Job ID = 14171251 SRX = SRX9986126 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19495316 spots for SRR13591545/SRR13591545.sra Written 19495316 spots for SRR13591545/SRR13591545.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171712 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:52 19495316 reads; of these: 19495316 (100.00%) were unpaired; of these: 1398870 (7.18%) aligned 0 times 15324665 (78.61%) aligned exactly 1 time 2771781 (14.22%) aligned >1 times 92.82% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5826465 / 18096446 = 0.3220 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, 11 Dec 2021 10:52:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 11 Dec 2021 10:52:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:52:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:52:47: 1000000 INFO @ Sat, 11 Dec 2021 10:52:52: 2000000 INFO @ Sat, 11 Dec 2021 10:52:57: 3000000 INFO @ Sat, 11 Dec 2021 10:53:02: 4000000 INFO @ Sat, 11 Dec 2021 10:53:07: 5000000 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, 11 Dec 2021 10:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 11 Dec 2021 10:53:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:53:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:53:11: 6000000 INFO @ Sat, 11 Dec 2021 10:53:16: 7000000 INFO @ Sat, 11 Dec 2021 10:53:20: 8000000 INFO @ Sat, 11 Dec 2021 10:53:22: 1000000 INFO @ Sat, 11 Dec 2021 10:53:25: 9000000 INFO @ Sat, 11 Dec 2021 10:53:30: 10000000 INFO @ Sat, 11 Dec 2021 10:53:33: 2000000 INFO @ Sat, 11 Dec 2021 10:53:35: 11000000 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, 11 Dec 2021 10:53:40: 12000000 INFO @ Sat, 11 Dec 2021 10:53:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:53:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:53:41: #1 total tags in treatment: 12269981 INFO @ Sat, 11 Dec 2021 10:53:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:53:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 10:53:41: #1 tags after filtering in treatment: 12269981 INFO @ Sat, 11 Dec 2021 10:53:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:53:41: #1 finished! INFO @ Sat, 11 Dec 2021 10:53:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 11 Dec 2021 10:53:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:53:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:53:42: #2 number of paired peaks: 306 WARNING @ Sat, 11 Dec 2021 10:53:42: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sat, 11 Dec 2021 10:53:42: start model_add_line... INFO @ Sat, 11 Dec 2021 10:53:42: start X-correlation... INFO @ Sat, 11 Dec 2021 10:53:42: end of X-cor INFO @ Sat, 11 Dec 2021 10:53:42: #2 finished! INFO @ Sat, 11 Dec 2021 10:53:42: #2 predicted fragment length is 268 bps INFO @ Sat, 11 Dec 2021 10:53:42: #2 alternative fragment length(s) may be 3,268,290,313 bps INFO @ Sat, 11 Dec 2021 10:53:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.05_model.r INFO @ Sat, 11 Dec 2021 10:53:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:53:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:53:45: 3000000 INFO @ Sat, 11 Dec 2021 10:53:49: 1000000 INFO @ Sat, 11 Dec 2021 10:53:54: 4000000 INFO @ Sat, 11 Dec 2021 10:53:57: 2000000 INFO @ Sat, 11 Dec 2021 10:54:04: 5000000 INFO @ Sat, 11 Dec 2021 10:54:06: 3000000 INFO @ Sat, 11 Dec 2021 10:54:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:54:13: 4000000 INFO @ Sat, 11 Dec 2021 10:54:13: 6000000 INFO @ Sat, 11 Dec 2021 10:54:19: 5000000 INFO @ Sat, 11 Dec 2021 10:54:21: 7000000 INFO @ Sat, 11 Dec 2021 10:54:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:54:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.05_summits.bed INFO @ Sat, 11 Dec 2021 10:54:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5949 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:54:26: 6000000 INFO @ Sat, 11 Dec 2021 10:54:29: 8000000 INFO @ Sat, 11 Dec 2021 10:54:31: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:54:36: 8000000 INFO @ Sat, 11 Dec 2021 10:54:37: 9000000 INFO @ Sat, 11 Dec 2021 10:54:41: 9000000 INFO @ Sat, 11 Dec 2021 10:54:45: 10000000 INFO @ Sat, 11 Dec 2021 10:54:46: 10000000 INFO @ Sat, 11 Dec 2021 10:54:51: 11000000 INFO @ Sat, 11 Dec 2021 10:54:53: 11000000 INFO @ Sat, 11 Dec 2021 10:54:56: 12000000 INFO @ Sat, 11 Dec 2021 10:54:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:54:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:54:58: #1 total tags in treatment: 12269981 INFO @ Sat, 11 Dec 2021 10:54:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:54:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 10:54:58: #1 tags after filtering in treatment: 12269981 INFO @ Sat, 11 Dec 2021 10:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:54:58: #1 finished! INFO @ Sat, 11 Dec 2021 10:54:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:54:58: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:54:59: #2 number of paired peaks: 306 WARNING @ Sat, 11 Dec 2021 10:54:59: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sat, 11 Dec 2021 10:54:59: start model_add_line... INFO @ Sat, 11 Dec 2021 10:54:59: start X-correlation... INFO @ Sat, 11 Dec 2021 10:54:59: end of X-cor INFO @ Sat, 11 Dec 2021 10:54:59: #2 finished! INFO @ Sat, 11 Dec 2021 10:54:59: #2 predicted fragment length is 268 bps INFO @ Sat, 11 Dec 2021 10:54:59: #2 alternative fragment length(s) may be 3,268,290,313 bps INFO @ Sat, 11 Dec 2021 10:54:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.20_model.r INFO @ Sat, 11 Dec 2021 10:54:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:54:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:54:59: 12000000 INFO @ Sat, 11 Dec 2021 10:55:01: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:55:01: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:55:01: #1 total tags in treatment: 12269981 INFO @ Sat, 11 Dec 2021 10:55:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:55:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 10:55:01: #1 tags after filtering in treatment: 12269981 INFO @ Sat, 11 Dec 2021 10:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:55:01: #1 finished! INFO @ Sat, 11 Dec 2021 10:55:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:55:03: #2 number of paired peaks: 306 WARNING @ Sat, 11 Dec 2021 10:55:03: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sat, 11 Dec 2021 10:55:03: start model_add_line... INFO @ Sat, 11 Dec 2021 10:55:03: start X-correlation... INFO @ Sat, 11 Dec 2021 10:55:03: end of X-cor INFO @ Sat, 11 Dec 2021 10:55:03: #2 finished! INFO @ Sat, 11 Dec 2021 10:55:03: #2 predicted fragment length is 268 bps INFO @ Sat, 11 Dec 2021 10:55:03: #2 alternative fragment length(s) may be 3,268,290,313 bps INFO @ Sat, 11 Dec 2021 10:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.10_model.r INFO @ Sat, 11 Dec 2021 10:55:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:55:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:55:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.20_summits.bed INFO @ Sat, 11 Dec 2021 10:55:44: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (512 records, 4 fields): 78 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986126/SRX9986126.10_summits.bed INFO @ Sat, 11 Dec 2021 10:56:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2271 records, 4 fields): 3 millis CompletedMACS2peakCalling