Job ID = 6508482 SRX = SRX287904 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:55:08 prefetch.2.10.7: 1) Downloading 'SRR870093'... 2020-06-26T14:55:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:56:37 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:56:37 prefetch.2.10.7: 1) 'SRR870093' was downloaded successfully Read 16839930 spots for SRR870093/SRR870093.sra Written 16839930 spots for SRR870093/SRR870093.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: 00:04:50 16839930 reads; of these: 16839930 (100.00%) were unpaired; of these: 1076651 (6.39%) aligned 0 times 11678216 (69.35%) aligned exactly 1 time 4085063 (24.26%) aligned >1 times 93.61% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 1924959 / 15763279 = 0.1221 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 @ Sat, 27 Jun 2020 00:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.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 @ Sat, 27 Jun 2020 00:06:46: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:06:46: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:06:53: 1000000 INFO @ Sat, 27 Jun 2020 00:06:59: 2000000 INFO @ Sat, 27 Jun 2020 00:07:05: 3000000 INFO @ Sat, 27 Jun 2020 00:07:11: 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 @ Sat, 27 Jun 2020 00:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.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 @ Sat, 27 Jun 2020 00:07:16: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:07:16: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:07:18: 5000000 INFO @ Sat, 27 Jun 2020 00:07:25: 1000000 INFO @ Sat, 27 Jun 2020 00:07:26: 6000000 INFO @ Sat, 27 Jun 2020 00:07:33: 2000000 INFO @ Sat, 27 Jun 2020 00:07:33: 7000000 INFO @ Sat, 27 Jun 2020 00:07:41: 8000000 INFO @ Sat, 27 Jun 2020 00:07:42: 3000000 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 @ Sat, 27 Jun 2020 00:07:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.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 @ Sat, 27 Jun 2020 00:07:46: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:07:46: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:07:48: 9000000 INFO @ Sat, 27 Jun 2020 00:07:50: 4000000 INFO @ Sat, 27 Jun 2020 00:07:54: 1000000 INFO @ Sat, 27 Jun 2020 00:07:56: 10000000 INFO @ Sat, 27 Jun 2020 00:07:59: 5000000 INFO @ Sat, 27 Jun 2020 00:08:02: 2000000 INFO @ Sat, 27 Jun 2020 00:08:04: 11000000 INFO @ Sat, 27 Jun 2020 00:08:08: 6000000 INFO @ Sat, 27 Jun 2020 00:08:10: 3000000 INFO @ Sat, 27 Jun 2020 00:08:12: 12000000 INFO @ Sat, 27 Jun 2020 00:08:16: 7000000 INFO @ Sat, 27 Jun 2020 00:08:18: 4000000 INFO @ Sat, 27 Jun 2020 00:08:20: 13000000 INFO @ Sat, 27 Jun 2020 00:08:25: 8000000 INFO @ Sat, 27 Jun 2020 00:08:26: 5000000 INFO @ Sat, 27 Jun 2020 00:08:27: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:08:27: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:08:27: #1 total tags in treatment: 13838320 INFO @ Sat, 27 Jun 2020 00:08:27: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:08:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:08:28: #1 tags after filtering in treatment: 13838320 INFO @ Sat, 27 Jun 2020 00:08:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:08:28: #1 finished! INFO @ Sat, 27 Jun 2020 00:08:28: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:08:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:08:29: #2 number of paired peaks: 667 WARNING @ Sat, 27 Jun 2020 00:08:29: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Sat, 27 Jun 2020 00:08:29: start model_add_line... INFO @ Sat, 27 Jun 2020 00:08:29: start X-correlation... INFO @ Sat, 27 Jun 2020 00:08:29: end of X-cor INFO @ Sat, 27 Jun 2020 00:08:29: #2 finished! INFO @ Sat, 27 Jun 2020 00:08:29: #2 predicted fragment length is 135 bps INFO @ Sat, 27 Jun 2020 00:08:29: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 27 Jun 2020 00:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.05_model.r INFO @ Sat, 27 Jun 2020 00:08:29: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:08:33: 9000000 INFO @ Sat, 27 Jun 2020 00:08:34: 6000000 INFO @ Sat, 27 Jun 2020 00:08:41: 7000000 INFO @ Sat, 27 Jun 2020 00:08:42: 10000000 INFO @ Sat, 27 Jun 2020 00:08:49: 8000000 INFO @ Sat, 27 Jun 2020 00:08:50: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:08:57: 9000000 INFO @ Sat, 27 Jun 2020 00:08:59: 12000000 INFO @ Sat, 27 Jun 2020 00:09:00: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:09:04: 10000000 INFO @ Sat, 27 Jun 2020 00:09:08: 13000000 INFO @ Sat, 27 Jun 2020 00:09:12: 11000000 INFO @ Sat, 27 Jun 2020 00:09:15: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:09:15: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:09:15: #1 total tags in treatment: 13838320 INFO @ Sat, 27 Jun 2020 00:09:15: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:09:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:09:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:09:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:09:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.05_summits.bed INFO @ Sat, 27 Jun 2020 00:09:15: Done! INFO @ Sat, 27 Jun 2020 00:09:16: #1 tags after filtering in treatment: 13838320 INFO @ Sat, 27 Jun 2020 00:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:09:16: #1 finished! INFO @ Sat, 27 Jun 2020 00:09:16: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:09:16: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (656 chroms): 2 millis pass2 - checking and writing primary data (4770 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:09:17: #2 number of paired peaks: 667 WARNING @ Sat, 27 Jun 2020 00:09:17: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Sat, 27 Jun 2020 00:09:17: start model_add_line... INFO @ Sat, 27 Jun 2020 00:09:17: start X-correlation... INFO @ Sat, 27 Jun 2020 00:09:17: end of X-cor INFO @ Sat, 27 Jun 2020 00:09:17: #2 finished! INFO @ Sat, 27 Jun 2020 00:09:17: #2 predicted fragment length is 135 bps INFO @ Sat, 27 Jun 2020 00:09:17: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 27 Jun 2020 00:09:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.10_model.r INFO @ Sat, 27 Jun 2020 00:09:17: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:09:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:09:19: 12000000 INFO @ Sat, 27 Jun 2020 00:09:25: 13000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:09:31: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:09:31: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:09:31: #1 total tags in treatment: 13838320 INFO @ Sat, 27 Jun 2020 00:09:31: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:09:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:09:32: #1 tags after filtering in treatment: 13838320 INFO @ Sat, 27 Jun 2020 00:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:09:32: #1 finished! INFO @ Sat, 27 Jun 2020 00:09:32: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:09:33: #2 number of paired peaks: 667 WARNING @ Sat, 27 Jun 2020 00:09:33: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Sat, 27 Jun 2020 00:09:33: start model_add_line... INFO @ Sat, 27 Jun 2020 00:09:33: start X-correlation... INFO @ Sat, 27 Jun 2020 00:09:33: end of X-cor INFO @ Sat, 27 Jun 2020 00:09:33: #2 finished! INFO @ Sat, 27 Jun 2020 00:09:33: #2 predicted fragment length is 135 bps INFO @ Sat, 27 Jun 2020 00:09:33: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 27 Jun 2020 00:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.20_model.r INFO @ Sat, 27 Jun 2020 00:09:33: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:09:49: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:10:03: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:10:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:10:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:10:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.10_summits.bed INFO @ Sat, 27 Jun 2020 00:10:05: Done! pass1 - making usageList (572 chroms): 1 millis pass2 - checking and writing primary data (3297 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:10:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:10:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:10:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287904/SRX287904.20_summits.bed INFO @ Sat, 27 Jun 2020 00:10:18: Done! pass1 - making usageList (445 chroms): 2 millis pass2 - checking and writing primary data (2123 records, 4 fields): 14 millis CompletedMACS2peakCalling