Job ID = 6453146 SRX = SRX104968 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:21:32 prefetch.2.10.7: 1) Downloading 'SRR363412'... 2020-06-21T08:21:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:25 prefetch.2.10.7: 'SRR363412' is valid 2020-06-21T08:24:25 prefetch.2.10.7: 1) 'SRR363412' was downloaded successfully Read 23835354 spots for SRR363412/SRR363412.sra Written 23835354 spots for SRR363412/SRR363412.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: 00:05:28 23835354 reads; of these: 23835354 (100.00%) were unpaired; of these: 992895 (4.17%) aligned 0 times 17175606 (72.06%) aligned exactly 1 time 5666853 (23.77%) aligned >1 times 95.83% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 3081679 / 22842459 = 0.1349 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 17:35:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.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 17:35:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:35:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:35:41: 1000000 INFO @ Sun, 21 Jun 2020 17:35:47: 2000000 INFO @ Sun, 21 Jun 2020 17:35:52: 3000000 INFO @ Sun, 21 Jun 2020 17:35:58: 4000000 INFO @ Sun, 21 Jun 2020 17:36:03: 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 17:36:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.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 17:36:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:36:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:36:09: 6000000 INFO @ Sun, 21 Jun 2020 17:36:12: 1000000 INFO @ Sun, 21 Jun 2020 17:36:14: 7000000 INFO @ Sun, 21 Jun 2020 17:36:18: 2000000 INFO @ Sun, 21 Jun 2020 17:36:20: 8000000 INFO @ Sun, 21 Jun 2020 17:36:24: 3000000 INFO @ Sun, 21 Jun 2020 17:36:26: 9000000 INFO @ Sun, 21 Jun 2020 17:36:30: 4000000 INFO @ Sun, 21 Jun 2020 17:36:32: 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 17:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.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 17:36:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:36:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:36:36: 5000000 INFO @ Sun, 21 Jun 2020 17:36:38: 11000000 INFO @ Sun, 21 Jun 2020 17:36:42: 6000000 INFO @ Sun, 21 Jun 2020 17:36:42: 1000000 INFO @ Sun, 21 Jun 2020 17:36:44: 12000000 INFO @ Sun, 21 Jun 2020 17:36:48: 7000000 INFO @ Sun, 21 Jun 2020 17:36:48: 2000000 INFO @ Sun, 21 Jun 2020 17:36:51: 13000000 INFO @ Sun, 21 Jun 2020 17:36:54: 8000000 INFO @ Sun, 21 Jun 2020 17:36:54: 3000000 INFO @ Sun, 21 Jun 2020 17:36:56: 14000000 INFO @ Sun, 21 Jun 2020 17:37:00: 9000000 INFO @ Sun, 21 Jun 2020 17:37:00: 4000000 INFO @ Sun, 21 Jun 2020 17:37:02: 15000000 INFO @ Sun, 21 Jun 2020 17:37:06: 10000000 INFO @ Sun, 21 Jun 2020 17:37:06: 5000000 INFO @ Sun, 21 Jun 2020 17:37:08: 16000000 INFO @ Sun, 21 Jun 2020 17:37:12: 11000000 INFO @ Sun, 21 Jun 2020 17:37:12: 6000000 INFO @ Sun, 21 Jun 2020 17:37:15: 17000000 INFO @ Sun, 21 Jun 2020 17:37:18: 12000000 INFO @ Sun, 21 Jun 2020 17:37:19: 7000000 INFO @ Sun, 21 Jun 2020 17:37:22: 18000000 INFO @ Sun, 21 Jun 2020 17:37:24: 13000000 INFO @ Sun, 21 Jun 2020 17:37:25: 8000000 INFO @ Sun, 21 Jun 2020 17:37:28: 19000000 INFO @ Sun, 21 Jun 2020 17:37:30: 14000000 INFO @ Sun, 21 Jun 2020 17:37:31: 9000000 INFO @ Sun, 21 Jun 2020 17:37:33: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:37:33: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:37:33: #1 total tags in treatment: 19760780 INFO @ Sun, 21 Jun 2020 17:37:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:33: #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 17:37:34: #1 tags after filtering in treatment: 19760779 INFO @ Sun, 21 Jun 2020 17:37:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:35: #2 number of paired peaks: 896 WARNING @ Sun, 21 Jun 2020 17:37:35: Fewer paired peaks (896) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 896 pairs to build model! INFO @ Sun, 21 Jun 2020 17:37:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:35: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:37:35: #2 alternative fragment length(s) may be 2,126,167 bps INFO @ Sun, 21 Jun 2020 17:37:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.05_model.r INFO @ Sun, 21 Jun 2020 17:37:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:37:36: 15000000 INFO @ Sun, 21 Jun 2020 17:37:37: 10000000 INFO @ Sun, 21 Jun 2020 17:37:42: 16000000 INFO @ Sun, 21 Jun 2020 17:37:43: 11000000 INFO @ Sun, 21 Jun 2020 17:37:48: 17000000 INFO @ Sun, 21 Jun 2020 17:37:49: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:37:54: 18000000 INFO @ Sun, 21 Jun 2020 17:37:55: 13000000 INFO @ Sun, 21 Jun 2020 17:38:00: 19000000 INFO @ Sun, 21 Jun 2020 17:38:01: 14000000 INFO @ Sun, 21 Jun 2020 17:38:05: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:38:05: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:38:05: #1 total tags in treatment: 19760780 INFO @ Sun, 21 Jun 2020 17:38:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:05: #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 17:38:06: #1 tags after filtering in treatment: 19760779 INFO @ Sun, 21 Jun 2020 17:38:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:06: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:07: 15000000 INFO @ Sun, 21 Jun 2020 17:38:07: #2 number of paired peaks: 896 WARNING @ Sun, 21 Jun 2020 17:38:07: Fewer paired peaks (896) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 896 pairs to build model! INFO @ Sun, 21 Jun 2020 17:38:07: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:07: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:07: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:07: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:07: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:38:07: #2 alternative fragment length(s) may be 2,126,167 bps INFO @ Sun, 21 Jun 2020 17:38:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.10_model.r INFO @ Sun, 21 Jun 2020 17:38:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:12: 16000000 INFO @ Sun, 21 Jun 2020 17:38:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:18: 17000000 INFO @ Sun, 21 Jun 2020 17:38:24: 18000000 INFO @ Sun, 21 Jun 2020 17:38:30: 19000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:38:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.05_summits.bed INFO @ Sun, 21 Jun 2020 17:38:33: Done! pass1 - making usageList (488 chroms): 1 millis pass2 - checking and writing primary data (1896 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:34: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:38:34: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:38:34: #1 total tags in treatment: 19760780 INFO @ Sun, 21 Jun 2020 17:38:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:34: #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 17:38:35: #1 tags after filtering in treatment: 19760779 INFO @ Sun, 21 Jun 2020 17:38:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:36: #2 number of paired peaks: 896 WARNING @ Sun, 21 Jun 2020 17:38:36: Fewer paired peaks (896) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 896 pairs to build model! INFO @ Sun, 21 Jun 2020 17:38:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:36: #2 predicted fragment length is 126 bps INFO @ Sun, 21 Jun 2020 17:38:36: #2 alternative fragment length(s) may be 2,126,167 bps INFO @ Sun, 21 Jun 2020 17:38:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.20_model.r INFO @ Sun, 21 Jun 2020 17:38:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.10_summits.bed INFO @ Sun, 21 Jun 2020 17:39:06: Done! pass1 - making usageList (235 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:39:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104968/SRX104968.20_summits.bed INFO @ Sun, 21 Jun 2020 17:39:37: Done! pass1 - making usageList (117 chroms): 3 millis pass2 - checking and writing primary data (218 records, 4 fields): 4 millis CompletedMACS2peakCalling