Job ID = 6453832 SRX = SRX151960 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:31:11 prefetch.2.10.7: 1) Downloading 'SRR504794'... 2020-06-21T08:31:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:06 prefetch.2.10.7: 'SRR504794' is valid 2020-06-21T08:32:06 prefetch.2.10.7: 1) 'SRR504794' was downloaded successfully Read 6073606 spots for SRR504794/SRR504794.sra Written 6073606 spots for SRR504794/SRR504794.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: 00:01:12 6073606 reads; of these: 6073606 (100.00%) were unpaired; of these: 351403 (5.79%) aligned 0 times 4391642 (72.31%) aligned exactly 1 time 1330561 (21.91%) aligned >1 times 94.21% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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_rmdupse_core] 773864 / 5722203 = 0.1352 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 17:35:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.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 17:35:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:35:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:35:16: 1000000 INFO @ Sun, 21 Jun 2020 17:35:21: 2000000 INFO @ Sun, 21 Jun 2020 17:35:27: 3000000 INFO @ Sun, 21 Jun 2020 17:35:33: 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 17:35:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.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 17:35:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:35:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:35:40: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:35:40: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:35:40: #1 total tags in treatment: 4948339 INFO @ Sun, 21 Jun 2020 17:35:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:40: #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 17:35:40: #1 tags after filtering in treatment: 4948291 INFO @ Sun, 21 Jun 2020 17:35:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:41: #2 number of paired peaks: 4020 INFO @ Sun, 21 Jun 2020 17:35:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:41: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 17:35:41: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 17:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.05_model.r INFO @ Sun, 21 Jun 2020 17:35:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:35:46: 1000000 INFO @ Sun, 21 Jun 2020 17:35:51: 2000000 INFO @ Sun, 21 Jun 2020 17:35:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:35:57: 3000000 INFO @ Sun, 21 Jun 2020 17:36:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:36:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:36:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.05_summits.bed INFO @ Sun, 21 Jun 2020 17:36:00: Done! pass1 - making usageList (215 chroms): 1 millis pass2 - checking and writing primary data (5824 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:36:03: 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 17:36:09: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:36:09: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:36:09: #1 total tags in treatment: 4948339 INFO @ Sun, 21 Jun 2020 17:36:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:36:09: #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 17:36:09: #1 tags after filtering in treatment: 4948291 INFO @ Sun, 21 Jun 2020 17:36:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:36:09: #1 finished! INFO @ Sun, 21 Jun 2020 17:36:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.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 17:36:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:36:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:36:10: #2 number of paired peaks: 4020 INFO @ Sun, 21 Jun 2020 17:36:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:36:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:36:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:36:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:36:10: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 17:36:10: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 17:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.10_model.r INFO @ Sun, 21 Jun 2020 17:36:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:36:16: 1000000 INFO @ Sun, 21 Jun 2020 17:36:21: 2000000 INFO @ Sun, 21 Jun 2020 17:36:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:36:27: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.10_summits.bed INFO @ Sun, 21 Jun 2020 17:36:30: Done! pass1 - making usageList (167 chroms): 2 millis pass2 - checking and writing primary data (4307 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:36:33: 4000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:36:39: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:36:39: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:36:39: #1 total tags in treatment: 4948339 INFO @ Sun, 21 Jun 2020 17:36:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:36:39: #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 17:36:40: #1 tags after filtering in treatment: 4948291 INFO @ Sun, 21 Jun 2020 17:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:36:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:36:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:36:40: #2 number of paired peaks: 4020 INFO @ Sun, 21 Jun 2020 17:36:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:36:40: start X-correlation... INFO @ Sun, 21 Jun 2020 17:36:40: end of X-cor INFO @ Sun, 21 Jun 2020 17:36:40: #2 finished! INFO @ Sun, 21 Jun 2020 17:36:40: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 17:36:40: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 17:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.20_model.r INFO @ Sun, 21 Jun 2020 17:36:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:36:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151960/SRX151960.20_summits.bed INFO @ Sun, 21 Jun 2020 17:37:00: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (2726 records, 4 fields): 7 millis CompletedMACS2peakCalling