Job ID = 6508761 SRX = SRX467117 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:53:07 prefetch.2.10.7: 1) Downloading 'SRR1164541'... 2020-06-26T14:53:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:54:40 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:54:41 prefetch.2.10.7: 'SRR1164541' is valid 2020-06-26T14:54:41 prefetch.2.10.7: 1) 'SRR1164541' was downloaded successfully Read 14826548 spots for SRR1164541/SRR1164541.sra Written 14826548 spots for SRR1164541/SRR1164541.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: 00:03:42 14826548 reads; of these: 14826548 (100.00%) were unpaired; of these: 930227 (6.27%) aligned 0 times 10821397 (72.99%) aligned exactly 1 time 3074924 (20.74%) aligned >1 times 93.73% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 1873787 / 13896321 = 0.1348 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 00:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.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 00:03:06: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:03:06: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:03:13: 1000000 INFO @ Sat, 27 Jun 2020 00:03:21: 2000000 INFO @ Sat, 27 Jun 2020 00:03:28: 3000000 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 00:03:35: 4000000 INFO @ Sat, 27 Jun 2020 00:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.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 00:03:36: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:03:36: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:03:43: 5000000 INFO @ Sat, 27 Jun 2020 00:03:44: 1000000 INFO @ Sat, 27 Jun 2020 00:03:50: 6000000 INFO @ Sat, 27 Jun 2020 00:03:51: 2000000 INFO @ Sat, 27 Jun 2020 00:03:58: 7000000 INFO @ Sat, 27 Jun 2020 00:03:59: 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 00:04:06: 8000000 INFO @ Sat, 27 Jun 2020 00:04:06: 4000000 INFO @ Sat, 27 Jun 2020 00:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.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 00:04:06: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:04:06: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:04:14: 9000000 INFO @ Sat, 27 Jun 2020 00:04:14: 5000000 INFO @ Sat, 27 Jun 2020 00:04:15: 1000000 INFO @ Sat, 27 Jun 2020 00:04:22: 10000000 INFO @ Sat, 27 Jun 2020 00:04:22: 6000000 INFO @ Sat, 27 Jun 2020 00:04:24: 2000000 INFO @ Sat, 27 Jun 2020 00:04:30: 7000000 INFO @ Sat, 27 Jun 2020 00:04:30: 11000000 INFO @ Sat, 27 Jun 2020 00:04:32: 3000000 INFO @ Sat, 27 Jun 2020 00:04:38: 8000000 INFO @ Sat, 27 Jun 2020 00:04:38: 12000000 INFO @ Sat, 27 Jun 2020 00:04:38: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:04:38: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:04:38: #1 total tags in treatment: 12022534 INFO @ Sat, 27 Jun 2020 00:04:38: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:04:38: #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 00:04:39: #1 tags after filtering in treatment: 12022443 INFO @ Sat, 27 Jun 2020 00:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:04:39: #1 finished! INFO @ Sat, 27 Jun 2020 00:04:39: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:04:40: 4000000 INFO @ Sat, 27 Jun 2020 00:04:40: #2 number of paired peaks: 5855 INFO @ Sat, 27 Jun 2020 00:04:40: start model_add_line... INFO @ Sat, 27 Jun 2020 00:04:40: start X-correlation... INFO @ Sat, 27 Jun 2020 00:04:40: end of X-cor INFO @ Sat, 27 Jun 2020 00:04:40: #2 finished! INFO @ Sat, 27 Jun 2020 00:04:40: #2 predicted fragment length is 203 bps INFO @ Sat, 27 Jun 2020 00:04:40: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 27 Jun 2020 00:04:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.05_model.r INFO @ Sat, 27 Jun 2020 00:04:40: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:04:46: 9000000 INFO @ Sat, 27 Jun 2020 00:04:47: 5000000 INFO @ Sat, 27 Jun 2020 00:04:54: 10000000 INFO @ Sat, 27 Jun 2020 00:04:55: 6000000 INFO @ Sat, 27 Jun 2020 00:05:02: 11000000 INFO @ Sat, 27 Jun 2020 00:05:03: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:05:10: 8000000 INFO @ Sat, 27 Jun 2020 00:05:11: 12000000 INFO @ Sat, 27 Jun 2020 00:05:11: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:05:11: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:05:11: #1 total tags in treatment: 12022534 INFO @ Sat, 27 Jun 2020 00:05:11: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:05:11: #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 00:05:11: #1 tags after filtering in treatment: 12022443 INFO @ Sat, 27 Jun 2020 00:05:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:05:11: #1 finished! INFO @ Sat, 27 Jun 2020 00:05:11: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:05:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:05:13: #2 number of paired peaks: 5855 INFO @ Sat, 27 Jun 2020 00:05:13: start model_add_line... INFO @ Sat, 27 Jun 2020 00:05:13: start X-correlation... INFO @ Sat, 27 Jun 2020 00:05:13: end of X-cor INFO @ Sat, 27 Jun 2020 00:05:13: #2 finished! INFO @ Sat, 27 Jun 2020 00:05:13: #2 predicted fragment length is 203 bps INFO @ Sat, 27 Jun 2020 00:05:13: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 27 Jun 2020 00:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.10_model.r INFO @ Sat, 27 Jun 2020 00:05:13: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:05:13: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:05:17: 9000000 INFO @ Sat, 27 Jun 2020 00:05:25: 10000000 INFO @ Sat, 27 Jun 2020 00:05:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:05:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:05:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.05_summits.bed INFO @ Sat, 27 Jun 2020 00:05:30: Done! pass1 - making usageList (232 chroms): 1 millis pass2 - checking and writing primary data (6796 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:05:32: 11000000 INFO @ Sat, 27 Jun 2020 00:05:39: 12000000 INFO @ Sat, 27 Jun 2020 00:05:40: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:05:40: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:05:40: #1 total tags in treatment: 12022534 INFO @ Sat, 27 Jun 2020 00:05:40: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:05:40: #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 00:05:40: #1 tags after filtering in treatment: 12022443 INFO @ Sat, 27 Jun 2020 00:05:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:05:40: #1 finished! INFO @ Sat, 27 Jun 2020 00:05:40: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:05:41: #2 number of paired peaks: 5855 INFO @ Sat, 27 Jun 2020 00:05:41: start model_add_line... INFO @ Sat, 27 Jun 2020 00:05:42: start X-correlation... INFO @ Sat, 27 Jun 2020 00:05:42: end of X-cor INFO @ Sat, 27 Jun 2020 00:05:42: #2 finished! INFO @ Sat, 27 Jun 2020 00:05:42: #2 predicted fragment length is 203 bps INFO @ Sat, 27 Jun 2020 00:05:42: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 27 Jun 2020 00:05:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.20_model.r INFO @ Sat, 27 Jun 2020 00:05:42: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:05:48: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:06:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:06:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:06:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.10_summits.bed INFO @ Sat, 27 Jun 2020 00:06:07: Done! pass1 - making usageList (187 chroms): 1 millis pass2 - checking and writing primary data (5526 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:06:15: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:06:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:06:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:06:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467117/SRX467117.20_summits.bed INFO @ Sat, 27 Jun 2020 00:06:32: Done! pass1 - making usageList (124 chroms): 1 millis pass2 - checking and writing primary data (4042 records, 4 fields): 9 millis CompletedMACS2peakCalling