Job ID = 6456338 SRX = SRX3380787 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:41:08 prefetch.2.10.7: 1) Downloading 'SRR6278150'... 2020-06-21T10:41:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:43:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:43:41 prefetch.2.10.7: 'SRR6278150' is valid 2020-06-21T10:43:41 prefetch.2.10.7: 1) 'SRR6278150' was downloaded successfully 2020-06-21T10:43:41 prefetch.2.10.7: 'SRR6278150' has 0 unresolved dependencies Read 19217803 spots for SRR6278150/SRR6278150.sra Written 19217803 spots for SRR6278150/SRR6278150.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: 00:03:50 19217803 reads; of these: 19217803 (100.00%) were unpaired; of these: 1466280 (7.63%) aligned 0 times 16185631 (84.22%) aligned exactly 1 time 1565892 (8.15%) aligned >1 times 92.37% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 1670481 / 17751523 = 0.0941 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 19:52:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.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 19:52:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:09: 1000000 INFO @ Sun, 21 Jun 2020 19:52:14: 2000000 INFO @ Sun, 21 Jun 2020 19:52:20: 3000000 INFO @ Sun, 21 Jun 2020 19:52:25: 4000000 INFO @ Sun, 21 Jun 2020 19:52:30: 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 19:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.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 19:52:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:36: 6000000 INFO @ Sun, 21 Jun 2020 19:52:38: 1000000 INFO @ Sun, 21 Jun 2020 19:52:41: 7000000 INFO @ Sun, 21 Jun 2020 19:52:44: 2000000 INFO @ Sun, 21 Jun 2020 19:52:47: 8000000 INFO @ Sun, 21 Jun 2020 19:52:49: 3000000 INFO @ Sun, 21 Jun 2020 19:52:52: 9000000 INFO @ Sun, 21 Jun 2020 19:52:54: 4000000 INFO @ Sun, 21 Jun 2020 19:52:58: 10000000 INFO @ Sun, 21 Jun 2020 19:52:59: 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 19:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.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 19:53:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:04: 11000000 INFO @ Sun, 21 Jun 2020 19:53:04: 6000000 INFO @ Sun, 21 Jun 2020 19:53:09: 1000000 INFO @ Sun, 21 Jun 2020 19:53:09: 7000000 INFO @ Sun, 21 Jun 2020 19:53:09: 12000000 INFO @ Sun, 21 Jun 2020 19:53:14: 8000000 INFO @ Sun, 21 Jun 2020 19:53:15: 2000000 INFO @ Sun, 21 Jun 2020 19:53:15: 13000000 INFO @ Sun, 21 Jun 2020 19:53:19: 9000000 INFO @ Sun, 21 Jun 2020 19:53:20: 3000000 INFO @ Sun, 21 Jun 2020 19:53:22: 14000000 INFO @ Sun, 21 Jun 2020 19:53:24: 10000000 INFO @ Sun, 21 Jun 2020 19:53:26: 4000000 INFO @ Sun, 21 Jun 2020 19:53:28: 15000000 INFO @ Sun, 21 Jun 2020 19:53:29: 11000000 INFO @ Sun, 21 Jun 2020 19:53:31: 5000000 INFO @ Sun, 21 Jun 2020 19:53:34: 16000000 INFO @ Sun, 21 Jun 2020 19:53:34: 12000000 INFO @ Sun, 21 Jun 2020 19:53:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:53:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:53:34: #1 total tags in treatment: 16081042 INFO @ Sun, 21 Jun 2020 19:53:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:34: #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 19:53:35: #1 tags after filtering in treatment: 16081000 INFO @ Sun, 21 Jun 2020 19:53:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:36: #2 number of paired peaks: 803 WARNING @ Sun, 21 Jun 2020 19:53:36: Fewer paired peaks (803) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 803 pairs to build model! INFO @ Sun, 21 Jun 2020 19:53:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:36: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 19:53:36: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 21 Jun 2020 19:53:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.05_model.r INFO @ Sun, 21 Jun 2020 19:53:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:37: 6000000 INFO @ Sun, 21 Jun 2020 19:53:39: 13000000 INFO @ Sun, 21 Jun 2020 19:53:42: 7000000 INFO @ Sun, 21 Jun 2020 19:53:44: 14000000 INFO @ Sun, 21 Jun 2020 19:53:48: 8000000 INFO @ Sun, 21 Jun 2020 19:53:49: 15000000 INFO @ Sun, 21 Jun 2020 19:53:53: 9000000 INFO @ Sun, 21 Jun 2020 19:53:54: 16000000 INFO @ Sun, 21 Jun 2020 19:53:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:53:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:53:55: #1 total tags in treatment: 16081042 INFO @ Sun, 21 Jun 2020 19:53:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:55: #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 19:53:55: #1 tags after filtering in treatment: 16081000 INFO @ Sun, 21 Jun 2020 19:53:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:57: #2 number of paired peaks: 803 WARNING @ Sun, 21 Jun 2020 19:53:57: Fewer paired peaks (803) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 803 pairs to build model! INFO @ Sun, 21 Jun 2020 19:53:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:57: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 19:53:57: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 21 Jun 2020 19:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.10_model.r INFO @ Sun, 21 Jun 2020 19:53:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:59: 10000000 INFO @ Sun, 21 Jun 2020 19:54:04: 11000000 INFO @ Sun, 21 Jun 2020 19:54:09: 12000000 INFO @ Sun, 21 Jun 2020 19:54:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:15: 13000000 INFO @ Sun, 21 Jun 2020 19:54:20: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:54:26: 15000000 INFO @ Sun, 21 Jun 2020 19:54:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.05_summits.bed INFO @ Sun, 21 Jun 2020 19:54:31: Done! pass1 - making usageList (84 chroms): 1 millis pass2 - checking and writing primary data (5685 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:54:31: 16000000 INFO @ Sun, 21 Jun 2020 19:54:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:54:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:54:32: #1 total tags in treatment: 16081042 INFO @ Sun, 21 Jun 2020 19:54:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:32: #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 19:54:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:32: #1 tags after filtering in treatment: 16081000 INFO @ Sun, 21 Jun 2020 19:54:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:33: #2 number of paired peaks: 803 WARNING @ Sun, 21 Jun 2020 19:54:33: Fewer paired peaks (803) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 803 pairs to build model! INFO @ Sun, 21 Jun 2020 19:54:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:34: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 19:54:34: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 21 Jun 2020 19:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.20_model.r INFO @ Sun, 21 Jun 2020 19:54:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.10_summits.bed INFO @ Sun, 21 Jun 2020 19:54:50: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (3209 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:55:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380787/SRX3380787.20_summits.bed INFO @ Sun, 21 Jun 2020 19:55:28: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (1131 records, 4 fields): 3 millis CompletedMACS2peakCalling