Job ID = 6453743 SRX = SRX1433380 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:47:17 prefetch.2.10.7: 1) Downloading 'SRR2919845'... 2020-06-21T08:47:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:50:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:50:04 prefetch.2.10.7: 1) 'SRR2919845' was downloaded successfully Read 32381362 spots for SRR2919845/SRR2919845.sra Written 32381362 spots for SRR2919845/SRR2919845.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: 00:08:48 32381362 reads; of these: 32381362 (100.00%) were unpaired; of these: 2172674 (6.71%) aligned 0 times 23491870 (72.55%) aligned exactly 1 time 6716818 (20.74%) aligned >1 times 93.29% overall alignment rate Time searching: 00:08:48 Overall time: 00:08:48 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 16 files... [bam_rmdupse_core] 11645803 / 30208688 = 0.3855 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 18:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.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 18:05:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:47: 1000000 INFO @ Sun, 21 Jun 2020 18:05:52: 2000000 INFO @ Sun, 21 Jun 2020 18:05:57: 3000000 INFO @ Sun, 21 Jun 2020 18:06:03: 4000000 INFO @ Sun, 21 Jun 2020 18:06:08: 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 18:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.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 18:06:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:14: 6000000 INFO @ Sun, 21 Jun 2020 18:06:17: 1000000 INFO @ Sun, 21 Jun 2020 18:06:20: 7000000 INFO @ Sun, 21 Jun 2020 18:06:24: 2000000 INFO @ Sun, 21 Jun 2020 18:06:26: 8000000 INFO @ Sun, 21 Jun 2020 18:06:30: 3000000 INFO @ Sun, 21 Jun 2020 18:06:31: 9000000 INFO @ Sun, 21 Jun 2020 18:06:36: 4000000 INFO @ Sun, 21 Jun 2020 18:06:38: 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 18:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.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 18:06:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:42: 5000000 INFO @ Sun, 21 Jun 2020 18:06:44: 11000000 INFO @ Sun, 21 Jun 2020 18:06:47: 1000000 INFO @ Sun, 21 Jun 2020 18:06:48: 6000000 INFO @ Sun, 21 Jun 2020 18:06:50: 12000000 INFO @ Sun, 21 Jun 2020 18:06:53: 2000000 INFO @ Sun, 21 Jun 2020 18:06:54: 7000000 INFO @ Sun, 21 Jun 2020 18:06:56: 13000000 INFO @ Sun, 21 Jun 2020 18:06:59: 3000000 INFO @ Sun, 21 Jun 2020 18:07:00: 8000000 INFO @ Sun, 21 Jun 2020 18:07:02: 14000000 INFO @ Sun, 21 Jun 2020 18:07:06: 4000000 INFO @ Sun, 21 Jun 2020 18:07:06: 9000000 INFO @ Sun, 21 Jun 2020 18:07:08: 15000000 INFO @ Sun, 21 Jun 2020 18:07:12: 5000000 INFO @ Sun, 21 Jun 2020 18:07:12: 10000000 INFO @ Sun, 21 Jun 2020 18:07:15: 16000000 INFO @ Sun, 21 Jun 2020 18:07:18: 6000000 INFO @ Sun, 21 Jun 2020 18:07:19: 11000000 INFO @ Sun, 21 Jun 2020 18:07:21: 17000000 INFO @ Sun, 21 Jun 2020 18:07:25: 7000000 INFO @ Sun, 21 Jun 2020 18:07:25: 12000000 INFO @ Sun, 21 Jun 2020 18:07:28: 18000000 INFO @ Sun, 21 Jun 2020 18:07:31: 8000000 INFO @ Sun, 21 Jun 2020 18:07:31: 13000000 INFO @ Sun, 21 Jun 2020 18:07:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:07:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:07:32: #1 total tags in treatment: 18562885 INFO @ Sun, 21 Jun 2020 18:07:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:32: #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 18:07:32: #1 tags after filtering in treatment: 18562831 INFO @ Sun, 21 Jun 2020 18:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:33: #2 number of paired peaks: 834 WARNING @ Sun, 21 Jun 2020 18:07:33: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Sun, 21 Jun 2020 18:07:33: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:34: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 18:07:34: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 18:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.05_model.r INFO @ Sun, 21 Jun 2020 18:07:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:37: 9000000 INFO @ Sun, 21 Jun 2020 18:07:37: 14000000 INFO @ Sun, 21 Jun 2020 18:07:43: 10000000 INFO @ Sun, 21 Jun 2020 18:07:44: 15000000 INFO @ Sun, 21 Jun 2020 18:07:49: 11000000 INFO @ Sun, 21 Jun 2020 18:07:50: 16000000 INFO @ Sun, 21 Jun 2020 18:07:55: 12000000 INFO @ Sun, 21 Jun 2020 18:07:56: 17000000 INFO @ Sun, 21 Jun 2020 18:08:01: 13000000 INFO @ Sun, 21 Jun 2020 18:08:02: 18000000 INFO @ Sun, 21 Jun 2020 18:08:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:08:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:08:06: #1 total tags in treatment: 18562885 INFO @ Sun, 21 Jun 2020 18:08:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:06: #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 18:08:06: #1 tags after filtering in treatment: 18562831 INFO @ Sun, 21 Jun 2020 18:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:07: 14000000 INFO @ Sun, 21 Jun 2020 18:08:07: #2 number of paired peaks: 834 WARNING @ Sun, 21 Jun 2020 18:08:07: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Sun, 21 Jun 2020 18:08:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:08: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 18:08:08: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 18:08:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.10_model.r INFO @ Sun, 21 Jun 2020 18:08:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:13: 15000000 INFO @ Sun, 21 Jun 2020 18:08:15: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:08:19: 16000000 INFO @ Sun, 21 Jun 2020 18:08:24: 17000000 INFO @ Sun, 21 Jun 2020 18:08:29: 18000000 INFO @ Sun, 21 Jun 2020 18:08:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:08:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:08:33: #1 total tags in treatment: 18562885 INFO @ Sun, 21 Jun 2020 18:08:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:33: #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 18:08:33: #1 tags after filtering in treatment: 18562831 INFO @ Sun, 21 Jun 2020 18:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.05_summits.bed INFO @ Sun, 21 Jun 2020 18:08:34: Done! pass1 - making usageList (529 chroms): 2 millis pass2 - checking and writing primary data (6893 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:08:34: #2 number of paired peaks: 834 WARNING @ Sun, 21 Jun 2020 18:08:34: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Sun, 21 Jun 2020 18:08:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:35: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 18:08:35: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 18:08:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.20_model.r INFO @ Sun, 21 Jun 2020 18:08:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:09:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.10_summits.bed INFO @ Sun, 21 Jun 2020 18:09:06: Done! pass1 - making usageList (453 chroms): 2 millis pass2 - checking and writing primary data (4745 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:09:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433380/SRX1433380.20_summits.bed INFO @ Sun, 21 Jun 2020 18:09:34: Done! pass1 - making usageList (278 chroms): 1 millis pass2 - checking and writing primary data (2664 records, 4 fields): 10 millis CompletedMACS2peakCalling