Job ID = 14171339 SRX = SRX9986155 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15642258 spots for SRR13591566/SRR13591566.sra Written 15642258 spots for SRR13591566/SRR13591566.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171808 ("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: 00:04:13 15642258 reads; of these: 15642258 (100.00%) were unpaired; of these: 2292930 (14.66%) aligned 0 times 11233457 (71.81%) aligned exactly 1 time 2115871 (13.53%) aligned >1 times 85.34% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 3036867 / 13349328 = 0.2275 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 11:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.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 11:27:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:27:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:27:24: 1000000 INFO @ Sat, 11 Dec 2021 11:27:29: 2000000 INFO @ Sat, 11 Dec 2021 11:27:35: 3000000 INFO @ Sat, 11 Dec 2021 11:27:40: 4000000 INFO @ Sat, 11 Dec 2021 11:27:46: 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 11:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.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 11:27:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:27:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:27:51: 6000000 INFO @ Sat, 11 Dec 2021 11:27:53: 1000000 INFO @ Sat, 11 Dec 2021 11:27:57: 7000000 INFO @ Sat, 11 Dec 2021 11:27:59: 2000000 INFO @ Sat, 11 Dec 2021 11:28:02: 8000000 INFO @ Sat, 11 Dec 2021 11:28:04: 3000000 INFO @ Sat, 11 Dec 2021 11:28:08: 9000000 INFO @ Sat, 11 Dec 2021 11:28:09: 4000000 INFO @ Sat, 11 Dec 2021 11:28:13: 10000000 INFO @ Sat, 11 Dec 2021 11:28:15: 5000000 INFO @ Sat, 11 Dec 2021 11:28:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:28:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:28:15: #1 total tags in treatment: 10312461 INFO @ Sat, 11 Dec 2021 11:28:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:28:15: #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 11:28:15: #1 tags after filtering in treatment: 10312461 INFO @ Sat, 11 Dec 2021 11:28:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:28:15: #1 finished! INFO @ Sat, 11 Dec 2021 11:28:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:28:15: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... INFO @ Sat, 11 Dec 2021 11:28:16: #2 number of paired peaks: 469 WARNING @ Sat, 11 Dec 2021 11:28:16: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Sat, 11 Dec 2021 11:28:16: start model_add_line... INFO @ Sat, 11 Dec 2021 11:28:16: start X-correlation... 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 11:28:16: end of X-cor INFO @ Sat, 11 Dec 2021 11:28:16: #2 finished! INFO @ Sat, 11 Dec 2021 11:28:16: #2 predicted fragment length is 159 bps INFO @ Sat, 11 Dec 2021 11:28:16: #2 alternative fragment length(s) may be 1,25,121,159 bps INFO @ Sat, 11 Dec 2021 11:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.05_model.r INFO @ Sat, 11 Dec 2021 11:28:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.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 11:28:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:28:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:28:20: 6000000 INFO @ Sat, 11 Dec 2021 11:28:23: 1000000 INFO @ Sat, 11 Dec 2021 11:28:25: 7000000 INFO @ Sat, 11 Dec 2021 11:28:29: 2000000 INFO @ Sat, 11 Dec 2021 11:28:30: 8000000 INFO @ Sat, 11 Dec 2021 11:28:34: 3000000 INFO @ Sat, 11 Dec 2021 11:28:36: 9000000 INFO @ Sat, 11 Dec 2021 11:28:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:28:40: 4000000 INFO @ Sat, 11 Dec 2021 11:28:41: 10000000 INFO @ Sat, 11 Dec 2021 11:28:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:28:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:28:43: #1 total tags in treatment: 10312461 INFO @ Sat, 11 Dec 2021 11:28:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:28:43: #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 11:28:43: #1 tags after filtering in treatment: 10312461 INFO @ Sat, 11 Dec 2021 11:28:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:28:43: #1 finished! INFO @ Sat, 11 Dec 2021 11:28:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:28:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:28:43: #2 number of paired peaks: 469 WARNING @ Sat, 11 Dec 2021 11:28:43: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Sat, 11 Dec 2021 11:28:43: start model_add_line... INFO @ Sat, 11 Dec 2021 11:28:43: start X-correlation... INFO @ Sat, 11 Dec 2021 11:28:43: end of X-cor INFO @ Sat, 11 Dec 2021 11:28:43: #2 finished! INFO @ Sat, 11 Dec 2021 11:28:43: #2 predicted fragment length is 159 bps INFO @ Sat, 11 Dec 2021 11:28:43: #2 alternative fragment length(s) may be 1,25,121,159 bps INFO @ Sat, 11 Dec 2021 11:28:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.10_model.r INFO @ Sat, 11 Dec 2021 11:28:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:28:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:28:45: 5000000 INFO @ Sat, 11 Dec 2021 11:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.05_summits.bed INFO @ Sat, 11 Dec 2021 11:28:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1266 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:28:51: 6000000 INFO @ Sat, 11 Dec 2021 11:28:56: 7000000 INFO @ Sat, 11 Dec 2021 11:29:02: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:29:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:29:07: 9000000 INFO @ Sat, 11 Dec 2021 11:29:12: 10000000 INFO @ Sat, 11 Dec 2021 11:29:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:29:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:29:14: #1 total tags in treatment: 10312461 INFO @ Sat, 11 Dec 2021 11:29:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:29:14: #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 11:29:14: #1 tags after filtering in treatment: 10312461 INFO @ Sat, 11 Dec 2021 11:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:29:14: #1 finished! INFO @ Sat, 11 Dec 2021 11:29:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:29:15: #2 number of paired peaks: 469 WARNING @ Sat, 11 Dec 2021 11:29:15: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Sat, 11 Dec 2021 11:29:15: start model_add_line... INFO @ Sat, 11 Dec 2021 11:29:15: start X-correlation... INFO @ Sat, 11 Dec 2021 11:29:15: end of X-cor INFO @ Sat, 11 Dec 2021 11:29:15: #2 finished! INFO @ Sat, 11 Dec 2021 11:29:15: #2 predicted fragment length is 159 bps INFO @ Sat, 11 Dec 2021 11:29:15: #2 alternative fragment length(s) may be 1,25,121,159 bps INFO @ Sat, 11 Dec 2021 11:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.20_model.r INFO @ Sat, 11 Dec 2021 11:29:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.10_summits.bed INFO @ Sat, 11 Dec 2021 11:29:16: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (495 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:29:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:29:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:29:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:29:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986155/SRX9986155.20_summits.bed INFO @ Sat, 11 Dec 2021 11:29:46: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling