Job ID = 6457265 SRX = SRX4639145 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:28:11 prefetch.2.10.7: 1) Downloading 'SRR7784126'... 2020-06-21T11:28:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:32:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:32:47 prefetch.2.10.7: 1) 'SRR7784126' was downloaded successfully Read 45471418 spots for SRR7784126/SRR7784126.sra Written 45471418 spots for SRR7784126/SRR7784126.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: 00:08:09 45471418 reads; of these: 45471418 (100.00%) were unpaired; of these: 26438561 (58.14%) aligned 0 times 13818420 (30.39%) aligned exactly 1 time 5214437 (11.47%) aligned >1 times 41.86% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 15883006 / 19032857 = 0.8345 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 20:47:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.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 20:47:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:47:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:47:53: 1000000 INFO @ Sun, 21 Jun 2020 20:47:58: 2000000 INFO @ Sun, 21 Jun 2020 20:48:05: 3000000 INFO @ Sun, 21 Jun 2020 20:48:06: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:48:06: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:48:06: #1 total tags in treatment: 3149851 INFO @ Sun, 21 Jun 2020 20:48:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:48:06: #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 20:48:06: #1 tags after filtering in treatment: 3149756 INFO @ Sun, 21 Jun 2020 20:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:48:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:48:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:48:07: #2 number of paired peaks: 3928 INFO @ Sun, 21 Jun 2020 20:48:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:48:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:48:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:48:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:48:07: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 20:48:07: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 20:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.05_model.r INFO @ Sun, 21 Jun 2020 20:48:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:48:07: #3 Pre-compute pvalue-qvalue table... 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 20:48:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:48:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.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 20:48:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:48:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:48:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.05_summits.bed INFO @ Sun, 21 Jun 2020 20:48:20: Done! pass1 - making usageList (820 chroms): 2 millis pass2 - checking and writing primary data (4047 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:48:23: 1000000 INFO @ Sun, 21 Jun 2020 20:48:29: 2000000 INFO @ Sun, 21 Jun 2020 20:48:35: 3000000 INFO @ Sun, 21 Jun 2020 20:48:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:48:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:48:36: #1 total tags in treatment: 3149851 INFO @ Sun, 21 Jun 2020 20:48:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:48:36: #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 20:48:36: #1 tags after filtering in treatment: 3149756 INFO @ Sun, 21 Jun 2020 20:48:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:48:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:48:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:48:37: #2 number of paired peaks: 3928 INFO @ Sun, 21 Jun 2020 20:48:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:48:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:48:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:48:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:48:37: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 20:48:37: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 20:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.10_model.r INFO @ Sun, 21 Jun 2020 20:48:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:48:37: #3 Pre-compute pvalue-qvalue table... 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 20:48:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:48:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.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 20:48:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:48:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.10_summits.bed INFO @ Sun, 21 Jun 2020 20:48:51: Done! pass1 - making usageList (722 chroms): 2 millis pass2 - checking and writing primary data (2637 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:48:53: 1000000 INFO @ Sun, 21 Jun 2020 20:48:59: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:49:06: 3000000 INFO @ Sun, 21 Jun 2020 20:49:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:49:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:49:07: #1 total tags in treatment: 3149851 INFO @ Sun, 21 Jun 2020 20:49:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:49:07: #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 20:49:07: #1 tags after filtering in treatment: 3149756 INFO @ Sun, 21 Jun 2020 20:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:49:07: #1 finished! INFO @ Sun, 21 Jun 2020 20:49:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:49:08: #2 number of paired peaks: 3928 INFO @ Sun, 21 Jun 2020 20:49:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:49:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:49:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:49:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:49:08: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 20:49:08: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 20:49:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.20_model.r INFO @ Sun, 21 Jun 2020 20:49:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:49:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:49:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639145/SRX4639145.20_summits.bed INFO @ Sun, 21 Jun 2020 20:49:21: Done! pass1 - making usageList (555 chroms): 2 millis pass2 - checking and writing primary data (1285 records, 4 fields): 31 millis CompletedMACS2peakCalling