Job ID = 6458882 SRX = SRX5717050 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:49:55 prefetch.2.10.7: 1) Downloading 'SRR8936411'... 2020-06-21T12:49:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:53:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:53:03 prefetch.2.10.7: 1) 'SRR8936411' was downloaded successfully Read 23617781 spots for SRR8936411/SRR8936411.sra Written 23617781 spots for SRR8936411/SRR8936411.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:37 23617781 reads; of these: 23617781 (100.00%) were unpaired; of these: 3049984 (12.91%) aligned 0 times 16107313 (68.20%) aligned exactly 1 time 4460484 (18.89%) aligned >1 times 87.09% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 7045049 / 20567797 = 0.3425 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 22:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.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 22:05:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:05:31: 1000000 INFO @ Sun, 21 Jun 2020 22:05:37: 2000000 INFO @ Sun, 21 Jun 2020 22:05:43: 3000000 INFO @ Sun, 21 Jun 2020 22:05:48: 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 22:05:54: 5000000 INFO @ Sun, 21 Jun 2020 22:05:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.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 22:05:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:01: 6000000 INFO @ Sun, 21 Jun 2020 22:06:02: 1000000 INFO @ Sun, 21 Jun 2020 22:06:07: 7000000 INFO @ Sun, 21 Jun 2020 22:06:08: 2000000 INFO @ Sun, 21 Jun 2020 22:06:13: 8000000 INFO @ Sun, 21 Jun 2020 22:06:14: 3000000 INFO @ Sun, 21 Jun 2020 22:06:20: 9000000 INFO @ Sun, 21 Jun 2020 22:06:20: 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 @ Sun, 21 Jun 2020 22:06:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.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 22:06:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:26: 5000000 INFO @ Sun, 21 Jun 2020 22:06:27: 10000000 INFO @ Sun, 21 Jun 2020 22:06:32: 1000000 INFO @ Sun, 21 Jun 2020 22:06:33: 6000000 INFO @ Sun, 21 Jun 2020 22:06:34: 11000000 INFO @ Sun, 21 Jun 2020 22:06:39: 2000000 INFO @ Sun, 21 Jun 2020 22:06:40: 7000000 INFO @ Sun, 21 Jun 2020 22:06:40: 12000000 INFO @ Sun, 21 Jun 2020 22:06:45: 3000000 INFO @ Sun, 21 Jun 2020 22:06:46: 8000000 INFO @ Sun, 21 Jun 2020 22:06:47: 13000000 INFO @ Sun, 21 Jun 2020 22:06:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:06:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:06:51: #1 total tags in treatment: 13522748 INFO @ Sun, 21 Jun 2020 22:06:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:51: #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 22:06:52: #1 tags after filtering in treatment: 13522647 INFO @ Sun, 21 Jun 2020 22:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:52: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:52: 4000000 INFO @ Sun, 21 Jun 2020 22:06:53: #2 number of paired peaks: 1951 INFO @ Sun, 21 Jun 2020 22:06:53: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:53: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:53: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:53: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:53: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 22:06:53: #2 alternative fragment length(s) may be 0,164,195,219,254,261,284 bps INFO @ Sun, 21 Jun 2020 22:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.05_model.r INFO @ Sun, 21 Jun 2020 22:06:53: 9000000 INFO @ Sun, 21 Jun 2020 22:06:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:58: 5000000 INFO @ Sun, 21 Jun 2020 22:07:00: 10000000 INFO @ Sun, 21 Jun 2020 22:07:05: 6000000 INFO @ Sun, 21 Jun 2020 22:07:06: 11000000 INFO @ Sun, 21 Jun 2020 22:07:11: 7000000 INFO @ Sun, 21 Jun 2020 22:07:13: 12000000 INFO @ Sun, 21 Jun 2020 22:07:17: 8000000 INFO @ Sun, 21 Jun 2020 22:07:19: 13000000 INFO @ Sun, 21 Jun 2020 22:07:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:07:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:07:23: #1 total tags in treatment: 13522748 INFO @ Sun, 21 Jun 2020 22:07:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:23: #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 22:07:23: #1 tags after filtering in treatment: 13522647 INFO @ Sun, 21 Jun 2020 22:07:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:23: 9000000 INFO @ Sun, 21 Jun 2020 22:07:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:24: #2 number of paired peaks: 1951 INFO @ Sun, 21 Jun 2020 22:07:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:25: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 22:07:25: #2 alternative fragment length(s) may be 0,164,195,219,254,261,284 bps INFO @ Sun, 21 Jun 2020 22:07:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.10_model.r INFO @ Sun, 21 Jun 2020 22:07:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:07:30: 10000000 INFO @ Sun, 21 Jun 2020 22:07:36: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:07:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.05_summits.bed INFO @ Sun, 21 Jun 2020 22:07:38: Done! pass1 - making usageList (423 chroms): 2 millis pass2 - checking and writing primary data (2449 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:07:41: 12000000 INFO @ Sun, 21 Jun 2020 22:07:47: 13000000 INFO @ Sun, 21 Jun 2020 22:07:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:07:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:07:50: #1 total tags in treatment: 13522748 INFO @ Sun, 21 Jun 2020 22:07:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:50: #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 22:07:51: #1 tags after filtering in treatment: 13522647 INFO @ Sun, 21 Jun 2020 22:07:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:52: #2 number of paired peaks: 1951 INFO @ Sun, 21 Jun 2020 22:07:52: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:52: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:52: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:52: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:52: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 22:07:52: #2 alternative fragment length(s) may be 0,164,195,219,254,261,284 bps INFO @ Sun, 21 Jun 2020 22:07:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.20_model.r INFO @ Sun, 21 Jun 2020 22:07:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:07:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.10_summits.bed INFO @ Sun, 21 Jun 2020 22:08:08: Done! pass1 - making usageList (260 chroms): 1 millis pass2 - checking and writing primary data (827 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:08:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717050/SRX5717050.20_summits.bed INFO @ Sun, 21 Jun 2020 22:08:36: Done! pass1 - making usageList (101 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 7 millis CompletedMACS2peakCalling