Job ID = 6453138 SRX = SRX104961 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:21:17 prefetch.2.10.7: 1) Downloading 'SRR363405'... 2020-06-21T08:21:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:28:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:28:06 prefetch.2.10.7: 1) 'SRR363405' was downloaded successfully Read 41546488 spots for SRR363405/SRR363405.sra Written 41546488 spots for SRR363405/SRR363405.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: 00:08:02 41546488 reads; of these: 41546488 (100.00%) were unpaired; of these: 2711766 (6.53%) aligned 0 times 34793261 (83.75%) aligned exactly 1 time 4041461 (9.73%) aligned >1 times 93.47% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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] 13994789 / 38834722 = 0.3604 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 17:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.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 17:45:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:44: 1000000 INFO @ Sun, 21 Jun 2020 17:45:49: 2000000 INFO @ Sun, 21 Jun 2020 17:45:55: 3000000 INFO @ Sun, 21 Jun 2020 17:46:00: 4000000 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 17:46:06: 5000000 INFO @ Sun, 21 Jun 2020 17:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.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 17:46:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:12: 6000000 INFO @ Sun, 21 Jun 2020 17:46:13: 1000000 INFO @ Sun, 21 Jun 2020 17:46:18: 7000000 INFO @ Sun, 21 Jun 2020 17:46:18: 2000000 INFO @ Sun, 21 Jun 2020 17:46:23: 3000000 INFO @ Sun, 21 Jun 2020 17:46:23: 8000000 INFO @ Sun, 21 Jun 2020 17:46:28: 4000000 INFO @ Sun, 21 Jun 2020 17:46:29: 9000000 INFO @ Sun, 21 Jun 2020 17:46:33: 5000000 INFO @ Sun, 21 Jun 2020 17:46:35: 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 17:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.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 17:46:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:38: 6000000 INFO @ Sun, 21 Jun 2020 17:46:41: 11000000 INFO @ Sun, 21 Jun 2020 17:46:43: 1000000 INFO @ Sun, 21 Jun 2020 17:46:43: 7000000 INFO @ Sun, 21 Jun 2020 17:46:47: 12000000 INFO @ Sun, 21 Jun 2020 17:46:48: 2000000 INFO @ Sun, 21 Jun 2020 17:46:48: 8000000 INFO @ Sun, 21 Jun 2020 17:46:53: 13000000 INFO @ Sun, 21 Jun 2020 17:46:53: 3000000 INFO @ Sun, 21 Jun 2020 17:46:53: 9000000 INFO @ Sun, 21 Jun 2020 17:46:58: 4000000 INFO @ Sun, 21 Jun 2020 17:46:58: 10000000 INFO @ Sun, 21 Jun 2020 17:46:59: 14000000 INFO @ Sun, 21 Jun 2020 17:47:03: 11000000 INFO @ Sun, 21 Jun 2020 17:47:03: 5000000 INFO @ Sun, 21 Jun 2020 17:47:05: 15000000 INFO @ Sun, 21 Jun 2020 17:47:08: 12000000 INFO @ Sun, 21 Jun 2020 17:47:09: 6000000 INFO @ Sun, 21 Jun 2020 17:47:11: 16000000 INFO @ Sun, 21 Jun 2020 17:47:13: 13000000 INFO @ Sun, 21 Jun 2020 17:47:14: 7000000 INFO @ Sun, 21 Jun 2020 17:47:17: 17000000 INFO @ Sun, 21 Jun 2020 17:47:19: 14000000 INFO @ Sun, 21 Jun 2020 17:47:19: 8000000 INFO @ Sun, 21 Jun 2020 17:47:23: 18000000 INFO @ Sun, 21 Jun 2020 17:47:24: 15000000 INFO @ Sun, 21 Jun 2020 17:47:24: 9000000 INFO @ Sun, 21 Jun 2020 17:47:29: 16000000 INFO @ Sun, 21 Jun 2020 17:47:29: 10000000 INFO @ Sun, 21 Jun 2020 17:47:29: 19000000 INFO @ Sun, 21 Jun 2020 17:47:34: 17000000 INFO @ Sun, 21 Jun 2020 17:47:34: 11000000 INFO @ Sun, 21 Jun 2020 17:47:35: 20000000 INFO @ Sun, 21 Jun 2020 17:47:39: 18000000 INFO @ Sun, 21 Jun 2020 17:47:39: 12000000 INFO @ Sun, 21 Jun 2020 17:47:41: 21000000 INFO @ Sun, 21 Jun 2020 17:47:44: 19000000 INFO @ Sun, 21 Jun 2020 17:47:44: 13000000 INFO @ Sun, 21 Jun 2020 17:47:47: 22000000 INFO @ Sun, 21 Jun 2020 17:47:49: 20000000 INFO @ Sun, 21 Jun 2020 17:47:49: 14000000 INFO @ Sun, 21 Jun 2020 17:47:53: 23000000 INFO @ Sun, 21 Jun 2020 17:47:54: 21000000 INFO @ Sun, 21 Jun 2020 17:47:54: 15000000 INFO @ Sun, 21 Jun 2020 17:47:59: 24000000 INFO @ Sun, 21 Jun 2020 17:47:59: 22000000 INFO @ Sun, 21 Jun 2020 17:47:59: 16000000 INFO @ Sun, 21 Jun 2020 17:48:04: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:48:04: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:48:04: #1 total tags in treatment: 24839933 INFO @ Sun, 21 Jun 2020 17:48:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:04: #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 17:48:04: 23000000 INFO @ Sun, 21 Jun 2020 17:48:04: #1 tags after filtering in treatment: 24839928 INFO @ Sun, 21 Jun 2020 17:48:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:05: 17000000 INFO @ Sun, 21 Jun 2020 17:48:06: #2 number of paired peaks: 544 WARNING @ Sun, 21 Jun 2020 17:48:06: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:06: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 17:48:06: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 17:48:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.05_model.r INFO @ Sun, 21 Jun 2020 17:48:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:09: 24000000 INFO @ Sun, 21 Jun 2020 17:48:10: 18000000 INFO @ Sun, 21 Jun 2020 17:48:13: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:48:13: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:48:13: #1 total tags in treatment: 24839933 INFO @ Sun, 21 Jun 2020 17:48:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:13: #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 17:48:14: #1 tags after filtering in treatment: 24839928 INFO @ Sun, 21 Jun 2020 17:48:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:14: 19000000 INFO @ Sun, 21 Jun 2020 17:48:16: #2 number of paired peaks: 544 WARNING @ Sun, 21 Jun 2020 17:48:16: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:16: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:16: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:16: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:16: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 17:48:16: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 17:48:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.10_model.r INFO @ Sun, 21 Jun 2020 17:48:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:19: 20000000 INFO @ Sun, 21 Jun 2020 17:48:24: 21000000 INFO @ Sun, 21 Jun 2020 17:48:29: 22000000 INFO @ Sun, 21 Jun 2020 17:48:34: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:48:39: 24000000 INFO @ Sun, 21 Jun 2020 17:48:43: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:48:43: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:48:43: #1 total tags in treatment: 24839933 INFO @ Sun, 21 Jun 2020 17:48:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:43: #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 17:48:44: #1 tags after filtering in treatment: 24839928 INFO @ Sun, 21 Jun 2020 17:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:46: #2 number of paired peaks: 544 WARNING @ Sun, 21 Jun 2020 17:48:46: Fewer paired peaks (544) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 544 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:46: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:46: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:46: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:46: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:46: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 17:48:46: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 17:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.20_model.r INFO @ Sun, 21 Jun 2020 17:48:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:19: Done! pass1 - making usageList (186 chroms): 2 millis pass2 - checking and writing primary data (12071 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.10_summits.bed INFO @ Sun, 21 Jun 2020 17:49:25: Done! pass1 - making usageList (113 chroms): 2 millis pass2 - checking and writing primary data (7764 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:49:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104961/SRX104961.20_summits.bed INFO @ Sun, 21 Jun 2020 17:49:57: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (4674 records, 4 fields): 9 millis CompletedMACS2peakCalling