Job ID = 6454545 SRX = SRX231858 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:32:29 prefetch.2.10.7: 1) Downloading 'SRR696684'... 2020-06-21T09:32:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:53 prefetch.2.10.7: 'SRR696684' is valid 2020-06-21T09:33:53 prefetch.2.10.7: 1) 'SRR696684' was downloaded successfully Read 6136012 spots for SRR696684/SRR696684.sra Written 6136012 spots for SRR696684/SRR696684.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:45 6136012 reads; of these: 6136012 (100.00%) were unpaired; of these: 2832479 (46.16%) aligned 0 times 2747196 (44.77%) aligned exactly 1 time 556337 (9.07%) aligned >1 times 53.84% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 153162 / 3303533 = 0.0464 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:36:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.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 @ Sun, 21 Jun 2020 18:36:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:11: 1000000 INFO @ Sun, 21 Jun 2020 18:36:16: 2000000 INFO @ Sun, 21 Jun 2020 18:36:21: 3000000 INFO @ Sun, 21 Jun 2020 18:36:22: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:36:22: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:36:22: #1 total tags in treatment: 3150371 INFO @ Sun, 21 Jun 2020 18:36:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:36:22: #1 tags after filtering in treatment: 3150251 INFO @ Sun, 21 Jun 2020 18:36:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:23: #2 number of paired peaks: 591 WARNING @ Sun, 21 Jun 2020 18:36:23: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:23: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:36:23: #2 alternative fragment length(s) may be 98,492,545 bps INFO @ Sun, 21 Jun 2020 18:36:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.05_model.r INFO @ Sun, 21 Jun 2020 18:36:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.05_summits.bed INFO @ Sun, 21 Jun 2020 18:36:33: Done! pass1 - making usageList (113 chroms): 1 millis pass2 - checking and writing primary data (1445 records, 4 fields): 5 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.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 @ Sun, 21 Jun 2020 18:36:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:40: 1000000 INFO @ Sun, 21 Jun 2020 18:36:45: 2000000 INFO @ Sun, 21 Jun 2020 18:36:50: 3000000 INFO @ Sun, 21 Jun 2020 18:36:51: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:36:51: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:36:51: #1 total tags in treatment: 3150371 INFO @ Sun, 21 Jun 2020 18:36:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:36:52: #1 tags after filtering in treatment: 3150251 INFO @ Sun, 21 Jun 2020 18:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:52: #2 number of paired peaks: 591 WARNING @ Sun, 21 Jun 2020 18:36:52: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:52: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:36:52: #2 alternative fragment length(s) may be 98,492,545 bps INFO @ Sun, 21 Jun 2020 18:36:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.10_model.r INFO @ Sun, 21 Jun 2020 18:36:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.10_summits.bed INFO @ Sun, 21 Jun 2020 18:37:03: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:37:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.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 @ Sun, 21 Jun 2020 18:37:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:10: 1000000 INFO @ Sun, 21 Jun 2020 18:37:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:37:19: 3000000 INFO @ Sun, 21 Jun 2020 18:37:20: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:37:20: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:37:20: #1 total tags in treatment: 3150371 INFO @ Sun, 21 Jun 2020 18:37:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:37:20: #1 tags after filtering in treatment: 3150251 INFO @ Sun, 21 Jun 2020 18:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:21: #2 number of paired peaks: 591 WARNING @ Sun, 21 Jun 2020 18:37:21: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:21: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:37:21: #2 alternative fragment length(s) may be 98,492,545 bps INFO @ Sun, 21 Jun 2020 18:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.20_model.r INFO @ Sun, 21 Jun 2020 18:37:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:37:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231858/SRX231858.20_summits.bed INFO @ Sun, 21 Jun 2020 18:37:31: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 2 millis CompletedMACS2peakCalling