Job ID = 6455642 SRX = SRX287950 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:18:06 prefetch.2.10.7: 1) Downloading 'SRR870139'... 2020-06-21T10:18:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:02 prefetch.2.10.7: 1) 'SRR870139' was downloaded successfully Read 18066428 spots for SRR870139/SRR870139.sra Written 18066428 spots for SRR870139/SRR870139.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: 00:05:20 18066428 reads; of these: 18066428 (100.00%) were unpaired; of these: 1179511 (6.53%) aligned 0 times 10693916 (59.19%) aligned exactly 1 time 6193001 (34.28%) aligned >1 times 93.47% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 2908663 / 16886917 = 0.1722 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 19:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.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 19:33:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:47: 1000000 INFO @ Sun, 21 Jun 2020 19:33:53: 2000000 INFO @ Sun, 21 Jun 2020 19:33:59: 3000000 INFO @ Sun, 21 Jun 2020 19:34:05: 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 19:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.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 19:34:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:11: 5000000 INFO @ Sun, 21 Jun 2020 19:34:16: 1000000 INFO @ Sun, 21 Jun 2020 19:34:17: 6000000 INFO @ Sun, 21 Jun 2020 19:34:22: 2000000 INFO @ Sun, 21 Jun 2020 19:34:23: 7000000 INFO @ Sun, 21 Jun 2020 19:34:27: 3000000 INFO @ Sun, 21 Jun 2020 19:34:30: 8000000 INFO @ Sun, 21 Jun 2020 19:34:33: 4000000 INFO @ Sun, 21 Jun 2020 19:34:36: 9000000 INFO @ Sun, 21 Jun 2020 19:34:38: 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 19:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.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 19:34:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:42: 10000000 INFO @ Sun, 21 Jun 2020 19:34:44: 6000000 INFO @ Sun, 21 Jun 2020 19:34:47: 1000000 INFO @ Sun, 21 Jun 2020 19:34:49: 11000000 INFO @ Sun, 21 Jun 2020 19:34:49: 7000000 INFO @ Sun, 21 Jun 2020 19:34:53: 2000000 INFO @ Sun, 21 Jun 2020 19:34:55: 8000000 INFO @ Sun, 21 Jun 2020 19:34:55: 12000000 INFO @ Sun, 21 Jun 2020 19:34:59: 3000000 INFO @ Sun, 21 Jun 2020 19:35:00: 9000000 INFO @ Sun, 21 Jun 2020 19:35:01: 13000000 INFO @ Sun, 21 Jun 2020 19:35:05: 4000000 INFO @ Sun, 21 Jun 2020 19:35:06: 10000000 INFO @ Sun, 21 Jun 2020 19:35:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:08: #1 total tags in treatment: 13978254 INFO @ Sun, 21 Jun 2020 19:35:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:08: #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 19:35:08: #1 tags after filtering in treatment: 13978254 INFO @ Sun, 21 Jun 2020 19:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:09: #2 number of paired peaks: 936 WARNING @ Sun, 21 Jun 2020 19:35:09: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:09: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 19:35:09: #2 alternative fragment length(s) may be 4,122 bps INFO @ Sun, 21 Jun 2020 19:35:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.05_model.r INFO @ Sun, 21 Jun 2020 19:35:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:11: 5000000 INFO @ Sun, 21 Jun 2020 19:35:12: 11000000 INFO @ Sun, 21 Jun 2020 19:35:17: 12000000 INFO @ Sun, 21 Jun 2020 19:35:17: 6000000 INFO @ Sun, 21 Jun 2020 19:35:23: 13000000 INFO @ Sun, 21 Jun 2020 19:35:24: 7000000 INFO @ Sun, 21 Jun 2020 19:35:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:28: #1 total tags in treatment: 13978254 INFO @ Sun, 21 Jun 2020 19:35:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:28: #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 19:35:29: #1 tags after filtering in treatment: 13978254 INFO @ Sun, 21 Jun 2020 19:35:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:30: 8000000 INFO @ Sun, 21 Jun 2020 19:35:30: #2 number of paired peaks: 936 WARNING @ Sun, 21 Jun 2020 19:35:30: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:30: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 19:35:30: #2 alternative fragment length(s) may be 4,122 bps INFO @ Sun, 21 Jun 2020 19:35:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.10_model.r INFO @ Sun, 21 Jun 2020 19:35:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:36: 9000000 INFO @ Sun, 21 Jun 2020 19:35:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:42: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:35:48: 11000000 INFO @ Sun, 21 Jun 2020 19:35:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.05_summits.bed INFO @ Sun, 21 Jun 2020 19:35:53: Done! pass1 - making usageList (825 chroms): 1 millis pass2 - checking and writing primary data (3200 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:54: 12000000 INFO @ Sun, 21 Jun 2020 19:35:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:00: 13000000 INFO @ Sun, 21 Jun 2020 19:36:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:06: #1 total tags in treatment: 13978254 INFO @ Sun, 21 Jun 2020 19:36:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:06: #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 19:36:07: #1 tags after filtering in treatment: 13978254 INFO @ Sun, 21 Jun 2020 19:36:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:08: #2 number of paired peaks: 936 WARNING @ Sun, 21 Jun 2020 19:36:08: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:08: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 19:36:08: #2 alternative fragment length(s) may be 4,122 bps INFO @ Sun, 21 Jun 2020 19:36:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.20_model.r INFO @ Sun, 21 Jun 2020 19:36:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.10_summits.bed INFO @ Sun, 21 Jun 2020 19:36:14: Done! BigWig に変換しました。 pass1 - making usageList (681 chroms): 1 millis pass2 - checking and writing primary data (1917 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287950/SRX287950.20_summits.bed INFO @ Sun, 21 Jun 2020 19:36:50: Done! pass1 - making usageList (494 chroms): 1 millis pass2 - checking and writing primary data (1102 records, 4 fields): 13 millis CompletedMACS2peakCalling