Job ID = 6457117 SRX = SRX4451933 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:32:29 prefetch.2.10.7: 1) Downloading 'SRR7586077'... 2020-06-21T11:32:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:36:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:36:04 prefetch.2.10.7: 1) 'SRR7586077' was downloaded successfully 2020-06-21T11:36:04 prefetch.2.10.7: 'SRR7586077' has 0 unresolved dependencies Read 23504556 spots for SRR7586077/SRR7586077.sra Written 23504556 spots for SRR7586077/SRR7586077.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: 00:06:55 23504556 reads; of these: 23504556 (100.00%) were unpaired; of these: 4029368 (17.14%) aligned 0 times 16714453 (71.11%) aligned exactly 1 time 2760735 (11.75%) aligned >1 times 82.86% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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] 6141743 / 19475188 = 0.3154 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 20:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.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 20:50:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:07: 1000000 INFO @ Sun, 21 Jun 2020 20:50:14: 2000000 INFO @ Sun, 21 Jun 2020 20:50:21: 3000000 INFO @ Sun, 21 Jun 2020 20:50:27: 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 20:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.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 20:50:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:34: 5000000 INFO @ Sun, 21 Jun 2020 20:50:37: 1000000 INFO @ Sun, 21 Jun 2020 20:50:41: 6000000 INFO @ Sun, 21 Jun 2020 20:50:44: 2000000 INFO @ Sun, 21 Jun 2020 20:50:48: 7000000 INFO @ Sun, 21 Jun 2020 20:50:51: 3000000 INFO @ Sun, 21 Jun 2020 20:50:55: 8000000 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 20:50:58: 4000000 INFO @ Sun, 21 Jun 2020 20:51:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.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 20:51:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:02: 9000000 INFO @ Sun, 21 Jun 2020 20:51:06: 5000000 INFO @ Sun, 21 Jun 2020 20:51:06: 1000000 INFO @ Sun, 21 Jun 2020 20:51:09: 10000000 INFO @ Sun, 21 Jun 2020 20:51:13: 2000000 INFO @ Sun, 21 Jun 2020 20:51:13: 6000000 INFO @ Sun, 21 Jun 2020 20:51:17: 11000000 INFO @ Sun, 21 Jun 2020 20:51:19: 3000000 INFO @ Sun, 21 Jun 2020 20:51:20: 7000000 INFO @ Sun, 21 Jun 2020 20:51:24: 12000000 INFO @ Sun, 21 Jun 2020 20:51:24: 4000000 INFO @ Sun, 21 Jun 2020 20:51:27: 8000000 INFO @ Sun, 21 Jun 2020 20:51:31: 5000000 INFO @ Sun, 21 Jun 2020 20:51:31: 13000000 INFO @ Sun, 21 Jun 2020 20:51:33: #1 tag size is determined as 79 bps INFO @ Sun, 21 Jun 2020 20:51:33: #1 tag size = 79 INFO @ Sun, 21 Jun 2020 20:51:33: #1 total tags in treatment: 13333445 INFO @ Sun, 21 Jun 2020 20:51:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:33: #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 20:51:34: #1 tags after filtering in treatment: 13333283 INFO @ Sun, 21 Jun 2020 20:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:34: 9000000 INFO @ Sun, 21 Jun 2020 20:51:35: #2 number of paired peaks: 1554 INFO @ Sun, 21 Jun 2020 20:51:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:35: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 20:51:35: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 20:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.05_model.r INFO @ Sun, 21 Jun 2020 20:51:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:37: 6000000 INFO @ Sun, 21 Jun 2020 20:51:41: 10000000 INFO @ Sun, 21 Jun 2020 20:51:43: 7000000 INFO @ Sun, 21 Jun 2020 20:51:48: 8000000 INFO @ Sun, 21 Jun 2020 20:51:49: 11000000 INFO @ Sun, 21 Jun 2020 20:51:54: 9000000 INFO @ Sun, 21 Jun 2020 20:51:56: 12000000 INFO @ Sun, 21 Jun 2020 20:52:00: 10000000 INFO @ Sun, 21 Jun 2020 20:52:03: 13000000 INFO @ Sun, 21 Jun 2020 20:52:05: #1 tag size is determined as 79 bps INFO @ Sun, 21 Jun 2020 20:52:05: #1 tag size = 79 INFO @ Sun, 21 Jun 2020 20:52:05: #1 total tags in treatment: 13333445 INFO @ Sun, 21 Jun 2020 20:52:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:05: #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 20:52:06: #1 tags after filtering in treatment: 13333283 INFO @ Sun, 21 Jun 2020 20:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:07: 11000000 INFO @ Sun, 21 Jun 2020 20:52:07: #2 number of paired peaks: 1554 INFO @ Sun, 21 Jun 2020 20:52:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:07: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 20:52:07: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 20:52:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.10_model.r INFO @ Sun, 21 Jun 2020 20:52:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:52:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:12: 12000000 INFO @ Sun, 21 Jun 2020 20:52:18: 13000000 INFO @ Sun, 21 Jun 2020 20:52:20: #1 tag size is determined as 79 bps INFO @ Sun, 21 Jun 2020 20:52:20: #1 tag size = 79 INFO @ Sun, 21 Jun 2020 20:52:20: #1 total tags in treatment: 13333445 INFO @ Sun, 21 Jun 2020 20:52:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:52:21: #1 tags after filtering in treatment: 13333283 INFO @ Sun, 21 Jun 2020 20:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:22: #2 number of paired peaks: 1554 INFO @ Sun, 21 Jun 2020 20:52:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:22: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:22: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 20:52:22: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 20:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.20_model.r INFO @ Sun, 21 Jun 2020 20:52:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:52:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.05_summits.bed INFO @ Sun, 21 Jun 2020 20:52:23: Done! pass1 - making usageList (279 chroms): 2 millis pass2 - checking and writing primary data (5907 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:52:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:52:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.10_summits.bed INFO @ Sun, 21 Jun 2020 20:52:55: Done! pass1 - making usageList (180 chroms): 2 millis pass2 - checking and writing primary data (4632 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4451933/SRX4451933.20_summits.bed INFO @ Sun, 21 Jun 2020 20:53:10: Done! pass1 - making usageList (105 chroms): 1 millis pass2 - checking and writing primary data (3317 records, 4 fields): 8 millis CompletedMACS2peakCalling