Job ID = 6456340 SRX = SRX3380789 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:40:23 prefetch.2.10.7: 1) Downloading 'SRR6278152'... 2020-06-21T10:40:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:42:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:42:18 prefetch.2.10.7: 'SRR6278152' is valid 2020-06-21T10:42:18 prefetch.2.10.7: 1) 'SRR6278152' was downloaded successfully 2020-06-21T10:42:18 prefetch.2.10.7: 'SRR6278152' has 0 unresolved dependencies Read 17228089 spots for SRR6278152/SRR6278152.sra Written 17228089 spots for SRR6278152/SRR6278152.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: 00:03:57 17228089 reads; of these: 17228089 (100.00%) were unpaired; of these: 1164566 (6.76%) aligned 0 times 14603980 (84.77%) aligned exactly 1 time 1459543 (8.47%) aligned >1 times 93.24% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1337594 / 16063523 = 0.0833 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 19:50:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.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 19:50:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:39: 1000000 INFO @ Sun, 21 Jun 2020 19:50:44: 2000000 INFO @ Sun, 21 Jun 2020 19:50:50: 3000000 INFO @ Sun, 21 Jun 2020 19:50:55: 4000000 INFO @ Sun, 21 Jun 2020 19:51:01: 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 19:51:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.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 19:51:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:06: 6000000 INFO @ Sun, 21 Jun 2020 19:51:09: 1000000 INFO @ Sun, 21 Jun 2020 19:51:12: 7000000 INFO @ Sun, 21 Jun 2020 19:51:15: 2000000 INFO @ Sun, 21 Jun 2020 19:51:18: 8000000 INFO @ Sun, 21 Jun 2020 19:51:21: 3000000 INFO @ Sun, 21 Jun 2020 19:51:23: 9000000 INFO @ Sun, 21 Jun 2020 19:51:27: 4000000 INFO @ Sun, 21 Jun 2020 19:51:29: 10000000 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 19:51:33: 5000000 INFO @ Sun, 21 Jun 2020 19:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.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 19:51:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:35: 11000000 INFO @ Sun, 21 Jun 2020 19:51:38: 6000000 INFO @ Sun, 21 Jun 2020 19:51:40: 1000000 INFO @ Sun, 21 Jun 2020 19:51:41: 12000000 INFO @ Sun, 21 Jun 2020 19:51:44: 7000000 INFO @ Sun, 21 Jun 2020 19:51:46: 2000000 INFO @ Sun, 21 Jun 2020 19:51:47: 13000000 INFO @ Sun, 21 Jun 2020 19:51:50: 8000000 INFO @ Sun, 21 Jun 2020 19:51:52: 3000000 INFO @ Sun, 21 Jun 2020 19:51:53: 14000000 INFO @ Sun, 21 Jun 2020 19:51:56: 9000000 INFO @ Sun, 21 Jun 2020 19:51:57: 4000000 INFO @ Sun, 21 Jun 2020 19:51:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:51:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:51:58: #1 total tags in treatment: 14725929 INFO @ Sun, 21 Jun 2020 19:51:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:58: #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 19:51:58: #1 tags after filtering in treatment: 14725896 INFO @ Sun, 21 Jun 2020 19:51:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:59: #2 number of paired peaks: 827 WARNING @ Sun, 21 Jun 2020 19:51:59: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Sun, 21 Jun 2020 19:51:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:59: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 19:51:59: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 21 Jun 2020 19:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.05_model.r INFO @ Sun, 21 Jun 2020 19:51:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:52:02: 10000000 INFO @ Sun, 21 Jun 2020 19:52:03: 5000000 INFO @ Sun, 21 Jun 2020 19:52:08: 11000000 INFO @ Sun, 21 Jun 2020 19:52:09: 6000000 INFO @ Sun, 21 Jun 2020 19:52:14: 12000000 INFO @ Sun, 21 Jun 2020 19:52:15: 7000000 INFO @ Sun, 21 Jun 2020 19:52:20: 13000000 INFO @ Sun, 21 Jun 2020 19:52:21: 8000000 INFO @ Sun, 21 Jun 2020 19:52:26: 14000000 INFO @ Sun, 21 Jun 2020 19:52:27: 9000000 INFO @ Sun, 21 Jun 2020 19:52:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:52:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:52:30: #1 total tags in treatment: 14725929 INFO @ Sun, 21 Jun 2020 19:52:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:30: #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 19:52:31: #1 tags after filtering in treatment: 14725896 INFO @ Sun, 21 Jun 2020 19:52:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:32: #2 number of paired peaks: 827 WARNING @ Sun, 21 Jun 2020 19:52:32: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Sun, 21 Jun 2020 19:52:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:32: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 19:52:32: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 21 Jun 2020 19:52:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.10_model.r INFO @ Sun, 21 Jun 2020 19:52:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:52:32: 10000000 INFO @ Sun, 21 Jun 2020 19:52:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:38: 11000000 INFO @ Sun, 21 Jun 2020 19:52:43: 12000000 INFO @ Sun, 21 Jun 2020 19:52:49: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:52:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.05_summits.bed INFO @ Sun, 21 Jun 2020 19:52:54: Done! pass1 - making usageList (92 chroms): 2 millis pass2 - checking and writing primary data (5485 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:52:55: 14000000 INFO @ Sun, 21 Jun 2020 19:52:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:52:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:52:59: #1 total tags in treatment: 14725929 INFO @ Sun, 21 Jun 2020 19:52:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:59: #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 19:52:59: #1 tags after filtering in treatment: 14725896 INFO @ Sun, 21 Jun 2020 19:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:00: #2 number of paired peaks: 827 WARNING @ Sun, 21 Jun 2020 19:53:00: Fewer paired peaks (827) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 827 pairs to build model! INFO @ Sun, 21 Jun 2020 19:53:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:01: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 19:53:01: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 21 Jun 2020 19:53:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.20_model.r INFO @ Sun, 21 Jun 2020 19:53:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.10_summits.bed INFO @ Sun, 21 Jun 2020 19:53:28: Done! pass1 - making usageList (69 chroms): 1 millis pass2 - checking and writing primary data (2904 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:53:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380789/SRX3380789.20_summits.bed INFO @ Sun, 21 Jun 2020 19:53:57: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (983 records, 4 fields): 5 millis CompletedMACS2peakCalling