INFO @ Sat, 15 Jan 2022 16:50:58: start X-correlation... INFO @ Sat, 15 Jan 2022 16:50:58: end of X-cor INFO @ Sat, 15 Jan 2022 16:50:58: #2 finished! INFO @ Sat, 15 Jan 2022 16:50:58: #2 predicted fragment length is 211 bps INFO @ Sat, 15 Jan 2022 16:50:58: #2 alternative fragment length(s) may be 4,211 bps INFO @ Sat, 15 Jan 2022 16:50:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.10_model.r INFO @ Sat, 15 Jan 2022 16:50:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:50:59: 14000000 INFO @ Sat, 15 Jan 2022 16:51:06: 15000000 INFO @ Sat, 15 Jan 2022 16:51:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 16:51:14: 16000000 INFO @ Sat, 15 Jan 2022 16:51:21: 17000000 INFO @ Sat, 15 Jan 2022 16:51:28: 18000000 INFO @ Sat, 15 Jan 2022 16:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.05_peaks.xls INFO @ Sat, 15 Jan 2022 16:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.05_summits.bed INFO @ Sat, 15 Jan 2022 16:51:32: Done! pass1 - making usageList (124 chroms): 4 millis pass2 - checking and writing primary data (23380 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 16:51:36: 19000000 INFO @ Sat, 15 Jan 2022 16:51:43: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 16:51:43: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 16:51:43: #1 total tags in treatment: 19930979 INFO @ Sat, 15 Jan 2022 16:51:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:51:43: #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 16:51:43: #1 tags after filtering in treatment: 19930720 INFO @ Sat, 15 Jan 2022 16:51:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:51:43: #1 finished! INFO @ Sat, 15 Jan 2022 16:51:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:51:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 16:51:46: #2 number of paired peaks: 37626 INFO @ Sat, 15 Jan 2022 16:51:46: start model_add_line... INFO @ Sat, 15 Jan 2022 16:51:46: start X-correlation... INFO @ Sat, 15 Jan 2022 16:51:46: end of X-cor INFO @ Sat, 15 Jan 2022 16:51:46: #2 finished! INFO @ Sat, 15 Jan 2022 16:51:46: #2 predicted fragment length is 211 bps INFO @ Sat, 15 Jan 2022 16:51:46: #2 alternative fragment length(s) may be 4,211 bps INFO @ Sat, 15 Jan 2022 16:51:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.20_model.r INFO @ Sat, 15 Jan 2022 16:51:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:51:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:52:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.10_peaks.xls INFO @ Sat, 15 Jan 2022 16:52:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:52:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.10_summits.bed INFO @ Sat, 15 Jan 2022 16:52:13: Done! pass1 - making usageList (112 chroms): 4 millis pass2 - checking and writing primary data (20670 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 16:52:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 16:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.20_peaks.xls INFO @ Sat, 15 Jan 2022 16:53:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:53:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963484/SRX9963484.20_summits.bed INFO @ Sat, 15 Jan 2022 16:53:00: Done! pass1 - making usageList (97 chroms): 3 millis pass2 - checking and writing primary data (17765 records, 4 fields): 35 millis CompletedMACS2peakCalling