Job ID = 14167114 SRX = SRX4712936 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21088409 spots for SRR7874066/SRR7874066.sra Written 21088409 spots for SRR7874066/SRR7874066.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167552 ("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: 00:07:39 21088409 reads; of these: 21088409 (100.00%) were unpaired; of these: 756061 (3.59%) aligned 0 times 16041365 (76.07%) aligned exactly 1 time 4290983 (20.35%) aligned >1 times 96.41% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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 12 files... [bam_rmdupse_core] 3425469 / 20332348 = 0.1685 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 @ Fri, 10 Dec 2021 10:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.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 @ Fri, 10 Dec 2021 10:17:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:17:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:17:13: 1000000 INFO @ Fri, 10 Dec 2021 10:17:23: 2000000 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 @ Fri, 10 Dec 2021 10:17:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.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 @ Fri, 10 Dec 2021 10:17:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:17:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:17:33: 3000000 INFO @ Fri, 10 Dec 2021 10:17:40: 1000000 INFO @ Fri, 10 Dec 2021 10:17:43: 4000000 INFO @ Fri, 10 Dec 2021 10:17:50: 2000000 INFO @ Fri, 10 Dec 2021 10:17:53: 5000000 INFO @ Fri, 10 Dec 2021 10:17:58: 3000000 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 @ Fri, 10 Dec 2021 10:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.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 @ Fri, 10 Dec 2021 10:18:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:18:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:18:04: 6000000 INFO @ Fri, 10 Dec 2021 10:18:06: 4000000 INFO @ Fri, 10 Dec 2021 10:18:12: 1000000 INFO @ Fri, 10 Dec 2021 10:18:15: 7000000 INFO @ Fri, 10 Dec 2021 10:18:15: 5000000 INFO @ Fri, 10 Dec 2021 10:18:23: 2000000 INFO @ Fri, 10 Dec 2021 10:18:26: 8000000 INFO @ Fri, 10 Dec 2021 10:18:26: 6000000 INFO @ Fri, 10 Dec 2021 10:18:33: 3000000 INFO @ Fri, 10 Dec 2021 10:18:34: 7000000 INFO @ Fri, 10 Dec 2021 10:18:36: 9000000 INFO @ Fri, 10 Dec 2021 10:18:42: 8000000 INFO @ Fri, 10 Dec 2021 10:18:43: 4000000 INFO @ Fri, 10 Dec 2021 10:18:47: 10000000 INFO @ Fri, 10 Dec 2021 10:18:52: 9000000 INFO @ Fri, 10 Dec 2021 10:18:53: 5000000 INFO @ Fri, 10 Dec 2021 10:18:57: 11000000 INFO @ Fri, 10 Dec 2021 10:19:03: 10000000 INFO @ Fri, 10 Dec 2021 10:19:04: 6000000 INFO @ Fri, 10 Dec 2021 10:19:07: 12000000 INFO @ Fri, 10 Dec 2021 10:19:12: 11000000 INFO @ Fri, 10 Dec 2021 10:19:15: 7000000 INFO @ Fri, 10 Dec 2021 10:19:17: 13000000 INFO @ Fri, 10 Dec 2021 10:19:21: 12000000 INFO @ Fri, 10 Dec 2021 10:19:27: 8000000 INFO @ Fri, 10 Dec 2021 10:19:27: 14000000 INFO @ Fri, 10 Dec 2021 10:19:30: 13000000 INFO @ Fri, 10 Dec 2021 10:19:37: 15000000 INFO @ Fri, 10 Dec 2021 10:19:38: 9000000 INFO @ Fri, 10 Dec 2021 10:19:39: 14000000 INFO @ Fri, 10 Dec 2021 10:19:47: 16000000 INFO @ Fri, 10 Dec 2021 10:19:48: 10000000 INFO @ Fri, 10 Dec 2021 10:19:51: 15000000 INFO @ Fri, 10 Dec 2021 10:19:56: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:19:56: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:19:56: #1 total tags in treatment: 16906879 INFO @ Fri, 10 Dec 2021 10:19:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:19:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:19:57: #1 tags after filtering in treatment: 16906879 INFO @ Fri, 10 Dec 2021 10:19:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:19:57: #1 finished! INFO @ Fri, 10 Dec 2021 10:19:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:19:58: #2 number of paired peaks: 383 WARNING @ Fri, 10 Dec 2021 10:19:58: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Fri, 10 Dec 2021 10:19:58: start model_add_line... INFO @ Fri, 10 Dec 2021 10:19:58: start X-correlation... INFO @ Fri, 10 Dec 2021 10:19:58: 11000000 INFO @ Fri, 10 Dec 2021 10:19:58: end of X-cor INFO @ Fri, 10 Dec 2021 10:19:58: #2 finished! INFO @ Fri, 10 Dec 2021 10:19:58: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 10:19:58: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 10:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.05_model.r INFO @ Fri, 10 Dec 2021 10:19:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:19:58: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:20:04: 16000000 INFO @ Fri, 10 Dec 2021 10:20:08: 12000000 INFO @ Fri, 10 Dec 2021 10:20:13: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:20:13: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:20:13: #1 total tags in treatment: 16906879 INFO @ Fri, 10 Dec 2021 10:20:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:20:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:20:13: #1 tags after filtering in treatment: 16906879 INFO @ Fri, 10 Dec 2021 10:20:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:20:13: #1 finished! INFO @ Fri, 10 Dec 2021 10:20:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:20:14: #2 number of paired peaks: 383 WARNING @ Fri, 10 Dec 2021 10:20:14: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Fri, 10 Dec 2021 10:20:14: start model_add_line... INFO @ Fri, 10 Dec 2021 10:20:14: start X-correlation... INFO @ Fri, 10 Dec 2021 10:20:15: end of X-cor INFO @ Fri, 10 Dec 2021 10:20:15: #2 finished! INFO @ Fri, 10 Dec 2021 10:20:15: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 10:20:15: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 10:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.10_model.r INFO @ Fri, 10 Dec 2021 10:20:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:20:18: 13000000 INFO @ Fri, 10 Dec 2021 10:20:27: 14000000 INFO @ Fri, 10 Dec 2021 10:20:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:20:37: 15000000 INFO @ Fri, 10 Dec 2021 10:20:48: 16000000 INFO @ Fri, 10 Dec 2021 10:20:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:20:57: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:20:57: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:20:57: #1 total tags in treatment: 16906879 INFO @ Fri, 10 Dec 2021 10:20:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:20:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:20:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:20:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:20:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.05_summits.bed INFO @ Fri, 10 Dec 2021 10:20:57: Done! INFO @ Fri, 10 Dec 2021 10:20:57: #1 tags after filtering in treatment: 16906879 INFO @ Fri, 10 Dec 2021 10:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:20:57: #1 finished! INFO @ Fri, 10 Dec 2021 10:20:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:20:57: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8130 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:20:58: #2 number of paired peaks: 383 WARNING @ Fri, 10 Dec 2021 10:20:58: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Fri, 10 Dec 2021 10:20:58: start model_add_line... INFO @ Fri, 10 Dec 2021 10:20:59: start X-correlation... INFO @ Fri, 10 Dec 2021 10:20:59: end of X-cor INFO @ Fri, 10 Dec 2021 10:20:59: #2 finished! INFO @ Fri, 10 Dec 2021 10:20:59: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 10:20:59: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 10:20:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.20_model.r INFO @ Fri, 10 Dec 2021 10:20:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:20:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.10_summits.bed INFO @ Fri, 10 Dec 2021 10:21:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5600 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:21:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712936/SRX4712936.20_summits.bed INFO @ Fri, 10 Dec 2021 10:21:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3245 records, 4 fields): 6 millis CompletedMACS2peakCalling