Job ID = 6453879 SRX = SRX1550613 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:36:24 prefetch.2.10.7: 1) Downloading 'SRR3130869'... 2020-06-21T08:36:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:37:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:37:32 prefetch.2.10.7: 'SRR3130869' is valid 2020-06-21T08:37:32 prefetch.2.10.7: 1) 'SRR3130869' was downloaded successfully Read 4000000 spots for SRR3130869/SRR3130869.sra Written 4000000 spots for SRR3130869/SRR3130869.sra 2020-06-21T08:37:55 prefetch.2.10.7: 1) Downloading 'SRR3130870'... 2020-06-21T08:37:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:38:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:38:35 prefetch.2.10.7: 'SRR3130870' is valid 2020-06-21T08:38:35 prefetch.2.10.7: 1) 'SRR3130870' was downloaded successfully Read 4000000 spots for SRR3130870/SRR3130870.sra Written 4000000 spots for SRR3130870/SRR3130870.sra 2020-06-21T08:38:57 prefetch.2.10.7: 1) Downloading 'SRR3130871'... 2020-06-21T08:38:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:39:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:39:49 prefetch.2.10.7: 'SRR3130871' is valid 2020-06-21T08:39:49 prefetch.2.10.7: 1) 'SRR3130871' was downloaded successfully Read 4000000 spots for SRR3130871/SRR3130871.sra Written 4000000 spots for SRR3130871/SRR3130871.sra 2020-06-21T08:40:11 prefetch.2.10.7: 1) Downloading 'SRR3130872'... 2020-06-21T08:40:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:40:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:40:39 prefetch.2.10.7: 'SRR3130872' is valid 2020-06-21T08:40:39 prefetch.2.10.7: 1) 'SRR3130872' was downloaded successfully Read 4000000 spots for SRR3130872/SRR3130872.sra Written 4000000 spots for SRR3130872/SRR3130872.sra 2020-06-21T08:41:01 prefetch.2.10.7: 1) Downloading 'SRR3130873'... 2020-06-21T08:41:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:41:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:41:39 prefetch.2.10.7: 'SRR3130873' is valid 2020-06-21T08:41:39 prefetch.2.10.7: 1) 'SRR3130873' was downloaded successfully Read 4000000 spots for SRR3130873/SRR3130873.sra Written 4000000 spots for SRR3130873/SRR3130873.sra 2020-06-21T08:42:01 prefetch.2.10.7: 1) Downloading 'SRR3130874'... 2020-06-21T08:42:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:42:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:42:29 prefetch.2.10.7: 'SRR3130874' is valid 2020-06-21T08:42:29 prefetch.2.10.7: 1) 'SRR3130874' was downloaded successfully Read 864387 spots for SRR3130874/SRR3130874.sra Written 864387 spots for SRR3130874/SRR3130874.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:35 20864387 reads; of these: 20864387 (100.00%) were unpaired; of these: 1137574 (5.45%) aligned 0 times 15550554 (74.53%) aligned exactly 1 time 4176259 (20.02%) aligned >1 times 94.55% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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_sort_core] merging from 12 files... [bam_rmdupse_core] 3182265 / 19726813 = 0.1613 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 17:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.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 17:53:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:46: 1000000 INFO @ Sun, 21 Jun 2020 17:53:51: 2000000 INFO @ Sun, 21 Jun 2020 17:53:56: 3000000 INFO @ Sun, 21 Jun 2020 17:54:01: 4000000 INFO @ Sun, 21 Jun 2020 17:54:07: 5000000 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 17:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.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 17:54:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:12: 6000000 INFO @ Sun, 21 Jun 2020 17:54:16: 1000000 INFO @ Sun, 21 Jun 2020 17:54:18: 7000000 INFO @ Sun, 21 Jun 2020 17:54:22: 2000000 INFO @ Sun, 21 Jun 2020 17:54:23: 8000000 INFO @ Sun, 21 Jun 2020 17:54:27: 3000000 INFO @ Sun, 21 Jun 2020 17:54:29: 9000000 INFO @ Sun, 21 Jun 2020 17:54:33: 4000000 INFO @ Sun, 21 Jun 2020 17:54:35: 10000000 INFO @ Sun, 21 Jun 2020 17:54:39: 5000000 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 17:54:40: 11000000 INFO @ Sun, 21 Jun 2020 17:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.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 17:54:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:44: 6000000 INFO @ Sun, 21 Jun 2020 17:54:46: 12000000 INFO @ Sun, 21 Jun 2020 17:54:46: 1000000 INFO @ Sun, 21 Jun 2020 17:54:50: 7000000 INFO @ Sun, 21 Jun 2020 17:54:52: 13000000 INFO @ Sun, 21 Jun 2020 17:54:52: 2000000 INFO @ Sun, 21 Jun 2020 17:54:56: 8000000 INFO @ Sun, 21 Jun 2020 17:54:57: 3000000 INFO @ Sun, 21 Jun 2020 17:54:58: 14000000 INFO @ Sun, 21 Jun 2020 17:55:01: 9000000 INFO @ Sun, 21 Jun 2020 17:55:03: 4000000 INFO @ Sun, 21 Jun 2020 17:55:03: 15000000 INFO @ Sun, 21 Jun 2020 17:55:07: 10000000 INFO @ Sun, 21 Jun 2020 17:55:09: 5000000 INFO @ Sun, 21 Jun 2020 17:55:09: 16000000 INFO @ Sun, 21 Jun 2020 17:55:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:55:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:55:12: #1 total tags in treatment: 16544548 INFO @ Sun, 21 Jun 2020 17:55:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:12: #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 17:55:12: 11000000 INFO @ Sun, 21 Jun 2020 17:55:13: #1 tags after filtering in treatment: 16544547 INFO @ Sun, 21 Jun 2020 17:55:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:14: #2 number of paired peaks: 790 WARNING @ Sun, 21 Jun 2020 17:55:14: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Sun, 21 Jun 2020 17:55:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:14: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 17:55:14: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 17:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.05_model.r INFO @ Sun, 21 Jun 2020 17:55:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:14: 6000000 INFO @ Sun, 21 Jun 2020 17:55:18: 12000000 INFO @ Sun, 21 Jun 2020 17:55:20: 7000000 INFO @ Sun, 21 Jun 2020 17:55:24: 13000000 INFO @ Sun, 21 Jun 2020 17:55:26: 8000000 INFO @ Sun, 21 Jun 2020 17:55:30: 14000000 INFO @ Sun, 21 Jun 2020 17:55:31: 9000000 INFO @ Sun, 21 Jun 2020 17:55:35: 15000000 INFO @ Sun, 21 Jun 2020 17:55:37: 10000000 INFO @ Sun, 21 Jun 2020 17:55:41: 16000000 INFO @ Sun, 21 Jun 2020 17:55:42: 11000000 INFO @ Sun, 21 Jun 2020 17:55:44: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:55:44: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:55:44: #1 total tags in treatment: 16544548 INFO @ Sun, 21 Jun 2020 17:55:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:44: #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 17:55:45: #1 tags after filtering in treatment: 16544547 INFO @ Sun, 21 Jun 2020 17:55:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:46: #2 number of paired peaks: 790 WARNING @ Sun, 21 Jun 2020 17:55:46: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Sun, 21 Jun 2020 17:55:46: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:46: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:46: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:46: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:46: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 17:55:46: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 17:55:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.10_model.r INFO @ Sun, 21 Jun 2020 17:55:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:48: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:55:53: 13000000 INFO @ Sun, 21 Jun 2020 17:55:59: 14000000 INFO @ Sun, 21 Jun 2020 17:56:04: 15000000 INFO @ Sun, 21 Jun 2020 17:56:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.05_summits.bed INFO @ Sun, 21 Jun 2020 17:56:05: Done! pass1 - making usageList (572 chroms): 2 millis pass2 - checking and writing primary data (6389 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:56:10: 16000000 INFO @ Sun, 21 Jun 2020 17:56:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:56:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:56:13: #1 total tags in treatment: 16544548 INFO @ Sun, 21 Jun 2020 17:56:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:13: #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 17:56:13: #1 tags after filtering in treatment: 16544547 INFO @ Sun, 21 Jun 2020 17:56:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:14: #2 number of paired peaks: 790 WARNING @ Sun, 21 Jun 2020 17:56:14: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:14: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 17:56:14: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 17:56:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.20_model.r INFO @ Sun, 21 Jun 2020 17:56:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:56:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.10_summits.bed INFO @ Sun, 21 Jun 2020 17:56:36: Done! pass1 - making usageList (497 chroms): 2 millis pass2 - checking and writing primary data (3580 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:56:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550613/SRX1550613.20_summits.bed INFO @ Sun, 21 Jun 2020 17:57:04: Done! pass1 - making usageList (430 chroms): 1 millis pass2 - checking and writing primary data (2017 records, 4 fields): 13 millis CompletedMACS2peakCalling