Job ID = 6508370 SRX = SRX2592454 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:38:19 prefetch.2.10.7: 1) Downloading 'SRR5289731'... 2020-06-26T14:38:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:44:20 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:44:20 prefetch.2.10.7: 1) 'SRR5289731' was downloaded successfully Read 16467723 spots for SRR5289731/SRR5289731.sra Written 16467723 spots for SRR5289731/SRR5289731.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: 00:07:51 16467723 reads; of these: 16467723 (100.00%) were unpaired; of these: 1919627 (11.66%) aligned 0 times 9307203 (56.52%) aligned exactly 1 time 5240893 (31.83%) aligned >1 times 88.34% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 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] 6096236 / 14548096 = 0.4190 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 @ Fri, 26 Jun 2020 23:58:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.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 @ Fri, 26 Jun 2020 23:58:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:58:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:58:13: 1000000 INFO @ Fri, 26 Jun 2020 23:58:19: 2000000 INFO @ Fri, 26 Jun 2020 23:58:24: 3000000 INFO @ Fri, 26 Jun 2020 23:58:30: 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 @ Fri, 26 Jun 2020 23:58:35: 5000000 INFO @ Fri, 26 Jun 2020 23:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.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 @ Fri, 26 Jun 2020 23:58:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:58:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:58:41: 6000000 INFO @ Fri, 26 Jun 2020 23:58:45: 1000000 INFO @ Fri, 26 Jun 2020 23:58:48: 7000000 INFO @ Fri, 26 Jun 2020 23:58:51: 2000000 INFO @ Fri, 26 Jun 2020 23:58:54: 8000000 INFO @ Fri, 26 Jun 2020 23:58:57: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:58:57: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:58:57: #1 total tags in treatment: 8451860 INFO @ Fri, 26 Jun 2020 23:58:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:58:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:58:57: 3000000 INFO @ Fri, 26 Jun 2020 23:58:57: #1 tags after filtering in treatment: 8451745 INFO @ Fri, 26 Jun 2020 23:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:58:57: #1 finished! INFO @ Fri, 26 Jun 2020 23:58:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:58:58: #2 number of paired peaks: 1173 INFO @ Fri, 26 Jun 2020 23:58:58: start model_add_line... INFO @ Fri, 26 Jun 2020 23:58:59: start X-correlation... INFO @ Fri, 26 Jun 2020 23:58:59: end of X-cor INFO @ Fri, 26 Jun 2020 23:58:59: #2 finished! INFO @ Fri, 26 Jun 2020 23:58:59: #2 predicted fragment length is 191 bps INFO @ Fri, 26 Jun 2020 23:58:59: #2 alternative fragment length(s) may be 68,191 bps INFO @ Fri, 26 Jun 2020 23:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.05_model.r INFO @ Fri, 26 Jun 2020 23:58:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:59:03: 4000000 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 @ Fri, 26 Jun 2020 23:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.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 @ Fri, 26 Jun 2020 23:59:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:59:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:59:08: 5000000 INFO @ Fri, 26 Jun 2020 23:59:14: 1000000 INFO @ Fri, 26 Jun 2020 23:59:15: 6000000 INFO @ Fri, 26 Jun 2020 23:59:20: 2000000 INFO @ Fri, 26 Jun 2020 23:59:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:59:21: 7000000 INFO @ Fri, 26 Jun 2020 23:59:26: 3000000 INFO @ Fri, 26 Jun 2020 23:59:27: 8000000 INFO @ Fri, 26 Jun 2020 23:59:30: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:59:30: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:59:30: #1 total tags in treatment: 8451860 INFO @ Fri, 26 Jun 2020 23:59:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:59:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:59:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:59:31: #1 tags after filtering in treatment: 8451745 INFO @ Fri, 26 Jun 2020 23:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:59:31: #1 finished! INFO @ Fri, 26 Jun 2020 23:59:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:59:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:59:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.05_summits.bed INFO @ Fri, 26 Jun 2020 23:59:32: 4000000 INFO @ Fri, 26 Jun 2020 23:59:32: Done! INFO @ Fri, 26 Jun 2020 23:59:32: #2 number of paired peaks: 1173 INFO @ Fri, 26 Jun 2020 23:59:32: start model_add_line... INFO @ Fri, 26 Jun 2020 23:59:32: start X-correlation... INFO @ Fri, 26 Jun 2020 23:59:32: end of X-cor INFO @ Fri, 26 Jun 2020 23:59:32: #2 finished! INFO @ Fri, 26 Jun 2020 23:59:32: #2 predicted fragment length is 191 bps INFO @ Fri, 26 Jun 2020 23:59:32: #2 alternative fragment length(s) may be 68,191 bps INFO @ Fri, 26 Jun 2020 23:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.10_model.r INFO @ Fri, 26 Jun 2020 23:59:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:59:32: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (806 chroms): 3 millis pass2 - checking and writing primary data (15225 records, 4 fields): 163 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:59:37: 5000000 INFO @ Fri, 26 Jun 2020 23:59:43: 6000000 INFO @ Fri, 26 Jun 2020 23:59:49: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:59:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:59:55: 8000000 INFO @ Fri, 26 Jun 2020 23:59:58: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:59:58: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:59:58: #1 total tags in treatment: 8451860 INFO @ Fri, 26 Jun 2020 23:59:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:59:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:59:59: #1 tags after filtering in treatment: 8451745 INFO @ Fri, 26 Jun 2020 23:59:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:59:59: #1 finished! INFO @ Fri, 26 Jun 2020 23:59:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:59:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:00:00: #2 number of paired peaks: 1173 INFO @ Sat, 27 Jun 2020 00:00:00: start model_add_line... INFO @ Sat, 27 Jun 2020 00:00:00: start X-correlation... INFO @ Sat, 27 Jun 2020 00:00:00: end of X-cor INFO @ Sat, 27 Jun 2020 00:00:00: #2 finished! INFO @ Sat, 27 Jun 2020 00:00:00: #2 predicted fragment length is 191 bps INFO @ Sat, 27 Jun 2020 00:00:00: #2 alternative fragment length(s) may be 68,191 bps INFO @ Sat, 27 Jun 2020 00:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.20_model.r INFO @ Sat, 27 Jun 2020 00:00:00: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.10_summits.bed INFO @ Sat, 27 Jun 2020 00:00:04: Done! pass1 - making usageList (658 chroms): 4 millis pass2 - checking and writing primary data (12310 records, 4 fields): 50 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:00:21: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592454/SRX2592454.20_summits.bed INFO @ Sat, 27 Jun 2020 00:00:31: Done! pass1 - making usageList (486 chroms): 3 millis pass2 - checking and writing primary data (9029 records, 4 fields): 37 millis CompletedMACS2peakCalling