Job ID = 6455011 SRX = SRX2618556 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:31:29 prefetch.2.10.7: 1) Downloading 'SRR5319110'... 2020-06-21T09:31:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:34:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:34:07 prefetch.2.10.7: 'SRR5319110' is valid 2020-06-21T09:34:07 prefetch.2.10.7: 1) 'SRR5319110' was downloaded successfully 2020-06-21T09:34:07 prefetch.2.10.7: 'SRR5319110' has 0 unresolved dependencies Read 20209629 spots for SRR5319110/SRR5319110.sra Written 20209629 spots for SRR5319110/SRR5319110.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: 00:06:01 20209629 reads; of these: 20209629 (100.00%) were unpaired; of these: 925715 (4.58%) aligned 0 times 14077778 (69.66%) aligned exactly 1 time 5206136 (25.76%) aligned >1 times 95.42% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 3503145 / 19283914 = 0.1817 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 18:46:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.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 18:46:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:06: 1000000 INFO @ Sun, 21 Jun 2020 18:46:12: 2000000 INFO @ Sun, 21 Jun 2020 18:46:17: 3000000 INFO @ Sun, 21 Jun 2020 18:46:22: 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 18:46:28: 5000000 INFO @ Sun, 21 Jun 2020 18:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.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 18:46:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:34: 6000000 INFO @ Sun, 21 Jun 2020 18:46:34: 1000000 INFO @ Sun, 21 Jun 2020 18:46:39: 7000000 INFO @ Sun, 21 Jun 2020 18:46:40: 2000000 INFO @ Sun, 21 Jun 2020 18:46:45: 8000000 INFO @ Sun, 21 Jun 2020 18:46:46: 3000000 INFO @ Sun, 21 Jun 2020 18:46:51: 9000000 INFO @ Sun, 21 Jun 2020 18:46:52: 4000000 INFO @ Sun, 21 Jun 2020 18:46:57: 10000000 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 18:46:58: 5000000 INFO @ Sun, 21 Jun 2020 18:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.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 18:46:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:02: 11000000 INFO @ Sun, 21 Jun 2020 18:47:04: 6000000 INFO @ Sun, 21 Jun 2020 18:47:06: 1000000 INFO @ Sun, 21 Jun 2020 18:47:08: 12000000 INFO @ Sun, 21 Jun 2020 18:47:10: 7000000 INFO @ Sun, 21 Jun 2020 18:47:12: 2000000 INFO @ Sun, 21 Jun 2020 18:47:15: 13000000 INFO @ Sun, 21 Jun 2020 18:47:16: 8000000 INFO @ Sun, 21 Jun 2020 18:47:18: 3000000 INFO @ Sun, 21 Jun 2020 18:47:21: 14000000 INFO @ Sun, 21 Jun 2020 18:47:22: 9000000 INFO @ Sun, 21 Jun 2020 18:47:24: 4000000 INFO @ Sun, 21 Jun 2020 18:47:26: 15000000 INFO @ Sun, 21 Jun 2020 18:47:28: 10000000 INFO @ Sun, 21 Jun 2020 18:47:30: 5000000 INFO @ Sun, 21 Jun 2020 18:47:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:47:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:47:31: #1 total tags in treatment: 15780769 INFO @ Sun, 21 Jun 2020 18:47:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:31: #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 18:47:32: #1 tags after filtering in treatment: 15780769 INFO @ Sun, 21 Jun 2020 18:47:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:33: #2 number of paired peaks: 3200 INFO @ Sun, 21 Jun 2020 18:47:33: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:34: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 18:47:34: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 18:47:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.05_model.r INFO @ Sun, 21 Jun 2020 18:47:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:34: 11000000 INFO @ Sun, 21 Jun 2020 18:47:36: 6000000 INFO @ Sun, 21 Jun 2020 18:47:39: 12000000 INFO @ Sun, 21 Jun 2020 18:47:42: 7000000 INFO @ Sun, 21 Jun 2020 18:47:46: 13000000 INFO @ Sun, 21 Jun 2020 18:47:48: 8000000 INFO @ Sun, 21 Jun 2020 18:47:51: 14000000 INFO @ Sun, 21 Jun 2020 18:47:54: 9000000 INFO @ Sun, 21 Jun 2020 18:47:57: 15000000 INFO @ Sun, 21 Jun 2020 18:47:59: 10000000 INFO @ Sun, 21 Jun 2020 18:48:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:48:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:48:02: #1 total tags in treatment: 15780769 INFO @ Sun, 21 Jun 2020 18:48:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:02: #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 18:48:03: #1 tags after filtering in treatment: 15780769 INFO @ Sun, 21 Jun 2020 18:48:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:04: #2 number of paired peaks: 3200 INFO @ Sun, 21 Jun 2020 18:48:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:04: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 18:48:04: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 18:48:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.10_model.r INFO @ Sun, 21 Jun 2020 18:48:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:05: 11000000 INFO @ Sun, 21 Jun 2020 18:48:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:10: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:48:16: 13000000 INFO @ Sun, 21 Jun 2020 18:48:21: 14000000 INFO @ Sun, 21 Jun 2020 18:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.05_summits.bed INFO @ Sun, 21 Jun 2020 18:48:26: Done! pass1 - making usageList (684 chroms): 2 millis pass2 - checking and writing primary data (7921 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:48:27: 15000000 INFO @ Sun, 21 Jun 2020 18:48:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:48:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:48:31: #1 total tags in treatment: 15780769 INFO @ Sun, 21 Jun 2020 18:48:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:31: #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 18:48:31: #1 tags after filtering in treatment: 15780769 INFO @ Sun, 21 Jun 2020 18:48:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:33: #2 number of paired peaks: 3200 INFO @ Sun, 21 Jun 2020 18:48:33: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:33: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 18:48:33: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 18:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.20_model.r INFO @ Sun, 21 Jun 2020 18:48:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.10_summits.bed INFO @ Sun, 21 Jun 2020 18:48:57: Done! pass1 - making usageList (596 chroms): 2 millis pass2 - checking and writing primary data (7286 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618556/SRX2618556.20_summits.bed INFO @ Sun, 21 Jun 2020 18:49:25: Done! pass1 - making usageList (478 chroms): 1 millis pass2 - checking and writing primary data (6202 records, 4 fields): 21 millis CompletedMACS2peakCalling