Job ID = 14170372 SRX = SRX9720907 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30260391 spots for SRR13291897/SRR13291897.sra Written 30260391 spots for SRR13291897/SRR13291897.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170777 ("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: 00:08:57 30260391 reads; of these: 30260391 (100.00%) were unpaired; of these: 2500623 (8.26%) aligned 0 times 20412591 (67.46%) aligned exactly 1 time 7347177 (24.28%) aligned >1 times 91.74% overall alignment rate Time searching: 00:08:57 Overall time: 00:08:57 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] 5310357 / 27759768 = 0.1913 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 06:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.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 06:40:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:32: 1000000 INFO @ Sat, 11 Dec 2021 06:40:37: 2000000 INFO @ Sat, 11 Dec 2021 06:40:43: 3000000 INFO @ Sat, 11 Dec 2021 06:40:48: 4000000 INFO @ Sat, 11 Dec 2021 06:40:53: 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 06:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.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 06:40:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:59: 6000000 INFO @ Sat, 11 Dec 2021 06:41:03: 1000000 INFO @ Sat, 11 Dec 2021 06:41:05: 7000000 INFO @ Sat, 11 Dec 2021 06:41:08: 2000000 INFO @ Sat, 11 Dec 2021 06:41:11: 8000000 INFO @ Sat, 11 Dec 2021 06:41:14: 3000000 INFO @ Sat, 11 Dec 2021 06:41:17: 9000000 INFO @ Sat, 11 Dec 2021 06:41:20: 4000000 INFO @ Sat, 11 Dec 2021 06:41:23: 10000000 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 06:41:26: 5000000 INFO @ Sat, 11 Dec 2021 06:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.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 06:41:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:41:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:41:29: 11000000 INFO @ Sat, 11 Dec 2021 06:41:33: 6000000 INFO @ Sat, 11 Dec 2021 06:41:34: 1000000 INFO @ Sat, 11 Dec 2021 06:41:35: 12000000 INFO @ Sat, 11 Dec 2021 06:41:40: 7000000 INFO @ Sat, 11 Dec 2021 06:41:41: 2000000 INFO @ Sat, 11 Dec 2021 06:41:42: 13000000 INFO @ Sat, 11 Dec 2021 06:41:46: 8000000 INFO @ Sat, 11 Dec 2021 06:41:48: 3000000 INFO @ Sat, 11 Dec 2021 06:41:49: 14000000 INFO @ Sat, 11 Dec 2021 06:41:53: 9000000 INFO @ Sat, 11 Dec 2021 06:41:55: 4000000 INFO @ Sat, 11 Dec 2021 06:41:55: 15000000 INFO @ Sat, 11 Dec 2021 06:42:00: 10000000 INFO @ Sat, 11 Dec 2021 06:42:02: 16000000 INFO @ Sat, 11 Dec 2021 06:42:02: 5000000 INFO @ Sat, 11 Dec 2021 06:42:06: 11000000 INFO @ Sat, 11 Dec 2021 06:42:09: 17000000 INFO @ Sat, 11 Dec 2021 06:42:09: 6000000 INFO @ Sat, 11 Dec 2021 06:42:13: 12000000 INFO @ Sat, 11 Dec 2021 06:42:16: 18000000 INFO @ Sat, 11 Dec 2021 06:42:17: 7000000 INFO @ Sat, 11 Dec 2021 06:42:20: 13000000 INFO @ Sat, 11 Dec 2021 06:42:22: 19000000 INFO @ Sat, 11 Dec 2021 06:42:24: 8000000 INFO @ Sat, 11 Dec 2021 06:42:26: 14000000 INFO @ Sat, 11 Dec 2021 06:42:29: 20000000 INFO @ Sat, 11 Dec 2021 06:42:31: 9000000 INFO @ Sat, 11 Dec 2021 06:42:33: 15000000 INFO @ Sat, 11 Dec 2021 06:42:36: 21000000 INFO @ Sat, 11 Dec 2021 06:42:38: 10000000 INFO @ Sat, 11 Dec 2021 06:42:40: 16000000 INFO @ Sat, 11 Dec 2021 06:42:42: 22000000 INFO @ Sat, 11 Dec 2021 06:42:45: 11000000 INFO @ Sat, 11 Dec 2021 06:42:45: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:45: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:45: #1 total tags in treatment: 22449411 INFO @ Sat, 11 Dec 2021 06:42:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:45: #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 06:42:46: #1 tags after filtering in treatment: 22449411 INFO @ Sat, 11 Dec 2021 06:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:46: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:46: 17000000 INFO @ Sat, 11 Dec 2021 06:42:47: #2 number of paired peaks: 691 WARNING @ Sat, 11 Dec 2021 06:42:47: Fewer paired peaks (691) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 691 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:47: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:47: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:47: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:47: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:47: #2 predicted fragment length is 197 bps INFO @ Sat, 11 Dec 2021 06:42:47: #2 alternative fragment length(s) may be 197 bps INFO @ Sat, 11 Dec 2021 06:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.05_model.r INFO @ Sat, 11 Dec 2021 06:42:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:52: 12000000 INFO @ Sat, 11 Dec 2021 06:42:53: 18000000 INFO @ Sat, 11 Dec 2021 06:42:59: 13000000 INFO @ Sat, 11 Dec 2021 06:43:00: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:43:06: 20000000 INFO @ Sat, 11 Dec 2021 06:43:06: 14000000 INFO @ Sat, 11 Dec 2021 06:43:13: 21000000 INFO @ Sat, 11 Dec 2021 06:43:14: 15000000 INFO @ Sat, 11 Dec 2021 06:43:20: 22000000 INFO @ Sat, 11 Dec 2021 06:43:21: 16000000 INFO @ Sat, 11 Dec 2021 06:43:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:43:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:43:23: #1 total tags in treatment: 22449411 INFO @ Sat, 11 Dec 2021 06:43:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:43:23: #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 06:43:23: #1 tags after filtering in treatment: 22449411 INFO @ Sat, 11 Dec 2021 06:43:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:43:23: #1 finished! INFO @ Sat, 11 Dec 2021 06:43:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:43:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:43:25: #2 number of paired peaks: 691 WARNING @ Sat, 11 Dec 2021 06:43:25: Fewer paired peaks (691) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 691 pairs to build model! INFO @ Sat, 11 Dec 2021 06:43:25: start model_add_line... INFO @ Sat, 11 Dec 2021 06:43:25: start X-correlation... INFO @ Sat, 11 Dec 2021 06:43:25: end of X-cor INFO @ Sat, 11 Dec 2021 06:43:25: #2 finished! INFO @ Sat, 11 Dec 2021 06:43:25: #2 predicted fragment length is 197 bps INFO @ Sat, 11 Dec 2021 06:43:25: #2 alternative fragment length(s) may be 197 bps INFO @ Sat, 11 Dec 2021 06:43:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.10_model.r INFO @ Sat, 11 Dec 2021 06:43:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:43:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:43:27: 17000000 INFO @ Sat, 11 Dec 2021 06:43:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:43:34: 18000000 INFO @ Sat, 11 Dec 2021 06:43:41: 19000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:43:47: 20000000 INFO @ Sat, 11 Dec 2021 06:43:53: 21000000 INFO @ Sat, 11 Dec 2021 06:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.05_summits.bed INFO @ Sat, 11 Dec 2021 06:43:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7825 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:44:00: 22000000 INFO @ Sat, 11 Dec 2021 06:44:03: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:44:03: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:44:03: #1 total tags in treatment: 22449411 INFO @ Sat, 11 Dec 2021 06:44:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:44:03: #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 06:44:03: #1 tags after filtering in treatment: 22449411 INFO @ Sat, 11 Dec 2021 06:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:44:03: #1 finished! INFO @ Sat, 11 Dec 2021 06:44:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:44:05: #2 number of paired peaks: 691 WARNING @ Sat, 11 Dec 2021 06:44:05: Fewer paired peaks (691) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 691 pairs to build model! INFO @ Sat, 11 Dec 2021 06:44:05: start model_add_line... INFO @ Sat, 11 Dec 2021 06:44:05: start X-correlation... INFO @ Sat, 11 Dec 2021 06:44:05: end of X-cor INFO @ Sat, 11 Dec 2021 06:44:05: #2 finished! INFO @ Sat, 11 Dec 2021 06:44:05: #2 predicted fragment length is 197 bps INFO @ Sat, 11 Dec 2021 06:44:05: #2 alternative fragment length(s) may be 197 bps INFO @ Sat, 11 Dec 2021 06:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.20_model.r INFO @ Sat, 11 Dec 2021 06:44:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:44:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.10_summits.bed INFO @ Sat, 11 Dec 2021 06:44:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6274 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:44:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:45:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720907/SRX9720907.20_summits.bed INFO @ Sat, 11 Dec 2021 06:45:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4649 records, 4 fields): 6 millis CompletedMACS2peakCalling