Job ID = 6457492 SRX = SRX4664647 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:35:30 prefetch.2.10.7: 1) Downloading 'SRR7813074'... 2020-06-21T11:35:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:39:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:39:06 prefetch.2.10.7: 1) 'SRR7813074' was downloaded successfully Read 27801470 spots for SRR7813074/SRR7813074.sra Written 27801470 spots for SRR7813074/SRR7813074.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: 00:08:00 27801470 reads; of these: 27801470 (100.00%) were unpaired; of these: 792814 (2.85%) aligned 0 times 19666042 (70.74%) aligned exactly 1 time 7342614 (26.41%) aligned >1 times 97.15% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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 12 files... [bam_rmdupse_core] 10149034 / 27008656 = 0.3758 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 20:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.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 20:53:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:53:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:53:30: 1000000 INFO @ Sun, 21 Jun 2020 20:53:36: 2000000 INFO @ Sun, 21 Jun 2020 20:53:41: 3000000 INFO @ Sun, 21 Jun 2020 20:53:47: 4000000 INFO @ Sun, 21 Jun 2020 20:53:52: 5000000 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 20:53:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.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 20:53:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:53:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:53:58: 6000000 INFO @ Sun, 21 Jun 2020 20:54:01: 1000000 INFO @ Sun, 21 Jun 2020 20:54:04: 7000000 INFO @ Sun, 21 Jun 2020 20:54:07: 2000000 INFO @ Sun, 21 Jun 2020 20:54:10: 8000000 INFO @ Sun, 21 Jun 2020 20:54:12: 3000000 INFO @ Sun, 21 Jun 2020 20:54:16: 9000000 INFO @ Sun, 21 Jun 2020 20:54:18: 4000000 INFO @ Sun, 21 Jun 2020 20:54:22: 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 20:54:24: 5000000 INFO @ Sun, 21 Jun 2020 20:54:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.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 20:54:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:54:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:54:28: 11000000 INFO @ Sun, 21 Jun 2020 20:54:30: 6000000 INFO @ Sun, 21 Jun 2020 20:54:31: 1000000 INFO @ Sun, 21 Jun 2020 20:54:35: 12000000 INFO @ Sun, 21 Jun 2020 20:54:36: 7000000 INFO @ Sun, 21 Jun 2020 20:54:37: 2000000 INFO @ Sun, 21 Jun 2020 20:54:41: 13000000 INFO @ Sun, 21 Jun 2020 20:54:42: 8000000 INFO @ Sun, 21 Jun 2020 20:54:43: 3000000 INFO @ Sun, 21 Jun 2020 20:54:47: 14000000 INFO @ Sun, 21 Jun 2020 20:54:48: 9000000 INFO @ Sun, 21 Jun 2020 20:54:49: 4000000 INFO @ Sun, 21 Jun 2020 20:54:53: 15000000 INFO @ Sun, 21 Jun 2020 20:54:54: 10000000 INFO @ Sun, 21 Jun 2020 20:54:54: 5000000 INFO @ Sun, 21 Jun 2020 20:54:59: 16000000 INFO @ Sun, 21 Jun 2020 20:55:00: 11000000 INFO @ Sun, 21 Jun 2020 20:55:00: 6000000 INFO @ Sun, 21 Jun 2020 20:55:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:55:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:55:05: #1 total tags in treatment: 16859622 INFO @ Sun, 21 Jun 2020 20:55:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:55:05: #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 20:55:05: #1 tags after filtering in treatment: 16859568 INFO @ Sun, 21 Jun 2020 20:55:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:55:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:55:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:55:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:55:06: 12000000 INFO @ Sun, 21 Jun 2020 20:55:06: 7000000 INFO @ Sun, 21 Jun 2020 20:55:07: #2 number of paired peaks: 3149 INFO @ Sun, 21 Jun 2020 20:55:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:55:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:55:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:55:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:55:07: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 20:55:07: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 20:55:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.05_model.r INFO @ Sun, 21 Jun 2020 20:55:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:55:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:55:12: 13000000 INFO @ Sun, 21 Jun 2020 20:55:12: 8000000 INFO @ Sun, 21 Jun 2020 20:55:18: 14000000 INFO @ Sun, 21 Jun 2020 20:55:18: 9000000 INFO @ Sun, 21 Jun 2020 20:55:24: 15000000 INFO @ Sun, 21 Jun 2020 20:55:24: 10000000 INFO @ Sun, 21 Jun 2020 20:55:30: 11000000 INFO @ Sun, 21 Jun 2020 20:55:30: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:55:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:55:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:55:35: #1 total tags in treatment: 16859622 INFO @ Sun, 21 Jun 2020 20:55:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:55:35: #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 20:55:36: #1 tags after filtering in treatment: 16859568 INFO @ Sun, 21 Jun 2020 20:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:55:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:55:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:55:36: 12000000 INFO @ Sun, 21 Jun 2020 20:55:37: #2 number of paired peaks: 3149 INFO @ Sun, 21 Jun 2020 20:55:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:55:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:55:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:55:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:55:37: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 20:55:37: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 20:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.10_model.r INFO @ Sun, 21 Jun 2020 20:55:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:55:42: 13000000 INFO @ Sun, 21 Jun 2020 20:55:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:55:47: 14000000 INFO @ Sun, 21 Jun 2020 20:55:53: 15000000 INFO @ Sun, 21 Jun 2020 20:55:58: 16000000 INFO @ Sun, 21 Jun 2020 20:56:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:56:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:56:03: #1 total tags in treatment: 16859622 INFO @ Sun, 21 Jun 2020 20:56:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:56:03: #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 20:56:04: #1 tags after filtering in treatment: 16859568 INFO @ Sun, 21 Jun 2020 20:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:56:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:56:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:56:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:56:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:56:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.05_summits.bed INFO @ Sun, 21 Jun 2020 20:56:04: Done! pass1 - making usageList (649 chroms): 2 millis pass2 - checking and writing primary data (10478 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:56:05: #2 number of paired peaks: 3149 INFO @ Sun, 21 Jun 2020 20:56:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:56:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:56:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:56:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:56:05: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 20:56:05: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 20:56:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.20_model.r INFO @ Sun, 21 Jun 2020 20:56:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:56:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:56:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:56:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:56:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:56:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.10_summits.bed INFO @ Sun, 21 Jun 2020 20:56:36: Done! pass1 - making usageList (550 chroms): 2 millis pass2 - checking and writing primary data (8213 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:56:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:57:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:57:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:57:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664647/SRX4664647.20_summits.bed INFO @ Sun, 21 Jun 2020 20:57:02: Done! pass1 - making usageList (443 chroms): 2 millis pass2 - checking and writing primary data (5705 records, 4 fields): 16 millis CompletedMACS2peakCalling