Job ID = 6498310 SRX = SRX467121 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:19:46 prefetch.2.10.7: 1) Downloading 'SRR1164545'... 2020-06-25T23:19:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:22:25 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:22:25 prefetch.2.10.7: 1) 'SRR1164545' was downloaded successfully Read 17926413 spots for SRR1164545/SRR1164545.sra Written 17926413 spots for SRR1164545/SRR1164545.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: 00:00:01 Multiseed full-index search: 00:05:28 17926413 reads; of these: 17926413 (100.00%) were unpaired; of these: 921925 (5.14%) aligned 0 times 13188003 (73.57%) aligned exactly 1 time 3816485 (21.29%) aligned >1 times 94.86% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3315952 / 17004488 = 0.1950 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 08:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.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 08:33:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:33:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:33:42: 1000000 INFO @ Fri, 26 Jun 2020 08:33:48: 2000000 INFO @ Fri, 26 Jun 2020 08:33:55: 3000000 INFO @ Fri, 26 Jun 2020 08:34:01: 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 08:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.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 08:34:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:34:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:34:08: 5000000 INFO @ Fri, 26 Jun 2020 08:34:12: 1000000 INFO @ Fri, 26 Jun 2020 08:34:14: 6000000 INFO @ Fri, 26 Jun 2020 08:34:19: 2000000 INFO @ Fri, 26 Jun 2020 08:34:21: 7000000 INFO @ Fri, 26 Jun 2020 08:34:25: 3000000 INFO @ Fri, 26 Jun 2020 08:34:28: 8000000 INFO @ Fri, 26 Jun 2020 08:34:32: 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 08:34:35: 9000000 INFO @ Fri, 26 Jun 2020 08:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.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 08:34:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:34:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:34:39: 5000000 INFO @ Fri, 26 Jun 2020 08:34:42: 10000000 INFO @ Fri, 26 Jun 2020 08:34:43: 1000000 INFO @ Fri, 26 Jun 2020 08:34:46: 6000000 INFO @ Fri, 26 Jun 2020 08:34:49: 11000000 INFO @ Fri, 26 Jun 2020 08:34:49: 2000000 INFO @ Fri, 26 Jun 2020 08:34:52: 7000000 INFO @ Fri, 26 Jun 2020 08:34:56: 12000000 INFO @ Fri, 26 Jun 2020 08:34:56: 3000000 INFO @ Fri, 26 Jun 2020 08:34:59: 8000000 INFO @ Fri, 26 Jun 2020 08:35:02: 13000000 INFO @ Fri, 26 Jun 2020 08:35:02: 4000000 INFO @ Fri, 26 Jun 2020 08:35:06: 9000000 INFO @ Fri, 26 Jun 2020 08:35:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:35:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:35:07: #1 total tags in treatment: 13688536 INFO @ Fri, 26 Jun 2020 08:35:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:35:07: #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 08:35:07: #1 tags after filtering in treatment: 13688536 INFO @ Fri, 26 Jun 2020 08:35:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:35:07: #1 finished! INFO @ Fri, 26 Jun 2020 08:35:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:35:09: #2 number of paired peaks: 7565 INFO @ Fri, 26 Jun 2020 08:35:09: start model_add_line... INFO @ Fri, 26 Jun 2020 08:35:09: 5000000 INFO @ Fri, 26 Jun 2020 08:35:09: start X-correlation... INFO @ Fri, 26 Jun 2020 08:35:09: end of X-cor INFO @ Fri, 26 Jun 2020 08:35:09: #2 finished! INFO @ Fri, 26 Jun 2020 08:35:09: #2 predicted fragment length is 204 bps INFO @ Fri, 26 Jun 2020 08:35:09: #2 alternative fragment length(s) may be 3,204 bps INFO @ Fri, 26 Jun 2020 08:35:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.05_model.r INFO @ Fri, 26 Jun 2020 08:35:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:35:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:35:13: 10000000 INFO @ Fri, 26 Jun 2020 08:35:15: 6000000 INFO @ Fri, 26 Jun 2020 08:35:19: 11000000 INFO @ Fri, 26 Jun 2020 08:35:22: 7000000 INFO @ Fri, 26 Jun 2020 08:35:26: 12000000 INFO @ Fri, 26 Jun 2020 08:35:28: 8000000 INFO @ Fri, 26 Jun 2020 08:35:33: 13000000 INFO @ Fri, 26 Jun 2020 08:35:34: 9000000 INFO @ Fri, 26 Jun 2020 08:35:37: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:35:37: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:35:37: #1 total tags in treatment: 13688536 INFO @ Fri, 26 Jun 2020 08:35:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:35:37: #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 08:35:37: #1 tags after filtering in treatment: 13688536 INFO @ Fri, 26 Jun 2020 08:35:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:35:37: #1 finished! INFO @ Fri, 26 Jun 2020 08:35:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:35:39: #2 number of paired peaks: 7565 INFO @ Fri, 26 Jun 2020 08:35:39: start model_add_line... INFO @ Fri, 26 Jun 2020 08:35:39: start X-correlation... INFO @ Fri, 26 Jun 2020 08:35:39: end of X-cor INFO @ Fri, 26 Jun 2020 08:35:39: #2 finished! INFO @ Fri, 26 Jun 2020 08:35:39: #2 predicted fragment length is 204 bps INFO @ Fri, 26 Jun 2020 08:35:39: #2 alternative fragment length(s) may be 3,204 bps INFO @ Fri, 26 Jun 2020 08:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.10_model.r INFO @ Fri, 26 Jun 2020 08:35:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:35:40: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:35:46: 11000000 INFO @ Fri, 26 Jun 2020 08:35:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:35:52: 12000000 INFO @ Fri, 26 Jun 2020 08:35:58: 13000000 INFO @ Fri, 26 Jun 2020 08:36:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:36:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:36:02: #1 total tags in treatment: 13688536 INFO @ Fri, 26 Jun 2020 08:36:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:36:02: #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 08:36:02: #1 tags after filtering in treatment: 13688536 INFO @ Fri, 26 Jun 2020 08:36:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:36:02: #1 finished! INFO @ Fri, 26 Jun 2020 08:36:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:36:04: #2 number of paired peaks: 7565 INFO @ Fri, 26 Jun 2020 08:36:04: start model_add_line... INFO @ Fri, 26 Jun 2020 08:36:04: start X-correlation... INFO @ Fri, 26 Jun 2020 08:36:04: end of X-cor INFO @ Fri, 26 Jun 2020 08:36:04: #2 finished! INFO @ Fri, 26 Jun 2020 08:36:04: #2 predicted fragment length is 204 bps INFO @ Fri, 26 Jun 2020 08:36:04: #2 alternative fragment length(s) may be 3,204 bps INFO @ Fri, 26 Jun 2020 08:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.20_model.r INFO @ Fri, 26 Jun 2020 08:36:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:36:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.05_summits.bed INFO @ Fri, 26 Jun 2020 08:36:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10536 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:36:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.10_summits.bed INFO @ Fri, 26 Jun 2020 08:36:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6974 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:36:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467121/SRX467121.20_summits.bed INFO @ Fri, 26 Jun 2020 08:37:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3500 records, 4 fields): 5 millis CompletedMACS2peakCalling