Job ID = 14171375 SRX = SRX9986166 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20061360 spots for SRR13591520/SRR13591520.sra Written 20061360 spots for SRR13591520/SRR13591520.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171845 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:22 20061360 reads; of these: 20061360 (100.00%) were unpaired; of these: 2084768 (10.39%) aligned 0 times 15045563 (75.00%) aligned exactly 1 time 2931029 (14.61%) aligned >1 times 89.61% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 5039828 / 17976592 = 0.2804 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 11:36:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.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 11:36:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:36:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:36:17: 1000000 INFO @ Sat, 11 Dec 2021 11:36:22: 2000000 INFO @ Sat, 11 Dec 2021 11:36:26: 3000000 INFO @ Sat, 11 Dec 2021 11:36:31: 4000000 INFO @ Sat, 11 Dec 2021 11:36:36: 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 11:36:41: 6000000 INFO @ Sat, 11 Dec 2021 11:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.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 11:36:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:36:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:36:46: 7000000 INFO @ Sat, 11 Dec 2021 11:36:48: 1000000 INFO @ Sat, 11 Dec 2021 11:36:51: 8000000 INFO @ Sat, 11 Dec 2021 11:36:54: 2000000 INFO @ Sat, 11 Dec 2021 11:36:57: 9000000 INFO @ Sat, 11 Dec 2021 11:37:00: 3000000 INFO @ Sat, 11 Dec 2021 11:37:02: 10000000 INFO @ Sat, 11 Dec 2021 11:37:05: 4000000 INFO @ Sat, 11 Dec 2021 11:37:07: 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 11:37:11: 5000000 INFO @ Sat, 11 Dec 2021 11:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.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 11:37:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:37:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:37:12: 12000000 INFO @ Sat, 11 Dec 2021 11:37:17: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:37:17: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:37:17: #1 total tags in treatment: 12936764 INFO @ Sat, 11 Dec 2021 11:37:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:37:17: #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 11:37:17: #1 tags after filtering in treatment: 12936764 INFO @ Sat, 11 Dec 2021 11:37:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:37:17: #1 finished! INFO @ Sat, 11 Dec 2021 11:37:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:37:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:37:17: 6000000 INFO @ Sat, 11 Dec 2021 11:37:18: 1000000 INFO @ Sat, 11 Dec 2021 11:37:18: #2 number of paired peaks: 424 WARNING @ Sat, 11 Dec 2021 11:37:18: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 11 Dec 2021 11:37:18: start model_add_line... INFO @ Sat, 11 Dec 2021 11:37:18: start X-correlation... INFO @ Sat, 11 Dec 2021 11:37:18: end of X-cor INFO @ Sat, 11 Dec 2021 11:37:18: #2 finished! INFO @ Sat, 11 Dec 2021 11:37:18: #2 predicted fragment length is 140 bps INFO @ Sat, 11 Dec 2021 11:37:18: #2 alternative fragment length(s) may be 17,43,47,78,96,140,162,173,194,240,287,297,300,318,338,344,417,450,466,492,529,564 bps INFO @ Sat, 11 Dec 2021 11:37:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.05_model.r INFO @ Sat, 11 Dec 2021 11:37:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:37:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:37:24: 7000000 INFO @ Sat, 11 Dec 2021 11:37:24: 2000000 INFO @ Sat, 11 Dec 2021 11:37:29: 8000000 INFO @ Sat, 11 Dec 2021 11:37:30: 3000000 INFO @ Sat, 11 Dec 2021 11:37:35: 9000000 INFO @ Sat, 11 Dec 2021 11:37:36: 4000000 INFO @ Sat, 11 Dec 2021 11:37:41: 10000000 INFO @ Sat, 11 Dec 2021 11:37:41: 5000000 INFO @ Sat, 11 Dec 2021 11:37:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:37:47: 11000000 INFO @ Sat, 11 Dec 2021 11:37:47: 6000000 INFO @ Sat, 11 Dec 2021 11:37:53: 12000000 INFO @ Sat, 11 Dec 2021 11:37:53: 7000000 INFO @ Sat, 11 Dec 2021 11:37:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:37:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:37:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.05_summits.bed INFO @ Sat, 11 Dec 2021 11:37:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1071 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:37:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:37:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:37:58: #1 total tags in treatment: 12936764 INFO @ Sat, 11 Dec 2021 11:37:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:37:58: #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 11:37:58: #1 tags after filtering in treatment: 12936764 INFO @ Sat, 11 Dec 2021 11:37:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:37:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:37:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:37:59: 8000000 INFO @ Sat, 11 Dec 2021 11:37:59: #2 number of paired peaks: 424 WARNING @ Sat, 11 Dec 2021 11:37:59: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 11 Dec 2021 11:37:59: start model_add_line... INFO @ Sat, 11 Dec 2021 11:37:59: start X-correlation... INFO @ Sat, 11 Dec 2021 11:37:59: end of X-cor INFO @ Sat, 11 Dec 2021 11:37:59: #2 finished! INFO @ Sat, 11 Dec 2021 11:37:59: #2 predicted fragment length is 140 bps INFO @ Sat, 11 Dec 2021 11:37:59: #2 alternative fragment length(s) may be 17,43,47,78,96,140,162,173,194,240,287,297,300,318,338,344,417,450,466,492,529,564 bps INFO @ Sat, 11 Dec 2021 11:37:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.10_model.r INFO @ Sat, 11 Dec 2021 11:37:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:37:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:38:04: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:38:10: 10000000 INFO @ Sat, 11 Dec 2021 11:38:16: 11000000 INFO @ Sat, 11 Dec 2021 11:38:21: 12000000 INFO @ Sat, 11 Dec 2021 11:38:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:38:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:38:26: #1 total tags in treatment: 12936764 INFO @ Sat, 11 Dec 2021 11:38:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:26: #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 11:38:27: #1 tags after filtering in treatment: 12936764 INFO @ Sat, 11 Dec 2021 11:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:38:27: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:27: #2 number of paired peaks: 424 WARNING @ Sat, 11 Dec 2021 11:38:27: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 11 Dec 2021 11:38:27: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:27: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:28: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:28: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:28: #2 predicted fragment length is 140 bps INFO @ Sat, 11 Dec 2021 11:38:28: #2 alternative fragment length(s) may be 17,43,47,78,96,140,162,173,194,240,287,297,300,318,338,344,417,450,466,492,529,564 bps INFO @ Sat, 11 Dec 2021 11:38:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.20_model.r INFO @ Sat, 11 Dec 2021 11:38:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.10_summits.bed INFO @ Sat, 11 Dec 2021 11:38:34: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:38:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:39:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:39:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:39:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986166/SRX9986166.20_summits.bed INFO @ Sat, 11 Dec 2021 11:39:03: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 1 millis CompletedMACS2peakCalling